Term IRI Term label Parent term IRI Parent term label Alternative term Definition http://purl.obolibrary.org/obo/OBI_0002465 age since culture seeding measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum age of culture An age measurement datum that is the result of the measurement of the age of a cell since cultured (the process of seeding cells onto a culture dish). http://purl.obolibrary.org/obo/OBI_0002472 dbGaP study identifier http://purl.obolibrary.org/obo/IAO_0000577 centrally registered identifier symbol dbGaP accession number A central registered identifier symbol that denotes a specific study in dbGaP. http://purl.obolibrary.org/obo/OBI_0002475 number of PCR cycles during library construction http://purl.obolibrary.org/obo/IAO_0000027 data item library construction PCR cycles A data item that is the number of PCR cycles used during the construction of a sequencing library. http://purl.obolibrary.org/obo/OBI_0002479 sequence read length measurement datum http://purl.obolibrary.org/obo/IAO_0000109 measurement datum read length, read length measurement datum A measurement datum that is the result of the measurement of the number of bases in a DNA or RNA sequence. http://purl.obolibrary.org/obo/OBI_0002480 sequencing library input quantity measurement datum http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum library input amount A scalar measurement datum that indicates the amount of sequencing library used as input for a sequencer. http://purl.obolibrary.org/obo/OBI_0002482 specimen harvest quantity http://purl.obolibrary.org/obo/IAO_0000109 measurement datum harvest quantity A scalar measurement datum that indicates the amount of specimen collected. http://purl.obolibrary.org/obo/OBI_0002464 SRS identifier http://purl.obolibrary.org/obo/IAO_0000577 centrally registered identifier symbol SRA sample accession number An accession number that applies to a database record for an individual sample object in an NCBI Sequence Read Archive (SRA) submission. These records are imported from the NCBI BioSample database. http://purl.obolibrary.org/obo/OBI_0002485 transcript analysis by single-end sequencing assay http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay transcript analysis by single-end sequencing A sequencing assay that incorporates single-end reads and sequencing technology to determine transcripts, gene structures, and gene expressions. http://purl.obolibrary.org/obo/IAO_8000006 subset ontology module http://purl.obolibrary.org/obo/IAO_8000000 ontology module subset ontology An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. http://purl.obolibrary.org/obo/OBI_0002586 digital acquisition card http://purl.obolibrary.org/obo/OBI_0000968 device digital acquisition and digital generation card The digital acquisition card acts as the interface between the computer and a measurement device via the computer bus. It converts the signal generated by a measurement device (output from device) to a digital signal via an analog-to-digital converter, ADC. It also converts a digital signal to an analog signal via a digital-to-analog converter, DAC. This analog signal (e.g., stimulus) is fed to a measurement device (input to device). http://purl.obolibrary.org/obo/IAO_0000648 zone improvement plan code http://purl.obolibrary.org/obo/IAO_0000646 postal code ZIP code A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes. http://purl.obolibrary.org/obo/ONE_0000004 retrospective method for assessing dietary diversity http://purl.obolibrary.org/obo/ONE_0000002 retrospective dietary survey method Dietary Diversity Score (DDS) A retrospective dietary survey method that provides a score that represents a number of different foods, drinks and/or food groups consumed over a given reference period. http://purl.obolibrary.org/obo/ONE_0000007 Food Frequency Questionnaire method http://purl.obolibrary.org/obo/ONE_0000002 retrospective dietary survey method FFQ A retrospective dietary survey method that assesses the frequency with which foods and/or food groups are eaten over a certain time period. The questionnaire includes a food list (commonly close-ended), a frequency category section, and can be self- or interviewer administered. http://purl.obolibrary.org/obo/OBI_0002136 RNA Integrity Number calculation http://purl.obolibrary.org/obo/OBI_0200000 data transformation RIN calculation A data transformation using the RIN algorithm to generate a quality measure of RNA based on features from an electrophoretic trace. http://purl.obolibrary.org/obo/OBI_0002137 RNA Integrity Number value specification http://purl.obolibrary.org/obo/OBI_0001933 value specification RIN value specification A value specification that specifies the value of the RNA Integrity Number as a real value between 1 (most degraded) and 10 (most intact). http://purl.obolibrary.org/obo/OBI_0002142 Nanostring nCounter miRNA expression assay http://purl.obolibrary.org/obo/OBI_0001926 microRNA profiling assay microRNA counts A microRNA profiling assay using digital molecular barcoding technology to quantify target microRNA molecules without the need for amplification. http://purl.obolibrary.org/obo/OBI_0002143 bromouride labeling and sequencing after UV exposure http://purl.obolibrary.org/obo/OBI_0001271 RNA-seq assay BruUV-seq An RNA-seq assay to identify transcription start sites and active enhancer elements through isolation of bromouridine (Bru) labelled RNAs after UV light exposure introduces transcription-blocking lesions. http://purl.obolibrary.org/obo/OBI_0002144 extrachromosomal circular DNA sequencing assay http://purl.obolibrary.org/obo/OBI_0000626 DNA sequencing assay circulome-seq An assay which aims at identifying the endogenous population of extrachromosomal circular DNA originating from a subset of genomic loci and potentially having profound consequences on the regulatory and coding capabilities of these regions. The assay includes creation of a library out of the circular DNA molecules and subsequent sequencing using parallelized sequencing methods. http://purl.obolibrary.org/obo/OBI_0002146 HIV antibody assay http://purl.obolibrary.org/obo/OBI_0002145 antigen specific antibodies assay HIV I/II Ab assay An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) antigens. http://purl.obolibrary.org/obo/OBI_0002147 HIV group O antibody assay http://purl.obolibrary.org/obo/OBI_0002145 antigen specific antibodies assay HIV I/II Plus O assay An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) group O antigens. http://purl.obolibrary.org/obo/OBI_0002148 surface HBV antibody assay http://purl.obolibrary.org/obo/OBI_0002145 antigen specific antibodies assay HBsAb assay An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) surface antigens. http://purl.obolibrary.org/obo/OBI_0002149 core HBV antibody assay http://purl.obolibrary.org/obo/OBI_0002145 antigen specific antibodies assay HBcAb assay An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) core antigens. http://purl.obolibrary.org/obo/OBI_0002150 core HBV IgM antibody assay http://purl.obolibrary.org/obo/OBI_0002145 antigen specific antibodies assay HBcAb-IgM assay An antigen specific antibodies assay that is meant to detectimmunoglobulin M (IgM) antibodies that bind to hepatitis B virus (HBV) core antigens. http://purl.obolibrary.org/obo/OBI_0002151 HCV antibody assay http://purl.obolibrary.org/obo/OBI_0002145 antigen specific antibodies assay HCV Ab assay An antigen specific antibodies assay that is meant to detect antibodies that bind to Hepacivirus C (HCV) antigens. http://purl.obolibrary.org/obo/OBI_0002152 EBV IgG antibody assay http://purl.obolibrary.org/obo/OBI_0002145 antigen specific antibodies assay EBV IgG Ab assay An antigen specific antibodies assay that is meant to detect immunoglobulin G (IgG) antibodies that bind to Epstein-Barr virus (EBV) antigens. http://purl.obolibrary.org/obo/OBI_0002153 EBV IgM antibody assay http://purl.obolibrary.org/obo/OBI_0002145 antigen specific antibodies assay EBV IgM Ab assay An antigen specific antibodies assay that is meant to detect immunoglobulin M (IgM) antibodies that bind to Epstein-Barr virus (EBV) antigens. http://purl.obolibrary.org/obo/OBI_0002154 CMV antibody assay http://purl.obolibrary.org/obo/OBI_0002145 antigen specific antibodies assay CMV Ab assay An antigen specific antibodies assay that is meant to detect antibodies that bind to cytomegalovirus (CMV) antigens. http://purl.obolibrary.org/obo/OBI_0002155 venereal disease research laboratory test http://purl.obolibrary.org/obo/OBI_0000443 analyte assay VDRL test An analyte assay that is meant to detect general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. VDRL tests require a microscope and can be done on cerebrospinal fluid as well as blood. http://purl.obolibrary.org/obo/OBI_0002156 rapid plasma reagin test http://purl.obolibrary.org/obo/OBI_0000443 analyte assay RPR assay An analyte assay that is meant to detect with the aid of carbon or charcoal particles general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. RPR tests can be done without a microscope. http://purl.obolibrary.org/obo/OBI_0002157 HBV surface antigen assay http://purl.obolibrary.org/obo/OBI_0000443 analyte assay HBsAg assay An analyte assay that is meant to detect hepatitis B virus (HBV) surface antigens. http://purl.obolibrary.org/obo/OBI_0002158 HIV-1 nucleic acid testing http://purl.obolibrary.org/obo/OBI_0000443 analyte assay HIV-1 NAT An analyte assay that is meant to detect human immunodeficiency virus (HIV-1) nucleic acids. http://purl.obolibrary.org/obo/OBI_0002159 HCV nucleic acid testing http://purl.obolibrary.org/obo/OBI_0000443 analyte assay HCV NAT An analyte assay that is meant to detect hepatitis C virus (HCV) nucleic acids. http://purl.obolibrary.org/obo/OBI_0002160 multiplexed indexed T7 ChIP-seq assay http://purl.obolibrary.org/obo/OBI_0000716 ChIP-seq assay Mint-ChIP-seq A ChIP-seq assay which leverages T7 promoter amplification to allow low sample input and chromatin barcoding and pool-and-split multiplexing for high-throughput, quantitative profiling of chromatin states. http://purl.obolibrary.org/obo/OBI_0002161 systematic evolution of ligands by exponential enrichment assay http://purl.obolibrary.org/obo/OBI_0001146 binding assay SELEX A binding assay that identifies protein-binding sites on nucleic acids by selecting high-affinity target ligands from a randomized pool. The process is repeated in rounds, then the bound nucleic acids are separated from the unbound nucleic acids and amplified by PCR._ http://purl.obolibrary.org/obo/OBI_0002171 dot blot assay http://purl.obolibrary.org/obo/OBI_0000443 analyte assay dot blot analysis An analyte assay that detects molecules in a mixture dotted on a membrane using DNA probes or antibodies. http://purl.obolibrary.org/obo/OBI_0002172 Northwestern blot assay http://purl.obolibrary.org/obo/OBI_0001591 direct binding assay Northwestern assay A direct binding assay that detects interactions of labeled RNA with immobilized protein on a membrane. http://purl.obolibrary.org/obo/OBI_0002175 ATP bioluminescence assay http://purl.obolibrary.org/obo/OBI_0000443 analyte assay cell viability ATP quantitation assay An analyte assay that detects ATP concentration through light intensity when luciferase catalyzes the oxidation of luciferin in the presence of ATP, magnesium ions, and molecular oxygen. http://purl.obolibrary.org/obo/OBI_0002183 two electrode voltage clamp assay http://purl.obolibrary.org/obo/OBI_0002182 voltage clamp assay TEVC The two electrode voltage clamp (TEVC) method utilizes two low-resistance pipettes, one sensing voltage and the other injecting current. The microelectrodes are filled with conductive solution and inserted into the cell to artificially control membrane potential. The membrane acts as a dielectric as well as a resistor, while the fluids on either side of the membrane function as capacitors.[9] The microelectrodes compare the membrane potential against a command voltage, giving an accurate reproduction of the currents flowing across the membrane. Current readings can be used to analyze the electrical response of the cell to different applications. This technique is mainly used in the Oocyte preparation. http://purl.obolibrary.org/obo/OBI_0002184 cut open oocyte voltage clamp assay http://purl.obolibrary.org/obo/OBI_0002182 voltage clamp assay COVG The cut-open oocyte Vaseline gap (COVG) voltage-clamp technique is designed to solve weaknesses in the two elextrode voltage clamp by maximizing the benefits of the Xenopus oocyte expression system by improving on clamp speed, signal-to-noise ratio, and ability to effectively perfuse the oocyte. In this way, it was possible to combine the most popular transient expression system, and the associated benefits of molecular cloning and site-directed mutagenesis, with the superior voltage-clamp properties of cut-open cell techniques. http://purl.obolibrary.org/obo/OBI_0002186 electroencephalography http://purl.obolibrary.org/obo/OBI_0000454 extracellular electrophysiology recording assay EEG An extracellular electrophysiology assay where electrodes are mounted outside the brain (either on the surface of the scalp on onto the brain surface itself during surgery) to measure the electrical field over the external surface. http://purl.obolibrary.org/obo/IAO_0000580 looking up a centrally registered identifier http://purl.obolibrary.org/obo/OBI_0000011 planned process looking up a CRID A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol http://purl.obolibrary.org/obo/OBI_0001970 multiplexed sequencing library http://purl.obolibrary.org/obo/OBI_0000047 processed material DNA-barcoded sequencing library a multiplexed library is a material entity which is the output of a library preparation process that uses a ligation step to attach a unique multiplexing sequence identifier to a specific sample, then mixes several such tagged samples prior to the library amplification process proper. A multiplexed library allows the sequencing of several samples in one sequencing run. http://purl.obolibrary.org/obo/IAO_0000005 objective specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity goal specification A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. http://purl.obolibrary.org/obo/IAO_0000027 data item http://purl.obolibrary.org/obo/IAO_0000030 information content entity data An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. http://purl.obolibrary.org/obo/IAO_0000035 obsolete_study interpretation http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class conclusion A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses http://purl.obolibrary.org/obo/IAO_0000132 lot number http://purl.obolibrary.org/obo/IAO_0000028 symbol batch number A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots. http://purl.obolibrary.org/obo/IAO_0000184 scatter plot http://purl.obolibrary.org/obo/IAO_0000038 graph scattergraph A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. http://purl.obolibrary.org/obo/IAO_0000300 textual entity http://purl.obolibrary.org/obo/IAO_0000030 information content entity text A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. http://purl.obolibrary.org/obo/IAO_0000311 publication http://purl.obolibrary.org/obo/IAO_0000310 document published document A document that is the output of a publishing process. http://purl.obolibrary.org/obo/IAO_0000312 publication about an investigation http://purl.obolibrary.org/obo/IAO_0000311 publication scientific publication A publication that is about an investigation http://purl.obolibrary.org/obo/IAO_0000315 abstract http://purl.obolibrary.org/obo/IAO_0000314 document part precis A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes. http://purl.obolibrary.org/obo/IAO_0000316 introduction to a publication about an investigation http://purl.obolibrary.org/obo/IAO_0000314 document part overview A part of a publication about an investigation that is about the objective specification (why the investigation is being done) http://purl.obolibrary.org/obo/IAO_0000317 methods section http://purl.obolibrary.org/obo/IAO_0000314 document part experimental methods A part of a publication about an investigation that is about the study design of the investigation http://purl.obolibrary.org/obo/IAO_0000318 results section http://purl.obolibrary.org/obo/IAO_0000314 document part results A part of a publication about an investigation that is about a study design execution http://purl.obolibrary.org/obo/IAO_0000319 discussion section of a publication about an investigation http://purl.obolibrary.org/obo/IAO_0000314 document part discussions A part of a publication about an investigation that is about the study interpretation of the investigation http://purl.obolibrary.org/obo/IAO_0000320 references section http://purl.obolibrary.org/obo/IAO_0000314 document part reference list A part of a document that has citations as parts http://purl.obolibrary.org/obo/IAO_0000323 author contributions section http://purl.obolibrary.org/obo/IAO_0000314 document part contributorship A part of a publication that is about the specific contributions of each author http://purl.obolibrary.org/obo/IAO_0000324 acknowledgements section http://purl.obolibrary.org/obo/IAO_0000314 document part acknowledgment Part of a publication that is about the contributions of people or institutions other than the authors. http://purl.obolibrary.org/obo/IAO_0000325 footnote http://purl.obolibrary.org/obo/IAO_0000314 document part footnotes A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document. http://purl.obolibrary.org/obo/IAO_0000326 supplementary material to a document http://purl.obolibrary.org/obo/IAO_0000314 document part supplementary materials A part of a document that is segregated from the rest of the document due to its size http://purl.obolibrary.org/obo/IAO_0000573 line graph http://purl.obolibrary.org/obo/IAO_0000038 graph line chart A line graph is a type of graph created by connecting a series of data points together with a line. http://purl.obolibrary.org/obo/IAO_0000574 assigning a centrally registered identifier http://purl.obolibrary.org/obo/OBI_0000011 planned process assigning a CRID A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity http://purl.obolibrary.org/obo/IAO_0000575 associating information with a centrally registered identifier in its registry http://purl.obolibrary.org/obo/OBI_0000011 planned process associating information with a CRID in the CRID registry A planned process in which a CRID registry associates an information content entity with a CRID symbol http://purl.obolibrary.org/obo/IAO_0000577 centrally registered identifier symbol http://purl.obolibrary.org/obo/IAO_0000028 symbol CRID symbol A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. http://purl.obolibrary.org/obo/IAO_0000578 centrally registered identifier http://purl.obolibrary.org/obo/IAO_0020000 identifier CRID An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. http://purl.obolibrary.org/obo/IAO_0000579 centrally registered identifier registry http://purl.obolibrary.org/obo/IAO_0000100 data set CRID registry A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process. http://purl.obolibrary.org/obo/IAO_0000584 time sampled measurement data set http://purl.obolibrary.org/obo/IAO_0000100 data set experimental time series A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time. http://purl.obolibrary.org/obo/OBI_0000014 regulator role http://purl.obolibrary.org/obo/OBI_0000017 regulatory role regulator a regulatory role involved with making and/or enforcing relevant legislation and governmental orders http://purl.obolibrary.org/obo/OBI_0000018 material supplier role http://purl.obolibrary.org/obo/OBI_0000947 service provider role supplier a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. http://purl.obolibrary.org/obo/OBI_0000020 contract research organization role http://purl.obolibrary.org/obo/OBI_0000116 worker role contract research organization a worker role of carrying out the study according to the protocol document or study plan delivered by the PI, under the control of the study director. This role cannot make decisions about the study execution http://purl.obolibrary.org/obo/OBI_0000023 classified data set http://purl.obolibrary.org/obo/IAO_0000100 data set data set with assigned class labels A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels. http://purl.obolibrary.org/obo/OBI_0000025 reference substance role http://purl.obolibrary.org/obo/BFO_0000023 role reference substance a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference. http://purl.obolibrary.org/obo/OBI_0000026 cytological stain role http://purl.obolibrary.org/obo/OBI_0000250 dye role cytological stain A dye role that is realized when the stain is used to colour cells and or cellular components for the purposes of visualization http://purl.obolibrary.org/obo/OBI_0000032 clinical research coordinator role http://purl.obolibrary.org/obo/OBI_0000116 worker role clinical research coordinator a worker role comprised of handling the administrative duties of a trial or study. http://purl.obolibrary.org/obo/OBI_0000040 drug role http://purl.obolibrary.org/obo/BFO_0000023 role drug a role borne by a molecular entity and is realized in a process of absorption by an organism alters, or effects (or is assumed to effect) a function(s) which inhere in an organism http://purl.obolibrary.org/obo/OBI_0000048 chromatography device http://purl.obolibrary.org/obo/OBI_0002089 physical store chromatography instrument A device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a ""mobile phase"" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated. http://purl.obolibrary.org/obo/OBI_0000056 notified body role http://purl.obolibrary.org/obo/OBI_0000273 role of regulator of consumables and medical devices notified body Notified body is regulator of consumables and medical devices charged by the Competent Authority with verifying compliance of medical devices (not drugs) with the applicable Essential Requirements stated in the Medical Device Directive http://purl.obolibrary.org/obo/OBI_0000060 trial monitor role http://purl.obolibrary.org/obo/OBI_0000102 responsible party role trial monitor a responsible party involved in planning, overseeing the conduct of a study or study component, and interpreting data from a study http://purl.obolibrary.org/obo/OBI_0000064 positive reference substance role http://purl.obolibrary.org/obo/OBI_0000025 reference substance role positive reference substance a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "100%" response http://purl.obolibrary.org/obo/OBI_0000068 reporting party role http://purl.obolibrary.org/obo/OBI_0000202 investigation agent role submitter a study personnel role played by a party who reports the outcome of a study component http://purl.obolibrary.org/obo/OBI_0000070 assay http://purl.obolibrary.org/obo/OBI_0000011 planned process scientific observation A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. http://purl.obolibrary.org/obo/OBI_0000073 sample preparation for assay http://purl.obolibrary.org/obo/OBI_0000094 material processing study A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI. http://purl.obolibrary.org/obo/OBI_0000086 reagent role http://purl.obolibrary.org/obo/BFO_0000023 role reagent A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer. http://purl.obolibrary.org/obo/OBI_0000089 role of regulator of chemical manufacturer http://purl.obolibrary.org/obo/OBI_0000014 regulator role regulator of chemical manufacture a regulator involved with making and enforcing legislation and governmental orders relevant to chemical manufacture http://purl.obolibrary.org/obo/OBI_0000092 role of certified IRB professional http://purl.obolibrary.org/obo/OBI_0000016 regulation-assigned role certified IRB professional a role of which inheres in a Homo sapiens and realized during administration and oversight of the daily activities of Institutional Review Boards (IRBs) in the USA http://purl.obolibrary.org/obo/OBI_0000093 patient role http://purl.obolibrary.org/obo/BFO_0000023 role patient a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider http://purl.obolibrary.org/obo/OBI_0000094 material processing http://purl.obolibrary.org/obo/OBI_0000011 planned process material transformation A planned process which results in physical changes in a specified input material http://purl.obolibrary.org/obo/OBI_0000102 responsible party role http://purl.obolibrary.org/obo/OBI_0000202 investigation agent role responsible party a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study http://purl.obolibrary.org/obo/OBI_0000103 principal investigator role http://purl.obolibrary.org/obo/OBI_0000102 responsible party role principal investigator a responsible party role played by a person responsible for the overall conduct of a study http://purl.obolibrary.org/obo/OBI_0000110 pH indicator dye role http://purl.obolibrary.org/obo/OBI_0000250 dye role pH indicator dye the role of a dye that is realized when the dye is used in an experiment to measure the pH in a material entity http://purl.obolibrary.org/obo/OBI_0000116 worker role http://purl.obolibrary.org/obo/OBI_0000202 investigation agent role worker a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline http://purl.obolibrary.org/obo/OBI_0000140 obsolete_label role http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class label Label role is a role which inheres in a material entity and which is realized in a detection of label assay http://purl.obolibrary.org/obo/OBI_0000143 baseline participant role http://purl.obolibrary.org/obo/OBI_0000220 reference subject role baseline participant a reference participant role which is realized by making the reference to qualities at the start of the study or intervention http://purl.obolibrary.org/obo/OBI_0000144 role of independent data monitoring committee http://purl.obolibrary.org/obo/OBI_0000060 trial monitor role independent data monitoring committee a trial monitor role charged recommending whether to continue, modify, or end the trial http://purl.obolibrary.org/obo/OBI_0000145 pathologist role http://purl.obolibrary.org/obo/OBI_0000116 worker role Pathologist a worker role of being responsible for making the histopathology diagnoses associated with data from a study; this activity occurs outside the study timeline http://purl.obolibrary.org/obo/OBI_0000154 role of Institutional Review Board http://purl.obolibrary.org/obo/OBI_0000014 regulator role Internal Review Board the role of a organization that is realized by members reviewing study designs for their agreement with regulations http://purl.obolibrary.org/obo/OBI_0000161 crossover population role http://purl.obolibrary.org/obo/OBI_0000220 reference subject role crossover population a role realized when a participant serves as reference to itself http://purl.obolibrary.org/obo/OBI_0000162 complete nutrient role http://purl.obolibrary.org/obo/OBI_0000204 nutrient role complete nutrient A nutrient role that inheres in a material entity and is realized in the use of that material entity by an organism to provide all needed nourishment. http://purl.obolibrary.org/obo/OBI_0000163 radiolabel role http://purl.obolibrary.org/obo/OBI_0002743 molecular label role radiolabel a molecular label role which inheres in a material entity which is realized by the process of radioactivity detection http://purl.obolibrary.org/obo/OBI_0000169 placebo role http://purl.obolibrary.org/obo/OBI_0000214 negative reference substance role placebo a negative reference substance is a reference role in which the substance playing the reference substance role is physically similar in appearance to the test substance http://purl.obolibrary.org/obo/OBI_0000174 study group role http://purl.obolibrary.org/obo/BFO_0000023 role study group population a study population role where the bearer is a population of material entities and the role is realized in the implementation of a study design wherein the entities bearing the study population role are observed or subjected to intervention according to the study design and are biological replicates, i.e. they receive the same treatment under the protocol http://purl.obolibrary.org/obo/OBI_0000188 role of pathology review board http://purl.obolibrary.org/obo/OBI_0000116 worker role pathology review board a worker role comprised of providing a confirmed and consensus diagnosis for histopathology results obtained during the investigation http://purl.obolibrary.org/obo/OBI_0000192 microtiter plate http://purl.obolibrary.org/obo/OBI_0000967 container microplate A microtiter_plate is a flat plate with multiple wells used as small test tubes. http://purl.obolibrary.org/obo/OBI_0000196 role of impartial witness http://purl.obolibrary.org/obo/OBI_0000016 regulation-assigned role impartial witness a role which inheres in a Homo sapiens and is realized during a clinical trial - the impartial witness is independent of the trial and cannot be unfairly influenced by people involved with the trial http://purl.obolibrary.org/obo/OBI_00001975 chromatin immunoprecipitation http://purl.obolibrary.org/obo/OBI_0000690 immunoprecipitation ChIP An immunoprecipitation in which chromatin (i.e. packaged DNA which can include protein and RNA complexes) is cut into short regions, reversibly cross linked, and antibodies or tags are used to select for pieces of chromatin with desired characteristics. http://purl.obolibrary.org/obo/OBI_0000198 biological replicate role http://purl.obolibrary.org/obo/OBI_0000220 reference subject role biological replicate a reference participant role realized by equivalent treatment of participants http://purl.obolibrary.org/obo/OBI_0000202 investigation agent role http://purl.obolibrary.org/obo/BFO_0000023 role investigator A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing. http://purl.obolibrary.org/obo/OBI_0000204 nutrient role http://purl.obolibrary.org/obo/BFO_0000023 role nutrient a role that inheres in a material entity and is realized in the use of that material entity by an organism when it is used in that organism's metabolism and provides nourishment. http://purl.obolibrary.org/obo/OBI_0000207 obsolete health care provider role http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class health care provider a worker role of providing medical care either within or outside the study timeline http://purl.obolibrary.org/obo/OBI_0000211 proxy respondent role http://purl.obolibrary.org/obo/OBI_0000116 worker role proxy respondent Proxy respondent is a worker role of describing patient's symptoms or condition to medical personnel http://purl.obolibrary.org/obo/OBI_0000214 negative reference substance role http://purl.obolibrary.org/obo/OBI_0000025 reference substance role negative reference substance a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "no effect" response http://purl.obolibrary.org/obo/OBI_0000215 role of legally acceptable representative http://purl.obolibrary.org/obo/OBI_0000016 regulation-assigned role legally acceptable representative a role which inheres in a human or organization who are able subject to applicable law to consent, on behalf of a prospective subject, to the subject`s participation in as clinical trial. http://purl.obolibrary.org/obo/OBI_0000220 reference subject role http://purl.obolibrary.org/obo/OBI_0000097 participant under investigation role reference participant a reference subject role which inheres in an organism or entity of organismal origin so that the characteristics or responses of the participant playing the reference participant role are used for comparison or reference http://purl.obolibrary.org/obo/OBI_0000221 vital dye role http://purl.obolibrary.org/obo/OBI_0000250 dye role vital dye A dye role that is realized when used to detect live cells in an experiment http://purl.obolibrary.org/obo/OBI_0000224 sub-investigator role http://purl.obolibrary.org/obo/OBI_0000116 worker role sub-investigator a worker role authorized to make study-related decisions and carry out tasks related to the study; this role occurs during the study timeline http://purl.obolibrary.org/obo/OBI_0000234 trial statistician role http://purl.obolibrary.org/obo/OBI_0000116 worker role trial statistician a worker role that analyzes data obtained during a trial or study; this role occurs after the trial or study is completed or terminated. http://purl.obolibrary.org/obo/OBI_0000243 sponsor role http://purl.obolibrary.org/obo/OBI_0000102 responsible party role sponsor a responsible party role involved with any of the following activities: initiating, managing and funding a study http://purl.obolibrary.org/obo/OBI_0000248 feed role http://purl.obolibrary.org/obo/OBI_0000162 complete nutrient role feed a role that inheres in a material entity and is realized in the use of that material entity by lab animal to provide all needed nourishment. http://purl.obolibrary.org/obo/OBI_0000249 technical replicate role http://purl.obolibrary.org/obo/OBI_0000220 reference subject role technical replicate technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay http://purl.obolibrary.org/obo/OBI_0000250 dye role http://purl.obolibrary.org/obo/OBI_0002743 molecular label role dye A molecular label role which inheres in a material entity and which is realized in the process of detecting a molecular dye that imparts color to some material of interest. http://purl.obolibrary.org/obo/OBI_0000264 obsolete_sample population http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class recruited population A sample population is an object aggregate that is selected from the population, e.g. the fish in the net that were sampled from the lake, the people that responded to the call for volunteers. http://purl.obolibrary.org/obo/OBI_0000273 role of regulator of consumables and medical devices http://purl.obolibrary.org/obo/OBI_0000014 regulator role drug regulatoy authority a regulator involved with making and enforcing legislation and governmental orders relevant to the development, testing, manufacture and use of food, drugs and medical devices http://purl.obolibrary.org/obo/OBI_0000286 precipitate http://purl.obolibrary.org/obo/OBI_0000047 processed material precipited material a precipitate is a material entity which is output of a precipitation process http://purl.obolibrary.org/obo/OBI_0000291 transcription factor binding site assay http://purl.obolibrary.org/obo/OBI_0001146 binding assay TF binding An assay tthat determines DNA regions specifically recognized by proteins that function as transcription factors http://purl.obolibrary.org/obo/OBI_0000318 eluate http://purl.obolibrary.org/obo/OBI_0000047 processed material eluted material a eluate is a material entity which results from an elution, e.g. from a chromatography column. it has as part a material entity with role mobile phase http://purl.obolibrary.org/obo/OBI_0000366 metabolite profiling assay http://purl.obolibrary.org/obo/OBI_0000070 assay metabolomic assay An assay that detects and identifies chemical entities resulting from biochemical and cellular metabolism http://purl.obolibrary.org/obo/OBI_0000384 electricity supply function http://purl.obolibrary.org/obo/OBI_0000391 energy supply function power supply An electricity supply function is an energy supply function to transfer electricity from one source to another, typically a consumer of the electricity or as a stimulus during a neuroscience experiment. http://purl.obolibrary.org/obo/OBI_0000389 isoelectric focusing device http://purl.obolibrary.org/obo/OBI_0002089 physical store isoelectric focusing unit An isoelectric focusing device is a device in which isoelectric focusing can be performed. An isoelectric focussing device had the function to contain and control the contained environment and transfer electrical energy from a power supply to a separation medium and the charged material to be separated. http://purl.obolibrary.org/obo/OBI_0000392 information processor function http://purl.obolibrary.org/obo/BFO_0000034 function data processor function An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process. http://purl.obolibrary.org/obo/OBI_0000393 signal conversion function http://purl.obolibrary.org/obo/OBI_0000392 information processor function transduction function A signal conversion function is an information processor function which transforms a signal into another type of signal. For example an analog-to-digital_converter, Ac/Ac converter, a synapse converts electrical action potentials into an intermediate chemical signal. The post synapse converts it back into an electric one passed on to the axon. http://purl.obolibrary.org/obo/OBI_0000398 image creation device http://purl.obolibrary.org/obo/OBI_0000832 measurement device image acquisition device An image creation device is a device which captures a digitized image of an object http://purl.obolibrary.org/obo/OBI_0000415 polymerase chain reaction http://purl.obolibrary.org/obo/OBI_0600058 enzymatic amplification PCR PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified. http://purl.obolibrary.org/obo/OBI_0000423 extract http://purl.obolibrary.org/obo/OBI_0000047 processed material extracted material an extract is a material entity which results from an extraction process http://purl.obolibrary.org/obo/OBI_0000424 transcription profiling assay http://purl.obolibrary.org/obo/OBI_0000070 assay gene expression profiling An assay that determines gene expression and transcription activity using ribonucleic acids collected from a material entity. http://purl.obolibrary.org/obo/OBI_0000435 genotyping assay http://purl.obolibrary.org/obo/OBI_0000443 analyte assay genotype profiling An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions. http://purl.obolibrary.org/obo/OBI_0000456 material transformation objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification artifact creation objective an objective specifiction that creates an specific output object from input materials. http://purl.obolibrary.org/obo/OBI_0000466 thermal conductivity detector http://purl.obolibrary.org/obo/OBI_0000637 gas chromatography detector TCD, hot wire detector The most commonly used detector in preparative GC is the thermal conductivity detector (hot wire detector). Even this detector, however, is often too sensitive and has too high a flow impedance. Under such circumstances, the procedure mentioned above must be employed. The eluent from the preparative column is split and a small portion diverted through the detector (sometimes with further dilution with carrier gas to reduce sensitivity). http://purl.obolibrary.org/obo/OBI_0000480 Bruker high resolution probe http://purl.obolibrary.org/obo/OBI_0000561 Bruker NMR probe HR Probe BRUKER BIOSPIN's experienced Research & Development group not only delivers top-performance probes for the more common experiments, but also a wealth of special probes for almost any application. For high resolution (HR) NMR we offer probes with a variety of important characteristics and features. http://purl.obolibrary.org/obo/OBI_0000506 photoionization detector http://purl.obolibrary.org/obo/OBI_0000637 gas chromatography detector PID The selective determination of aromatic hydrocarbons or organo-heteroatom species is the job of the photoionization detector (PID). This device uses ultraviolet light as a means of ionizing an analyte exiting from a GC column. The ions produced by this process are collected by electrodes. The current generated is therefore a measure of the analyte concentration. f the amount of ionization is reproducible for a given compound, pressure, and light source then the current collected at the PID's reaction cell electrodes is reproducibly proportional to the amount of that compound entering the cell. The reason why the compounds that are routinely analyzed are either aromatic hydrocarbons or heteroatom containing compounds (like organosulfur or organophosphorus species) is because these species have ionization potentials (IP) that are within reach of commercially available UV lamps. The available lamp energies range from 8.3 to 11.7 ev, that is, lambda max ranging from 150 nm to 106 nm. Although most PIDs have only one lamp, lamps in the PID are exchanged depending on the compound selectivity required in the analysis. http://purl.obolibrary.org/obo/OBI_0000509 electron capture detector http://purl.obolibrary.org/obo/OBI_0000637 gas chromatography detector ECD The electron capture detector is a GC detector that uses a radioactive Beta emitter (electrons) to ionize some of the carrier gas and produce a current between a biased pair of electrodes. When organic molecules that contain electronegative functional groups, such as halogens, phosphorous, and nitro groups pass by the detector, they capture some of the electrons and reduce the current measured between the electrodes. http://purl.obolibrary.org/obo/OBI_0000520 clinical chemistry assay http://purl.obolibrary.org/obo/OBI_0000443 analyte assay detection of analyte in blood sample An analyte assay which uses analytical methods to produce measurements and data on the concentration of chemical parameters (analytes) present in a bodily fluid collected from an organism. http://purl.obolibrary.org/obo/OBI_0000521 flame ionization detector http://purl.obolibrary.org/obo/OBI_0000637 gas chromatography detector FID A flame ionization detector is a GC detector that consist of a hydrogen/air flame and a collector plate which are normally heated independently of the chromatographic oven. Heating is necessary in order to prevent condensation of water generated by the flame and also to prevent any hold-up of solutes as they pass from the column to the flame. There is an electrode above the flame to collect the ions formed at a hydrogen/air flame. The number of ions hitting the collector is measured and a signal is generated. Flame ionization detectors are most widely used and generally applicable for gas chromatography and hence is used for routine and general purpose analysis. It is easy to use but destructive of the sample. http://purl.obolibrary.org/obo/OBI_0000523 magic angle spinning rotor http://purl.obolibrary.org/obo/OBI_0000968 device MAS rotor A rotor device that holds the NMR sample and enables the adjustment of the orientation of the rotation axis for a sample in a NMR instrument in the magic angle. http://purl.obolibrary.org/obo/OBI_0000527 flow high resolution probe http://purl.obolibrary.org/obo/OBI_0000480 Bruker high resolution probe flow HR-probe Hyphenated analytical techniques combining mass spectrometry and chromatography are well-established laboratory tools. The combination of chromatography and NMR has also made its way into the analytical laboratory. Further developments even combine all three techniques into an LC-NMR/NMR-MS system. The use of solid phase extraction provides an efficient interface between chromatography and NMR with demands for special type of flow probes. http://purl.obolibrary.org/obo/OBI_0000537 copy number variation profiling assay http://purl.obolibrary.org/obo/OBI_0000070 assay CNV analysis An assay that determines lost or amplified genomic regions of DNA by comparing genomic DNA originating from tissues from the same or different individuals using specific techniques such as CGH, array CGH, SNP genotyping http://purl.obolibrary.org/obo/OBI_0000552 reverse transcribed polymerase chain reaction http://purl.obolibrary.org/obo/OBI_0600058 enzymatic amplification reverse transcription polymerase chain reaction reverse transcribe pcr is a process which allow amplification of cDNA during a pcr reaction while the cDNA results from a retrotranscription of messenger RNA isolated from a material entity. http://purl.obolibrary.org/obo/OBI_0000566 NMR instrument http://purl.obolibrary.org/obo/OBI_0000832 measurement device NMR instrument An Instrument which is used to carry out a NMR analysis of some sample. http://purl.obolibrary.org/obo/OBI_0000569 mass selective detector http://purl.obolibrary.org/obo/OBI_0000637 gas chromatography detector mass spectrometry detector A mass selective detector is a GC detector that uses mass spectrometry. It is based upon the ionization of solute molecules in the ion source and the separation of the ions generated on the basis of their mass/charge ratio by an analyzer unit. This may be a magnetic sector analyzer, a quadruple mass filter, or an ion trap. Ions are detected by a dynode electron multiplier. http://purl.obolibrary.org/obo/OBI_0000576 scattered molecular aggregate http://purl.obolibrary.org/obo/BFO_0000040 material entity Collective a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates http://purl.obolibrary.org/obo/OBI_0000588 flame photometric detector http://purl.obolibrary.org/obo/OBI_0000637 gas chromatography detector FPD The determination of sulfur or phosphorus containing compounds is the job of the flame photometric detector (FPD). This device uses the chemiluminescent reactions of these compounds in a hydrogen/air flame as a source of analytical information that is relatively specific for substances containing these two kinds of atoms. The emitting species for sulfur compounds is excited S2. The lambda max for emission of excited S2 is approximately 394 nm. The emitter for phosphorus compounds in the flame is excited HPO (lambda max = doublet 510-526 nm). In order to selectively detect one or the other family of compounds as it elutes from the GC column, an interference filter is used between the flame and the photomultiplier tube (PMT) to isolate the appropriate emission band. The drawback here being that the filter must be exchanged between chromatographic runs if the other family of compounds is to be detected. http://purl.obolibrary.org/obo/OBI_0000591 Bruker BEST NMR system http://purl.obolibrary.org/obo/OBI_0000464 Bruker autosampler Bruker Efficient Sample Transfer NMR The introduction of biological screening and combinatorial chemistry for chemical synthesis has also introduced new requirements for NMR automation, e.g., the use of well plates for sample input, increased demands on throughput, and the need for quick and simple interpretation of the acquired NMR data. http://purl.obolibrary.org/obo/OBI_0000595 pulsed amperometric detector http://purl.obolibrary.org/obo/OBI_0000832 measurement device PAD A chromatography detector as used by high-performance anion exchange chromatography that provides sensitive and specific detection of carbohydrates. Pulsed Electrochemical Detection (PED) allows simple, sensitive, and direct detection of numerous polar aliphatic compounds, especially carbohydrates. This technique exploits the electrocatalytic activity of noble metal electrode surfaces to oxidize various polar functional groups. In PED, multi-step potential-time waveforms at Au and Pt electrodes realize amperometric/coulometric detection while maintaining uniform and reproducible electrode activity. The response mechanisms in PED are dominated by the surface properties of the electrode, and, as a consequence, members of each chemical class of compounds produce virtually identical voltammetric responses. Thus, the full potential is realized when combined with high performance liquid chromatography (HPLC). http://purl.obolibrary.org/obo/OBI_0000607 high resolution magic angle spin probe http://purl.obolibrary.org/obo/OBI_0000480 Bruker high resolution probe high resolution MAS, hr-MAS Samples that are neither solid nor liquid, being of biological, chemical, or pharmaceutical interest, reveal highly resolved spectra when magic angle spinning is applied. The correct solution is a gradient, such that the field varies along the spinner axis. This so-called Magic Angle Gradient is employed in Brukers high resolution Magic Angle Spinning (hr-MAS) probes, and is implemented in such a way that it is compatible with the stator and does not interfere with the sample eject or insert. Bruker BioSpin has developed a series of dedicated probes for standard bore magnets to accommodate the rapidly expanding field of hr-MAS. These probes are available in double (e.g. 1H and 13C) and triple resonance (e.g. 1H, 13C, 15N) modes and come equipped with a deuterium lock channel. The probes have automatic sample ejection and insertion capability, with the availability of an optional sample changer, enabling fully automated sample runs. Probes can be equipped with an optional B0 gradient, directed along the magic angle, so that gradient spectroscopy can be done used. http://purl.obolibrary.org/obo/OBI_0000612 Bruker MATCH tube holder system http://purl.obolibrary.org/obo/OBI_0000484 NMR sample holder Bruker Multiple Adjustable Tube Clamp Holder The Bruker Multiple Adjustable Tube Clamp Holder MATCH system is a holder for 100 mm long NMR sample tubes with diameters ranging from micro tubes up to 5 mm NMR tubes. The MATCH insert fits into a standard 10 mm Bruker spinner and is suitable for all non-spinning applications.n The MATCH system provides an easy and cost efficient means of optimizing the signal-to-noise ratio of each sample. By matching the NMR tube diameter to the size of the sample, most of the sample can be placed in the active column of the NMR coil. This leads to an enhanced signal detection compared to diluting the same sample quantity in a larger tube. http://purl.obolibrary.org/obo/OBI_0000615 protein expression profiling assay http://purl.obolibrary.org/obo/OBI_0000070 assay proteomic analysis An assay that determines protein expression and translation activity using protein extracts collected from a material entity. http://purl.obolibrary.org/obo/OBI_0000616 high resolution probe with automatic tuning and matching http://purl.obolibrary.org/obo/OBI_0000480 Bruker high resolution probe High Resolution Probes with Automatic Tuning and Matching, HR_probe_with_ATM The Automatic Tuning and Matching (ATM) option for AVANCE spectrometers is available for double resonance probes in fixed-frequency and broadband tunable configurations with either direct or indirect detection. Thus, for multinuclear operation, as often required for applications in inorganic chemistry, ATM facilitates the accurate setting of 90 degree pulse widths on both observe and decoupling channels for each chosen nucleus and each individual sample - even with full automation. Triple resonance probes in fixed-frequency configurations, as typically used for inverse detection with high-field systems. http://purl.obolibrary.org/obo/OBI_0000623 NMR spectroscopy assay http://purl.obolibrary.org/obo/OBI_0000070 assay Nuclear magnetic resonance spectroscopy An assay that exploits the magnetic properties of certain nuclei (those with a spin) to resonate when placed in particular magnetic field conditions. Instruments recording NMR spectrum and sets of analysis can be used to deduce identity of chemical as well as composition of complex chemical mixtures. http://purl.obolibrary.org/obo/OBI_0000626 DNA sequencing assay http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay nucleotide sequencing A sequencing assay which determines information on the sequence of a DNA molecule. http://purl.obolibrary.org/obo/OBI_0000629 Bruker solid magic angle spinning probe http://purl.obolibrary.org/obo/OBI_0000561 Bruker NMR probe solid MAS probe Magic angle spinning, nowadays a routine technique for solids NMR, still offers the capability of innovation. The high mechanical performance of MAS probes in conjunction with efficient rf pulse techniques open new exciting fields in solids NMR of biological samples and in the field of quadrupolar nuclei. http://purl.obolibrary.org/obo/OBI_0000630 hematology assay http://purl.obolibrary.org/obo/OBI_0000070 assay haematology An assay that studies blood and blood producing organs using a variety of techniques and instruments http://purl.obolibrary.org/obo/OBI_0000634 DNA methylation profiling assay http://purl.obolibrary.org/obo/OBI_0002020 epigenetic modification assay DNA methylation profiling An assay that measures the state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion. http://purl.obolibrary.org/obo/OBI_0000637 gas chromatography detector http://purl.obolibrary.org/obo/OBI_0000481 chromatography detector FID A gas chromatography detector is a chromatography detector that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a gas chromatographic process and thus permits the senses to appreciate the nature of the separation. There is no LC detector that has an equivalent performance to the flame ionization detector (FID) used in GC. In general, LC detectors have sensitivities of two to three orders of magnitude less than their GC counterparts and linear dynamic ranges one to two orders of magnitude lower. Only highly specific LC detectors have sensitivities that can approach those of GC detectors. http://purl.obolibrary.org/obo/OBI_0000642 atomic emission detector http://purl.obolibrary.org/obo/OBI_0000637 gas chromatography detector AED Instead of measuring simple gas phase (carbon containing) ions created in a flame as with the flame ionization detector, or the change in background current because of electronegative element capture of thermal electrons as with the electron capture detector, the AED has a much wider applicability because it is based on the detection of atomic emissions. The strength of the AED lies in the detector's ability to simultaneously determine the atomic emissions of many of the elements in analytes that elute from a GC capillary column (called eluants or solutes in some books). As eluants come off the capillary column they are fed into a microwave powered plasma (or discharge) cavity where the compounds are destroyed and their atoms are excited by the energy of the plasma. The light that is emitted by the excited particles is separated into individual lines via a photodiode array. The associated computer then sorts out the individual emission lines and can produce chromatograms made up of peaks from eluants that contain only a specific element. http://purl.obolibrary.org/obo/OBI_0000648 clustered data set http://purl.obolibrary.org/obo/IAO_0000100 data set data set with assigned discovered class labels A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels. http://purl.obolibrary.org/obo/OBI_0000658 data representational model http://purl.obolibrary.org/obo/IAO_0000033 directive information entity data structure specification Data representational model is an information content entity of the relationships between data items. A data representational model is encoded in a data format specification such as for cytoscape or biopax. http://purl.obolibrary.org/obo/OBI_0000659 specimen collection process http://purl.obolibrary.org/obo/OBI_0000011 planned process specimen collection A planned process with the objective of collecting a specimen. http://purl.obolibrary.org/obo/OBI_0000661 enzyme-linked immunosorbent assay http://purl.obolibrary.org/obo/OBI_0000443 analyte assay ELISA An analyte assay where binding of an enzyme linked antibody to a material entity that is immobilized on solid support is detected utilizing a chemiluminescent reaction. Depending on the setup, the enzyme-linked antibody could be binding directly to the analyte, or it serves as a secondary antibody detecting binding of the primary antibody to the analyte. http://purl.obolibrary.org/obo/OBI_0000663 class prediction data transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation supervised classification data transformation A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction. http://purl.obolibrary.org/obo/OBI_0000665 obsolete intracellular cytokine staining assay http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class ICCS The measurement of cytokines within the cytoplasm of a cell by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer. http://purl.obolibrary.org/obo/OBI_0000667 obsolete MHC multimer staining assay http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class MHC tetramer assay An MHC multimer assay is an assay that detects T cells capable of binding the MHC:ligand complexes present in the multimer. The multimer is fluorescently labelled. The T cells bound to multimers are counted in a flow cytometer http://purl.obolibrary.org/obo/OBI_0000674 center value http://purl.obolibrary.org/obo/IAO_0000027 data item median A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data. http://purl.obolibrary.org/obo/OBI_0000675 statistical hypothesis test objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective hypothesis test objective is a data transformation objective where the aim is to estimate statistical significance with the aim of proving or disproving a hypothesis by means of some data transformation http://purl.obolibrary.org/obo/OBI_0000679 average value http://purl.obolibrary.org/obo/IAO_0000027 data item arithmetic mean A data item that is produced as the output of an averaging data transformation and represents the average value of the input data. http://purl.obolibrary.org/obo/OBI_0000689 454 Genome Sequence 20 http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer GS 20 is a DNA sequencer first manufactured by 454 Life Science Corporation in 2005, and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. http://purl.obolibrary.org/obo/OBI_0000693 MeDIP-seq assay http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay Methylated DNA immunoprecipitation sequencing assay A DNA methylation profiling assay that identifies methylated sites in genomic DNA and determines the methylation pattern that affect gene transcription using immunoprecipitation of methylated genomic DNA, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods. http://purl.obolibrary.org/obo/OBI_0000695 chain termination sequencing assay http://purl.obolibrary.org/obo/OBI_0000734 DNA sequencing by synthesis assay dye terminator sequencing A DNA sequencing assay which rely on the use of dideoxynucleotides used in 4 distinct sequencing reaction on the same DNA sample. The dideoxynucleotides, once incorporated in the complementary DNA strand being synthesized by the DNA polymerase prevent any further chain elongation. The newly generated sequences are resolved on a polyacrylamide gel using electrophoresis and labels (either fluorochrome or radioactivity) are used to determine the nucleotide present at a given position http://purl.obolibrary.org/obo/OBI_0000697 Helicos sequencing assay http://purl.obolibrary.org/obo/OBI_0000734 DNA sequencing by synthesis assay true single molecule sequencing A DNA sequencing by synthesis assay that identifiies the sequnece of billions of DNA molecules immobilized to a surface using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not require an amplification step and is typically able to produce reads of 25 base pair length. http://purl.obolibrary.org/obo/OBI_0000698 obsolete_DNA ligase http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class ligase A DNA ligase is an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule http://purl.obolibrary.org/obo/OBI_0000700 support vector machine http://purl.obolibrary.org/obo/OBI_0000663 class prediction data transformation SVM A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space. http://purl.obolibrary.org/obo/OBI_0000701 self-organizing map http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating SOM A self-organizing map (SOM) is an artificial neural network with objective class discovery that uses a neighborhood function to preserve the topological properties of a dataset to produce low-dimensional (typically 2) discretized representation of the training data set. A set of artificial neurons learn to map points in an input space to coordinates in an output space. The input space can have different dimensions and topology from the output space, and the SOM will attempt to preserve these. http://purl.obolibrary.org/obo/OBI_0000702 454 Genome Sequencer FLX http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer GS-FLX is a DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths. http://purl.obolibrary.org/obo/OBI_0000709 yeast artificial chromosome vector http://purl.obolibrary.org/obo/CHEBI_4705 double-stranded DNA YAC a double-stranded DNA that was engineered to contain a yeast origin of replication, encodes for a selectable gene product, contains a cloning site, and has yeast telomerase sequences http://purl.obolibrary.org/obo/OBI_0000711 library preparation http://purl.obolibrary.org/obo/OBI_0000094 material processing library construction is a process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors. http://purl.obolibrary.org/obo/OBI_0000716 ChIP-seq assay http://purl.obolibrary.org/obo/OBI_0001954 ChIP assay chromatin immunoprecipitation sequencing assay An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA sequencing step to identify which parts of DNA are part of the isolated chromatin http://purl.obolibrary.org/obo/OBI_0000722 paired-end library http://purl.obolibrary.org/obo/OBI_0000047 processed material paired-end tag (PET) library is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs http://purl.obolibrary.org/obo/OBI_0000724 Solexa sequencing assay http://purl.obolibrary.org/obo/OBI_0000734 DNA sequencing by synthesis assay reversible terminator sequencing A DNA sequencing by synthesis assay that identifies sequence information using DNA polymerase and reversible terminator, requiring immobilization of genomic DNA fragments onto a surface and a specific clonal amplification step known as bridge PCR. Reliance on a reversible terminator allows cycles of DNA chain extension by DNA polymerase and imaging without the need of electrophoretic separation of newly synthesized DNA fragment as with Sanger sequencing. http://purl.obolibrary.org/obo/OBI_0000727 k-nearest neighbors http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating k-NN A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned. http://purl.obolibrary.org/obo/OBI_0000736 single fragment library http://purl.obolibrary.org/obo/OBI_0000047 processed material fragment library is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs http://purl.obolibrary.org/obo/OBI_0000744 material sampling process http://purl.obolibrary.org/obo/OBI_0000659 specimen collection process sampling A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity http://purl.obolibrary.org/obo/OBI_0000747 material sample http://purl.obolibrary.org/obo/OBI_0100051 specimen sample population A material entity that has the material sample role http://purl.obolibrary.org/obo/OBI_0000749 CART http://purl.obolibrary.org/obo/OBI_0000707 decision tree building data transformation classification and regression trees A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure. http://purl.obolibrary.org/obo/OBI_0000750 study design independent variable http://purl.obolibrary.org/obo/IAO_0000033 directive information entity independent variable a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled http://purl.obolibrary.org/obo/OBI_0000751 study design dependent variable http://purl.obolibrary.org/obo/IAO_0000033 directive information entity dependent variable dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies. http://purl.obolibrary.org/obo/OBI_0000785 study design controlled variable http://purl.obolibrary.org/obo/IAO_0000033 directive information entity controlled variable Controlled variable specification is a part of a study design. They are the entities that could vary, but are kept constant to prevent their influence on the effect of the independent variable on the dependent. http://purl.obolibrary.org/obo/OBI_0000787 human antithrombin-III in blood assay http://purl.obolibrary.org/obo/OBI_0000443 analyte assay AT-III assay An assay that measures the amount of antithrombin III in blood. http://purl.obolibrary.org/obo/OBI_0000791 multiple testing correction objective http://purl.obolibrary.org/obo/OBI_0200186 error correction objective multiple comparison correction objective A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously http://purl.obolibrary.org/obo/OBI_0000795 glucometer http://purl.obolibrary.org/obo/OBI_0000832 measurement device glucose meter A measurement device with the function to measure and record the level/amount of glucose in a blood sample http://purl.obolibrary.org/obo/OBI_0000796 purification objective http://purl.obolibrary.org/obo/OBI_0000681 separation into different composition objective isolation objective The objective to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest http://purl.obolibrary.org/obo/OBI_0000801 spike train datum http://purl.obolibrary.org/obo/IAO_0000109 measurement datum spike train measurement A measurement datum which represents information about an ordered series of action potentials in an organism's CNS measured over time. http://purl.obolibrary.org/obo/OBI_0000805 antithrombin-III berichrome assay http://purl.obolibrary.org/obo/OBI_0000787 human antithrombin-III in blood assay AT-III assay An antithrombin-III (AT-III) assay in which exogenous bovine thrombin and heparin are added to test plasma to form a thrombin-heparin-AT complex. The residual thrombin not bound then hydrolyzes the p-nitroalanine substrate to produce a yellow color, which is read at 405 nm. The intensity of color produced is inversely proportional to the AT present. A calibration is done with standard human plasma reagent and results for a given specimen are reported as a percentage relative to the standard http://purl.obolibrary.org/obo/OBI_0000807 presentation of stimulus http://purl.obolibrary.org/obo/OBI_0000011 planned process stimulation of organism a planned process in which an organism is exposed to some stimulus with the intent to invoke an action http://purl.obolibrary.org/obo/OBI_0000816 micro electrode http://purl.obolibrary.org/obo/OBI_0000832 measurement device micro electrode measuring device An electrode of very fine caliber consisting usually of a fine wire or a glass tube of capillary diameter drawn to a fine point and filled with saline or a metal used in physiological experiments to stimulate or record action currents of extracellular or intracellular origin in the nervous system. http://purl.obolibrary.org/obo/OBI_0000820 activated partial thromboplastin time assay http://purl.obolibrary.org/obo/OBI_0000070 assay aPTT assay An assay that evaluates blood coagulation by measuring the time required for the appearance of fibrin strands following the mixing blood or plasma with phospholipid platelet substitute (e.g., crude cephalins, soybean phosphatides). It is a test of the intrinsic pathway (factors VIII, IX, XI, and XII) and the common pathway (fibrinogen, prothrombin, factors V and X) of blood coaguation . It is used as a screening test and to monitor heparin therapy. http://purl.obolibrary.org/obo/OBI_0000836 test tube http://purl.obolibrary.org/obo/OBI_0000967 container sample tube A test tube is a device consisting of a glass or plastic tubing, open at the top, usually with a rounded U-shaped bottom which has the function to contain material http://purl.obolibrary.org/obo/OBI_0000860 northern blot assay http://purl.obolibrary.org/obo/OBI_0000443 analyte assay northern blot An assay that determines the presence of gene transcripts by hybridizing labeled RNA or DNA probes against messenger RNAs isolated from tissue or cell cultures, resolved on denaturing gel, transfered by a blotting procedure to a solid support. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager. http://purl.obolibrary.org/obo/OBI_0000865 96-well neutralization assay http://purl.obolibrary.org/obo/OBI_0000872 serum neutralization of viral infectivity assay microneutralization assay A serum neutralization of viral infectivity assay which is performed in a 96-well plate. http://purl.obolibrary.org/obo/OBI_0000871 viral hemagglutination assay http://purl.obolibrary.org/obo/OBI_0000443 analyte assay viral haemagglutinin assay An assay that quantifies viruses by their hemagglutination activity. http://purl.obolibrary.org/obo/OBI_0000872 serum neutralization of viral infectivity assay http://purl.obolibrary.org/obo/OBI_0000443 analyte assay influenza neutralization assay An analyte assay that measures virus-neutralizing abilities of different sera. Different dilutions of serum are mixed with virus and used to infect cells. At the lower dilutions, antibodies will block infection, but at higher dilutions, there will be too few antibodies to have an effect.The neutralization titer is expressed as the reciprocal of the highest dilution at which virus infection is blocked. http://purl.obolibrary.org/obo/OBI_0000875 viral hemagglutination inhibition assay http://purl.obolibrary.org/obo/OBI_0000070 assay viral haemagglutinin inhibition assay An assay that measures the ability of an evaluant to inhibit hemagglutination by a virus. Hemagglutinin is a viral protein which binds to sialic acid receptors on cells or to erythrocytes, causing the cells to clump. Loss of clumping indicates hemagglutination inhibition by the evaluant. http://purl.obolibrary.org/obo/OBI_0000877 cell line immortalization http://purl.obolibrary.org/obo/OBI_0001867 establishing cell line 'establishing immortal cell line through directed genetic modification' an establishing cell line process whereby a mortal cell line is intentionally genetically modified to be capable of indefinite propagation and re-established as a new immortal cell line http://purl.obolibrary.org/obo/OBI_0000892 Southern blot assay http://purl.obolibrary.org/obo/OBI_0000443 analyte assay Southern blot An analyte assay that detects the presence of a specific sequence in a DNA sample, which has been digested by restriction enzymes, resolved by gel electrophoresis, and blotted to a solid support, followed by hybridization of a probe raised against a specific sequence and detected with fluorescence or radioactivity. http://purl.obolibrary.org/obo/OBI_0000893 real time polymerase chain reaction assay http://purl.obolibrary.org/obo/OBI_0002692 polymerase chain reaction assay quantitative real time polymerase chain reaction An assay, based on the PCR, that amplifies and simultaneously quantifies a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. http://purl.obolibrary.org/obo/OBI_0000906 induced hemagglutination http://purl.obolibrary.org/obo/OBI_0000094 material processing hemeagglutination The clumping or clustering of red blood cells caused by certain viruses, antibodies, or other substances http://purl.obolibrary.org/obo/OBI_0000911 real time reverse-transcription polymerase chain reaction assay http://purl.obolibrary.org/obo/OBI_0002692 polymerase chain reaction assay qRT-PCR An assay that uses a reverse transcription step (an RNA strand is reverse transcribed into its DNA complement using the enzyme reverse transcriptase) before a PCR assay. http://purl.obolibrary.org/obo/OBI_0000918 Dulbecco's modified Eagle medium http://purl.obolibrary.org/obo/OBI_0000079 culture medium DMEM A culture medium containing iron, phenol red, amino acids, salts, glucose and vitamins. http://purl.obolibrary.org/obo/OBI_0000919 animal euthanization http://purl.obolibrary.org/obo/OBI_0600006 killing animal sacrifice A process in which is the end of life of animal is brought about in accordance with local regulations on treatment of animal subjects and using a method which causes minimal pain and distress to the animal subject http://purl.obolibrary.org/obo/OBI_0000920 cytometric bead array assay http://purl.obolibrary.org/obo/OBI_0000443 analyte assay Luminex assay An analyte assay in which a series of beads coated with antibodies specific for different analytes and marked with discrete fluorescent labels are used to simultaneously capture and quantitate soluble analytes. http://purl.obolibrary.org/obo/OBI_0000930 calorimeter http://purl.obolibrary.org/obo/OBI_0000832 measurement device calorimetry instrument? A measurement device that is used to calculate the heat flow of a chemical reaction or physical change. http://purl.obolibrary.org/obo/OBI_0000933 positron emission tomography scanner http://purl.obolibrary.org/obo/OBI_0000398 image creation device PET scanner? A device that produces a three-dimensional image or picture of functional processes in the body. It detects pairs of gamma rays emitted indirectly by a positron-emitting radionuclide (tracer), which is introduced into the body on a biologically active molecule. http://purl.obolibrary.org/obo/OBI_0000938 categorical measurement datum http://purl.obolibrary.org/obo/IAO_0000109 measurement datum nominal mesurement datum A measurement datum that is reported on a categorical scale http://purl.obolibrary.org/obo/OBI_0000944 handedness assay http://purl.obolibrary.org/obo/OBI_0000070 assay handedness test An assay that measures the unequal distribution of fine motor skill between the left and right hands typically in human subjects by means of some questionnaire and scoring procedure. http://purl.obolibrary.org/obo/OBI_0000966 in live organism assay http://purl.obolibrary.org/obo/OBI_0000070 assay in vivo assay An assay in which a measurement is made by observing entities located in an organism. http://purl.obolibrary.org/obo/OBI_0000968 device http://purl.obolibrary.org/obo/OBI_0000047 processed material instrument A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. http://purl.obolibrary.org/obo/OBI_0000970 scalar score from composite inputs http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum questionaire score A measurement datum which is the result of combining multiple datum. For example, a mean or summary score. http://purl.obolibrary.org/obo/OBI_0000982 computed tomography scanner http://purl.obolibrary.org/obo/OBI_0000398 image creation device X-ray computed tomography scanner An image acquisition device that generates a three-dimensional image of the inside of an object from a large series of two-dimensional X-ray images taken around a single axis of rotation. http://purl.obolibrary.org/obo/OBI_0001002 Faraday cage http://purl.obolibrary.org/obo/OBI_0001034 environmental control device Faraday shield A device formed by conducting material or by a mesh of such material, that blocks out external static electric fields. http://purl.obolibrary.org/obo/OBI_0001005 RNASE CL3 structure mapping assay http://purl.obolibrary.org/obo/OBI_0001014 single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing single nucleotide resolution mapping assay using RNAse CL3 A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse CL3 as reagent and enzymatic probe. http://purl.obolibrary.org/obo/OBI_0001006 CMCT structure mapping assay http://purl.obolibrary.org/obo/OBI_0001017 single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing single nucleotide resolution mapping assay using CMCT probe A single-nucleotide-resolution nucleic acid structure mapping assay which uses CMCT as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure http://purl.obolibrary.org/obo/OBI_0001007 image creation http://purl.obolibrary.org/obo/OBI_0000011 planned process image acquisition A planned process that captures an image of an object. http://purl.obolibrary.org/obo/OBI_0001008 MPE-Fe(II) structure mapping assay http://purl.obolibrary.org/obo/OBI_0001017 single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing single nucleotide resolution mapping assay using Fe-MP probe A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using Fe-MP as reagent and chemical probe. http://purl.obolibrary.org/obo/OBI_0001011 ENU structure mapping assay http://purl.obolibrary.org/obo/OBI_0001017 single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing single nucleotide resolution mapping assay using ENU probe A single-nucleotide-resolution nucleic acid structure mapping assay that determines the secondary structure of a nucleic acid at the nucleotide resolution scale which uses ENU as reagent and chemical probe http://purl.obolibrary.org/obo/OBI_0001012 RNASE V1 structure mapping assay http://purl.obolibrary.org/obo/OBI_0001014 single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing single nucleotide resolution mapping assay using RNAse V1 A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse V1 as reagent and enzymatic probe http://purl.obolibrary.org/obo/OBI_0001015 DMS structure mapping assay http://purl.obolibrary.org/obo/OBI_0001017 single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing single nucleotide resolution mapping assay using DMS probe A single-nucleotide-resolution nucleic acid structure mapping assay which determins nucleic acid secondary structure at a nucleotide resolution scale using DMS as reagent and chemical probe http://purl.obolibrary.org/obo/OBI_0001016 DNASE 1 structure mapping assay http://purl.obolibrary.org/obo/OBI_0001014 single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing single nucleotide resolution mapping assay using DNAse I A single-nucleotide-resolution deoxyribonucleic acid structure mapping assay which uses DNAse 1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure http://purl.obolibrary.org/obo/OBI_0001018 Rhodium DNA structure mapping assay http://purl.obolibrary.org/obo/OBI_0001017 single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing single nucleotide resolution mapping assay using Rhodium probe A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Rhodium as reagent and chemical probe. http://purl.obolibrary.org/obo/OBI_0001019 RNA ADA I RNA structure mapping assay http://purl.obolibrary.org/obo/OBI_0001014 single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing single nucleotide resolution mapping assay using RNA adenosine deaminase I A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNA adenosine deaminase I as reagent and enzymatic probe. http://purl.obolibrary.org/obo/OBI_0001020 Lead structure mapping assay http://purl.obolibrary.org/obo/OBI_0001017 single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing single nucleotide resolution mapping assay using Lead probe A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using lead as reagent and chemical probe http://purl.obolibrary.org/obo/OBI_0001021 RNASE T2 structure mapping assay http://purl.obolibrary.org/obo/OBI_0001014 single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing single nucleotide resolution mapping assay using RNAse T2 A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse T2 as reagent and enzymatic probe http://purl.obolibrary.org/obo/OBI_0001023 Fe-BABE RNA structure mapping assay http://purl.obolibrary.org/obo/OBI_0001017 single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing single nucleotide resolution mapping assay using Fe-BABE probe A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic secondary structure at a nucleotide resolution scale using Fe-BABE as reagent and chemical probe. http://purl.obolibrary.org/obo/OBI_0001024 RNASE U2 structure mapping assay http://purl.obolibrary.org/obo/OBI_0001014 single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing single nucleotide resolution mapping assay using RNAse U2 A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAase U2 as reagent and enzymatic probe http://purl.obolibrary.org/obo/OBI_0001026 NMIA RNA structure mapping assay http://purl.obolibrary.org/obo/OBI_0001017 single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing single nucleotide resolution mapping assay using NMIA probe A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using NMIA as reagent and chemical probe http://purl.obolibrary.org/obo/OBI_0001027 Terbium RNA structure mapping assay http://purl.obolibrary.org/obo/OBI_0001017 single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing single nucleotide resolution mapping assay using Terbium probe A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Terbium as reagent and chemical probe http://purl.obolibrary.org/obo/OBI_0001029 OH-radical structure mapping assay http://purl.obolibrary.org/obo/OBI_0001017 single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing single nucleotide resolution mapping assay using OH-radical probe A single-nucleotide-resolution nucleic acid structure mapping assay hat determines nucleic acid secondary structure at a nucleotide resolution scale using hydroxyl radical as reagent and chemical probe http://purl.obolibrary.org/obo/OBI_0001030 RNASE T1 structure mapping assay http://purl.obolibrary.org/obo/OBI_0001014 single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing single nucleotide resolution mapping assay using RNAse T1 A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale uses RNAse T1 as reagent and enzymatic probe. http://purl.obolibrary.org/obo/OBI_0001031 array image creation http://purl.obolibrary.org/obo/OBI_0001007 image creation array image acquisition An image creation process that generate an image from the array. http://purl.obolibrary.org/obo/OBI_0001035 Nuclease S1 structure mapping assay http://purl.obolibrary.org/obo/OBI_0001014 single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing single nucleotide resolution mapping assay using Nuclease S1 A single-nucleotide-resolution deoxyribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using DNAse 1 as reagent and enzymatic probe. http://purl.obolibrary.org/obo/OBI_0001041 stabilization function http://purl.obolibrary.org/obo/BFO_0000034 function isolation function A stabilization function is a function that holds or isolates an entity such as an instrument or specimen steadfast or at an unfluctuating level or quantity. http://purl.obolibrary.org/obo/OBI_0001121 gel electrophoresis system http://purl.obolibrary.org/obo/OBI_0001053 electrophoresis system electrophoresis system A device that moves charged particles through a medium by using an electric field induced by electrodes. http://purl.obolibrary.org/obo/OBI_0001138 X-ray source http://purl.obolibrary.org/obo/OBI_0000968 device x-ray generator A device that is used to generate X-rays. http://purl.obolibrary.org/obo/OBI_0001143 labeled nucleic acid extract http://purl.obolibrary.org/obo/OBI_0000924 labeled specimen labeled extract a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments. http://purl.obolibrary.org/obo/OBI_0001158 age determination assay http://purl.obolibrary.org/obo/OBI_0000070 assay age measurement assay An assay that determines the duration of part of the life of an organism, where the initial time point is the beginning of some transitional state (such as birth or when planted). http://purl.obolibrary.org/obo/OBI_0001171 half life datum (t 1/2) http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum t 1/2 The time it takes for 50% of a class of stochastic processes to occur. http://purl.obolibrary.org/obo/OBI_0001174 passive immunization http://purl.obolibrary.org/obo/OBI_0600007 administering substance in vivo adoptive transfer The injection of immune effector material (antibodies, T cells or B cells) into an organism so that the organisms immune system gains its immune effector function to recognize specific antigens. http://purl.obolibrary.org/obo/OBI_0001178 efficacy of epitope intervention experiment http://purl.obolibrary.org/obo/OBI_0000070 assay efficacy of in vivo intervention An assay that tests if inducing an epitope specific immune response in an organism has an effect, such as the ability to prevent, treat or excarbate diseases in the organism. http://purl.obolibrary.org/obo/OBI_0001179 epitope protection from infectious challenge experiment http://purl.obolibrary.org/obo/OBI_0001184 epitope protection experiment protection from infectious challenge An epitope protection experiment in which the ability of the epitope to protect the host from an infection is assessed. http://purl.obolibrary.org/obo/OBI_0001183 epitope protection from tumor challenge experiment http://purl.obolibrary.org/obo/OBI_0001184 epitope protection experiment tumor burden after challenge An epitope protection experiment in which the ability of the epitope to protect the host from developing tumors is assessed. http://purl.obolibrary.org/obo/OBI_0001184 epitope protection experiment http://purl.obolibrary.org/obo/OBI_0001178 efficacy of epitope intervention experiment protection from challenge An efficacy of epitope intervention experiment that tests the efficacy of inducing an immune epitope response to prevent disease in a host. http://purl.obolibrary.org/obo/OBI_0001185 selectively maintained organism http://purl.obolibrary.org/obo/OBI_0100026 organism strain An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms http://purl.obolibrary.org/obo/OBI_0001186 epitope protection from infectious challenge experiment based on pathogen burden http://purl.obolibrary.org/obo/OBI_0001179 epitope protection from infectious challenge experiment pathogen urden after infectious challenge An epitope protection from infectious challenge experiment in which the readout is a reduction in the presence of pathogens in the host compared to controls. http://purl.obolibrary.org/obo/OBI_0001188 epitope disease exacerbation experiment http://purl.obolibrary.org/obo/OBI_0001178 efficacy of epitope intervention experiment exacerbation assay An efficacy of epitope intervention experiment that tests the ability of inducing an epitope immune response to increase the severity of an existing disease in the host. http://purl.obolibrary.org/obo/OBI_0001189 epitope protection experiment based on survival http://purl.obolibrary.org/obo/OBI_0001184 epitope protection experiment host survival after challenge An epitope protection experiment that determines the success of the epitope intervention based on increased survival of the host. http://purl.obolibrary.org/obo/OBI_0001190 epitope treatment experiment http://purl.obolibrary.org/obo/OBI_0001178 efficacy of epitope intervention experiment decreased disease symptoms after treatment An epitope intervention experiment that tests the ability of inducing an epitope immune response to treat an existing disease in the host. http://purl.obolibrary.org/obo/OBI_0001248 ChIP-chip assay http://purl.obolibrary.org/obo/OBI_0001954 ChIP assay ChIP-on-chip assay An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA microarray to identify which parts of DNA are part of the isolated chromatin http://purl.obolibrary.org/obo/OBI_0001271 RNA-seq assay http://purl.obolibrary.org/obo/OBI_0001177 RNA sequencing assay transcription profiling by high throughput sequencing An RNA sequencing assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance. http://purl.obolibrary.org/obo/OBI_0001307 tiling microarray http://purl.obolibrary.org/obo/OBI_0400148 DNA microarray genome tiling array A DNA microarray which has short fragments of nucleic acid immobilized on a substrate. These are designed to cover the whole genome of the target species. Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions. http://purl.obolibrary.org/obo/OBI_0001393 comparative genomic hybridization by array assay http://purl.obolibrary.org/obo/OBI_0001985 microarray assay array CGH An assay that measures changes in DNA sequence copy number using a microarray. For example the analysis of LOH in tumor cells vs a non diseased sample or the comparison of clinical isolated of disease causing bacteria. http://purl.obolibrary.org/obo/OBI_0001403 ChIP-chip design http://purl.obolibrary.org/obo/OBI_0001425 protein binding site identification design ChIP-on-chip design A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and DNA microarray (chip) assays. http://purl.obolibrary.org/obo/OBI_0001442 q-value http://purl.obolibrary.org/obo/OBI_0000071 quantitative confidence value FDR adjusted p-value A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant. To compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level. http://purl.obolibrary.org/obo/OBI_0001463 transcription profiling by array assay http://purl.obolibrary.org/obo/OBI_0000424 transcription profiling assay RNA profiling by array assay A transcription profiling assay that uses array technology. http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism http://purl.obolibrary.org/obo/OBI_0100051 specimen tissue specimen A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). http://purl.obolibrary.org/obo/OBI_0001486 disposition to be bound by an MHC protein complex http://purl.obolibrary.org/obo/BFO_0000016 disposition MHC ligand disposition Is the disposition borne by a material entity that is realized in a process of being bound in the antigen binding grove of an MHC protein complex. http://purl.obolibrary.org/obo/OBI_0001488 epitope tolerance induction experiment http://purl.obolibrary.org/obo/OBI_0001178 efficacy of epitope intervention experiment tolerance induction An efficacy of epitope intervention experiment that tests the ability of the intervention to decrease an existing immune response http://purl.obolibrary.org/obo/OBI_0001508 sampling time measurement datum http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum time point A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point. http://purl.obolibrary.org/obo/OBI_0001566 50% dissociation of binding temperature (Tm) http://purl.obolibrary.org/obo/OBI_0001181 binding datum melting temperature (Tm) A binding datum that specifies the temperature at which half of the binding partners are forming a complex and the other half are unbound. http://purl.obolibrary.org/obo/OBI_0001616 specimen identifier http://purl.obolibrary.org/obo/IAO_0000577 centrally registered identifier symbol specimen ID A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation. http://purl.obolibrary.org/obo/OBI_0001617 PubMed ID http://purl.obolibrary.org/obo/IAO_0000577 centrally registered identifier symbol PubMed Identifier A CRID symbol that is sufficient to look up a citation from the PubMed, a literature database of life sciences and biomedical information. http://purl.obolibrary.org/obo/OBI_0001619 specimen collection time measurement datum http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum collection date A time measurement datum that is the measure of the time when the specimens are collected. http://purl.obolibrary.org/obo/OBI_0001620 latitude coordinate measurement datum http://purl.obolibrary.org/obo/IAO_0000109 measurement datum latitude A measurement datum that is the measure of the latitude coordinate of a site. http://purl.obolibrary.org/obo/OBI_0001621 longitude coordinate measurement datum http://purl.obolibrary.org/obo/IAO_0000109 measurement datum longitude A measurement datum that is the measure of the longitude coordinate of a site. http://purl.obolibrary.org/obo/OBI_0001626 Bioinformatics Resource Center http://purl.obolibrary.org/obo/OBI_0000245 organization BRC An organization that is one of the Internet-based research centers established and funded by NIAID (the National Institute of Allergy and Infectious Diseases). The Bioinformatics Resource Centers (BRCs) were formed in response to the threats posed by emerging and re-emerging pathogens, particularly CDC Category A, B, and C pathogens, and their potential use in bioterrorism. The intention of NIAID in funding these bioinformatics centers is to assist researchers involved in the experimental characterization of such pathogens and the formation of drugs, vaccines, or diagnostic tools to combat them. http://purl.obolibrary.org/obo/OBI_0001670 RNA protection assay http://purl.obolibrary.org/obo/OBI_0000070 assay RNAse protection assay An assay that determines the presence and estimates abundance of transcript species by first creating an homo or heteroduplex by adding a specific, complementary sequence to the sequence of interest and then exposing the mixture of ribonuclease, which will degrade only single stranded molecules. A detection step will reveal if the sample contained a sequence of interest. http://purl.obolibrary.org/obo/OBI_0001671 electrophoretic mobility shift assay http://purl.obolibrary.org/obo/OBI_0001146 binding assay gel mobility shift assay An assay that measures information about Protein-DNA or Protein-RNA interactions using gel electrophoresis and relying on the fact the molecular interactions will cause the heterodimer to be retarded on the gel when compared to controls corresponding to protein extract alone and protein extract + neutral nucleic acid. http://purl.obolibrary.org/obo/OBI_0001673 nano-cap analysis of gene expression assay http://purl.obolibrary.org/obo/OBI_0000424 transcription profiling assay nano-CAGE A transcription profiling assay that is performed using a very low amount (nanogram scale) of mRNA samples using Cap analysis gene expression (CAGE). http://purl.obolibrary.org/obo/OBI_0001674 cap analysis of gene expression assay http://purl.obolibrary.org/obo/OBI_0002692 polymerase chain reaction assay CAGE A transcription profiling assay which measures RNA transcript abundances in biological samples by extracting 5' ends of capped transcripts, RTPCR and sequence those. Copy numbers of CAGE tags provide a way of quantification and provide a measure of expression of the transcriptome http://purl.obolibrary.org/obo/OBI_0001679 yeast 2-hybrid assay http://purl.obolibrary.org/obo/OBI_0001146 binding assay Y2H An assay that detects protein protein interactions and protein DNA interactions by testing for physical interactions (such as binding) between two proteins or a single protein and a DNA molecule, respectively. The premise behind the test is the activation of downstream reporter gene(s) by the binding of a transcription factor onto an upstream activating sequence (UAS). For two-hybrid screening, the transcription factor is split into two separate fragments, called the binding domain (BD) and activating domain (AD). The BD is the domain responsible for binding to the UAS and the AD is the domain responsible for the activation of transcription. The Y2H is thus a protein-fragment complementation assay. http://purl.obolibrary.org/obo/OBI_0001680 Sos-recruitment assay http://purl.obolibrary.org/obo/OBI_0001146 binding assay SRS A binding assay that detects interacting proteins for a targeted domain where mammalian guanyl nucleotide exchange factor (GEF) Sos is recruited to the Saccharomyces cerevisiae plasma membrane harboring a temperature-sensitive Ras GEF, Cdc25-2, allowing growth at the nonpermissive temperature using the Sos recruitment system, a kind of yeast 2 hybrid system. http://purl.obolibrary.org/obo/OBI_0001681 yeast one-hybrid assay http://purl.obolibrary.org/obo/OBI_0001146 binding assay Y1H An assay that determines protein DNA interactions using a single fusion protein in which the activating domain is linked directly to the binding domain. http://purl.obolibrary.org/obo/OBI_0001682 bacterial one-hybrid assay http://purl.obolibrary.org/obo/OBI_0001681 yeast one-hybrid assay B1H An assay that identifies the sequence-specific target site of a DNA-binding domain. In this system, a given transcription factor (TF) is expressed as a fusion to a subunit of RNA polymerase. In parallel, a library of randomized oligonucleotides representing potential TF target sequences, is cloned into a separate vector containing the selectable genes HIS3 and URA3. If the DNA-binding domain (bait) binds a potential DNA target site (prey) in vivo, it will recruit RNA polymerase to the promoter and activate transcription of the reporter genes in that clone. The two reporter genes, HIS3 and URA3, allow for positive and negative selections, respectively. At the end of the process, positive clones are sequenced and examined with motif-finding tools in order to resolve the favoured DNA target sequence http://purl.obolibrary.org/obo/OBI_0001683 chromosome organization assay by fluorescence in-situ hybridization http://purl.obolibrary.org/obo/OBI_0001686 in-situ hybridization assay FISH An in-situ hybridization assay that uses fluorescence to detect chromosomal integrity http://purl.obolibrary.org/obo/OBI_0001684 methylation-specific polymerase chain reaction assay http://purl.obolibrary.org/obo/OBI_0000070 assay MSP An assay that uses initial modification of DNA by sodium bisulfite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA. http://purl.obolibrary.org/obo/OBI_0001685 amplification of intermethylated sites assay http://purl.obolibrary.org/obo/OBI_0000634 DNA methylation profiling assay intermethylated site amplification An assay that estimates genome-wide DNA methylation and measures methylation of DNA sequences. AIMS is based on the differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers followed by restrained PCR amplification of methylated sequences. http://purl.obolibrary.org/obo/OBI_0001686 in-situ hybridization assay http://purl.obolibrary.org/obo/OBI_0000070 assay in situ hybridization An assay that localizes a specific DNA or RNA sequence within a portion or section of tissue using artificially induced nucleic hybridization. http://purl.obolibrary.org/obo/OBI_0001699 antibody cross-blocking assay http://purl.obolibrary.org/obo/OBI_0001593 competitive inhibition of binding assay antibody inhibition of antibody binding A competitive inhibition of binding assay in which two antibodies that are known to bind the same antigen are tested for the ability of one antibody to inhibit binding of the other antibody to the antigen, thereby determining if they have overlapping binding sites. http://purl.obolibrary.org/obo/OBI_0001755 selection criterion http://purl.obolibrary.org/obo/IAO_0000033 directive information entity selection rule A directive information entity which defines and states a principle of standard by which selection process may take place. http://purl.obolibrary.org/obo/OBI_0001848 chromatin interaction analysis by paired-end tag sequencing assay http://purl.obolibrary.org/obo/OBI_0002438 nuclear ligation assay ChIA-PET assay An assay that incorporates chromatin immunoprecipitation (ChIP)-based enrichment, chromatin proximity ligation, Paired-End Tags, and high-throughput sequencing to determine de novo long-range chromatin interactions genome-wide. http://purl.obolibrary.org/obo/OBI_0001849 structural analysis by paired-end tag sequencing assay http://purl.obolibrary.org/obo/OBI_0000626 DNA sequencing assay DNA-PET assay An assay that incorporates Paired-End Tags and sequencing technology to determine structural variants. http://purl.obolibrary.org/obo/OBI_0001850 transcript analysis by paired-end tag sequencing assay http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay RNA-PET assay A transcription profiling assay that determines transcripts, gene structures, and gene expressions using Paired-End Tags and sequencing technology. http://purl.obolibrary.org/obo/OBI_0001857 RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay RIP-seq assay An analyte assay that combines immunoprecipitation of an RNA-binding protein and RNA-seq to identify mRNAs associated with selected RNA binding proteins (RBPs). http://purl.obolibrary.org/obo/OBI_0001858 cross-linking immunoprecipitation high-throughput sequencing assay http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay CLIP-seq assay An analyte assay that employs UV-crosslinking between RNA and a protein, followed by immunoprecipitation with antibodies for the protein, fragmentation, and high-throughput screening for RNA sequences that interact with a particular RNA-binding protein. http://purl.obolibrary.org/obo/OBI_0001859 formaldehyde-assisted isolation of regulatory elements assay http://purl.obolibrary.org/obo/OBI_0000626 DNA sequencing assay FAIRE-seq assay An assay to determine the sequences of those DNA regions in the genome associated with regulatory activity. http://purl.obolibrary.org/obo/OBI_0001861 methylation-sensitive restriction enzyme sequencing assay http://purl.obolibrary.org/obo/OBI_0001266 DNA methylation profiling by high throughput sequencing assay MRE-seq assay An assay that identifies unmethylated CpGs using methylation sensitive restriction enzymes to fragment DNA. http://purl.obolibrary.org/obo/OBI_0001862 reduced representation bisulfite sequencing assay http://purl.obolibrary.org/obo/OBI_0000748 bisulfite sequencing assay reduced representation bisulfite-seq A bisulfite sequencing assay that identifies genomic methylation patterns using a bisulfite based protocol that enriches CG-rich parts of the genome. http://purl.obolibrary.org/obo/OBI_0001863 shotgun bisulfite-seq assay http://purl.obolibrary.org/obo/OBI_0000748 bisulfite sequencing assay whole-genome shotgun bisulfite sequencing A bisulfite sequencing assay that identifies methylated cytosines across the genome using high throughput sequencing. http://purl.obolibrary.org/obo/OBI_0001864 RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay RAMPAGE An transcription profiling assay that identifies transcription start sites (TSS), the quantification of their expression and the characterization of their transcripts using high throughput sequencing. http://purl.obolibrary.org/obo/OBI_0001868 genetic material http://purl.obolibrary.org/obo/CHEBI_33696 nucleic acid hereditary genetic material A nucleic acid macromolecule that is part of a cell or virion and is inherited from an immediate ancestor, or incorporated in a manner that it has the disposition to be replicated and inherited by descendants. http://purl.obolibrary.org/obo/OBI_0001875 cultured immune cell population http://purl.obolibrary.org/obo/OBI_0100060 cultured cell population immune cell culture sample a cultured cell population comprised of a single type of immune system cell http://purl.obolibrary.org/obo/OBI_0001877 random access memory http://purl.obolibrary.org/obo/IAO_0000178 material information bearer RAM Random-access memory (RAM) is a form of computer data storage. A random-access device allows stored data to be accessed directly in any random order. In contrast, other data storage media such as hard disks, CDs, DVDs and magnetic tape, as well as early primary memory types such as drum memory, read and write data only in a predetermined order, consecutively, because of mechanical design limitations. Therefore, the time to access a given data location varies significantly depending on its physical location http://purl.obolibrary.org/obo/OBI_0001905 secondary cultured cell population http://purl.obolibrary.org/obo/OBI_0100060 cultured cell population secondary cell culture sample A cultured cell population that is derived through one or more passages in culture. http://purl.obolibrary.org/obo/OBI_0001908 testable hypothesis http://purl.obolibrary.org/obo/IAO_0000030 information content entity hypothesis An information content entity that expresses an assertion that is intended to be tested. http://purl.obolibrary.org/obo/OBI_0001913 computation run time http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum computation run time datum computation run time is a time measurement datum which corresponds the time expressed in second, minute, hour necessary for a computer program to complete a process execution, for example genome assembly. It is an important metrics as it indicates the resource occupancy and computer program efficiency. http://purl.obolibrary.org/obo/OBI_0001914 multiplex ligation-mediated amplification http://purl.obolibrary.org/obo/OBI_0000415 polymerase chain reaction Multiplex ligation-dependent probe amplification A polymerase chain reaction that amplifies multiple targets with a single primer pair mediated by hybridization of a primer with its target sequence using ligation. http://purl.obolibrary.org/obo/OBI_0001915 DNA replication timing by array assay http://purl.obolibrary.org/obo/OBI_0002692 polymerase chain reaction assay Repli-chip assay An assay which quantifies the timing of DNA replication as a function of genome position using array technology. http://purl.obolibrary.org/obo/OBI_0001918 RNA-binding protein immunoprecipitation array profiling assay http://purl.obolibrary.org/obo/OBI_0001985 microarray assay RIP-chip assay An assay that combines immunoprecipitation of an RNA-binding protein and array technology to identify mRNAs associated with selected RNA binding proteins (RBPs). http://purl.obolibrary.org/obo/OBI_0001919 Carbon-copy chromosome conformation capture assay http://purl.obolibrary.org/obo/OBI_0002692 polymerase chain reaction assay 5C assay An assay that measures the organization of chromosomes at the genome-wide scale. http://purl.obolibrary.org/obo/OBI_0001920 DNA replication timing by sequencing assay http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay Repli-seq assay An assay in which timing of DNA replication is quantified as a function of genome position based on genome-wide sequencing. http://purl.obolibrary.org/obo/OBI_0001922 microRNA profiling by high throughput sequencing assay http://purl.obolibrary.org/obo/OBI_0001926 microRNA profiling assay microRNA-seq assay A microRNA profiling assay that analyzes the microRNA component of the transcriptome using high throughput sequencing technology. http://purl.obolibrary.org/obo/OBI_0001924 micrococcal nuclease digestion followed by high throughput sequencing assay http://purl.obolibrary.org/obo/OBI_0000626 DNA sequencing assay MNase-seq assay An assay that identifies nucleosome positioning by genome wide sequencing of regions sensitive to digestion by micrococal nuclease http://purl.obolibrary.org/obo/OBI_0001925 chromatin immunoprecipitation with exonuclease sequencing assay http://purl.obolibrary.org/obo/OBI_0000716 ChIP-seq assay ChIP-exo assay A ChIP-seq assay which uses immunoprecipitation to isolate protein bound DNA followed by an exonuclease step to degrade DNA that is not protein bound to provide greater resolution of the DNA binding site http://purl.obolibrary.org/obo/OBI_0001926 microRNA profiling assay http://purl.obolibrary.org/obo/OBI_0000424 transcription profiling assay microRNA expression assay A transcription profiling assay that quantifies the microRNA species within a biological sample. http://purl.obolibrary.org/obo/OBI_0001928 selection http://purl.obolibrary.org/obo/OBI_0000011 planned process selection process A planned process which results in the creation of group of entity from a larger group by the application of predefined criteria. http://purl.obolibrary.org/obo/OBI_0001940 N50 http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum weighted median item size the weighted median item size or N50 is a weighted median of the lengths of items, equal to the length of the longest item i such that the sum of the lengths of items greater than or equal in length to i is greater than or equal to half the length of all of the items. With regard to assemblies the items are typically contigs or scaffolds. It therefore denotes the ability of the software to create contigs and provides information about the resulting sequence assembly http://purl.obolibrary.org/obo/OBI_0001942 grant agency http://purl.obolibrary.org/obo/OBI_0000245 organization funding organization An organization that provides funding support for projects such as investigations. http://purl.obolibrary.org/obo/OBI_0001946 forward PCR primer http://purl.obolibrary.org/obo/CHEBI_16991 deoxyribonucleic acid sense primer A short oligonucleotide complementary to target DNA (5'->3' on plus strand) that acts as the leader for DNA extension in a PCR reaction. The polymerase starts replication at the 3'-end of the primer, and copies the opposite strand. A primer is characterized by its 'melting temperature' (Tm) and pairs of primers should have similar Tm. http://purl.obolibrary.org/obo/OBI_0001951 reverse PCR primer http://purl.obolibrary.org/obo/CHEBI_16991 deoxyribonucleic acid reverse primer A short oligonucleotide complementary to target DNA (5'->3' on minus strand) that acts as the leader for DNA extension in a PCR reaction. The polymerase starts replication at the 3'-end of the primer, and copies the opposite strand. A primer is characterized by its 'melting temperature' (Tm) and pairs of primers should have similar Tm. http://purl.obolibrary.org/obo/OBI_0001954 ChIP assay http://purl.obolibrary.org/obo/OBI_0000070 assay chromatin immunoprecipitation assay An assay in which portions of chromatin, the ordered and organized complex of DNA and its interaction partners that make up a chormosome, is extracted and purified by immunoprecipitation with antibodies or tags, and subsequently analyzed http://purl.obolibrary.org/obo/OBI_0001960 taxonomic diversity assessment by targeted gene survey http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay targeted gene survey DNA barcoding An assay that dteremines taxonomic and community diversity information by sequencing specific genomic regions used as marker of identity or diversity. http://purl.obolibrary.org/obo/OBI_0001964 decision-theoretic analysis objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification decision analysis objective An objective specification which what includes a description of two or more alternative actions to take in a particular situation and a metric that enables comparisons of the two actions. The objective specified is achieved in a planned process which includes a data transformation, the output of which is an identification of the 'best' choice according to the metric. http://purl.obolibrary.org/obo/OBI_0001971 Ion 316 Chip v2 http://purl.obolibrary.org/obo/OBI_0001973 ion semiconductor chip Ion PGM 316 Chip v2 An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 316 chip is compatible with the Ion Torrent PGM and has a run time of: 3.0 hours for 200 bp reads with an output of 30-50 Mb, 4.9 hours for 400 bp reads with an output of 60 Mb-1 Gb. http://purl.obolibrary.org/obo/OBI_0001972 Ion 318 Chip v2 http://purl.obolibrary.org/obo/OBI_0001973 ion semiconductor chip Ion PGM 318 Chip v2 An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 318 chip is compatible with the Ion Torrent PGM and has a run time of: 4.4 hours for 200 bp reads with an output of 60 Mb-1 Gb, 7.3 hours for 400 bp reads with an output of 1.2 Gb-2 Gb. http://purl.obolibrary.org/obo/OBI_0001973 ion semiconductor chip http://purl.obolibrary.org/obo/OBI_0000364 ion detector ion semiconductor An ion detector that is organized as an electronic circuit whose components, such as transistors and resistors, are etched or deposited on a single slice of semiconductor material to produce a chip. The specific chip detects ion charge induced when an ion passes by or hits a surface. http://purl.obolibrary.org/obo/OBI_0001974 Ion 314 Chip v2 http://purl.obolibrary.org/obo/OBI_0001973 ion semiconductor chip Ion PGM 314 Chip v2 An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 314 chip is compatible with the Ion Torrent PGM and has a run time of: 2.3 hours for 200 bp reads with an output of 30-50 Mb, 3.7 hours for 400 bp reads with an output of 60-100 Mb. http://purl.obolibrary.org/obo/OBI_0002000 Genome Analyzer IIx http://purl.obolibrary.org/obo/OBI_0000703 Illumina Genome Analyzer II Illumina GA IIx An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. http://purl.obolibrary.org/obo/OBI_0002001 Illumina HiSeq 2000 http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer HiSeq 2000 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. http://purl.obolibrary.org/obo/OBI_0002002 Illumina HiSeq 2500 http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer HiSeq 2500 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. http://purl.obolibrary.org/obo/OBI_0002003 MiSeq http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer Illumina MiSeq A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. http://purl.obolibrary.org/obo/OBI_0002004 Methylation 450K BeadChip http://purl.obolibrary.org/obo/OBI_0001870 Illumina methylation BeadChip Illumina Infinium Human Methylation 450K BeadChip A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 485,000 methylation sites per sample at single-nucleotide resolution. http://purl.obolibrary.org/obo/OBI_0002005 Methylation 27K BeadChip http://purl.obolibrary.org/obo/OBI_0001870 Illumina methylation BeadChip Illumina Infinium Human Methylation 27K BeadChip A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 27,000 CpG sites per sample at single-nucleotide resolution. http://purl.obolibrary.org/obo/OBI_0002006 1M-Duo Infinium HD BeadChip http://purl.obolibrary.org/obo/OBI_0001869 Illumina BeadChip Illumina Human 1M-Duo Infinium HD BeadChip A BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array integrates ~ 1 million markers per sample for genotyping, and copy number variation (CNV) and Cytogenetic analysis. http://purl.obolibrary.org/obo/OBI_0002007 SOLiD 3 Plus System http://purl.obolibrary.org/obo/OBI_0000696 AB SOLiD System Applied Biosystems SOLiD 3 Plus System A DNA sequencer which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. http://purl.obolibrary.org/obo/OBI_0002008 Mouse 385K Whole Genome CGH Tiling Array http://purl.obolibrary.org/obo/OBI_0001307 tiling microarray Nimblegen Mouse 385K Whole Genome CGH Tiling Array A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 385,000 features. http://purl.obolibrary.org/obo/OBI_0002009 Mouse 3x720K Whole Genome CGH Tiling Array http://purl.obolibrary.org/obo/OBI_0001307 tiling microarray Nimblegen Mouse 3x720K Whole Genome CGH Tiling Array A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 3x720,000 features. http://purl.obolibrary.org/obo/OBI_0002010 Human 3x720K Whole Genome CGH Tiling Array http://purl.obolibrary.org/obo/OBI_0001307 tiling microarray Nimblegen Human 3x720K Whole Genome CGH Tiling Array A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 3x720,000 features. http://purl.obolibrary.org/obo/OBI_0002011 Human 2.1M Whole-Genome CGH Tiling Array v2.0 http://purl.obolibrary.org/obo/OBI_0001307 tiling microarray Nimblegen Human 2.1M Whole-Genome CGH Tiling Array v2.0 A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 2.1 million features. http://purl.obolibrary.org/obo/OBI_0002012 PacBio RS II http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer Pacific Biosciences RS II A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. http://purl.obolibrary.org/obo/OBI_0002014 DNA methylation profiling by ChIP-chip assay http://purl.obolibrary.org/obo/OBI_0002020 epigenetic modification assay DNA methylation ChIP-chip An epigenetic modification assay that identifies sites of DNA methylation using ChIP-chip technologies. http://purl.obolibrary.org/obo/OBI_0002015 transcription profiling by MPSS assay http://purl.obolibrary.org/obo/OBI_0000424 transcription profiling assay expression MPSS A transcription profiling assay that uses Massive Parallel Signature Sequencing (MPSS). http://purl.obolibrary.org/obo/OBI_0002016 histone modification identification by ChIP-chip assay http://purl.obolibrary.org/obo/OBI_0002020 epigenetic modification assay histone modification ChIP-chip An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-chip techniques. http://purl.obolibrary.org/obo/OBI_0002017 histone modification identification by ChIP-Seq assay http://purl.obolibrary.org/obo/OBI_0002020 epigenetic modification assay histone modification ChIP-Seq An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-Seq techniques. http://purl.obolibrary.org/obo/OBI_0002018 transcription factor binding site identification by ChIP-chip assay http://purl.obolibrary.org/obo/OBI_0001248 ChIP-chip assay TF Binding ChIP-chip A transcription factor binding site assay that utilizes ChIP-chip technology. http://purl.obolibrary.org/obo/OBI_0002019 transcription factor binding site identification by ChIP-Seq assay http://purl.obolibrary.org/obo/OBI_0000716 ChIP-seq assay TF Binding ChIP-Seq A transcription factor binding site assay that utilizes ChIP-seq technology. http://purl.obolibrary.org/obo/OBI_0002021 NextSeq 500 http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer Illumina NextSeq 500 A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. http://purl.obolibrary.org/obo/OBI_0002022 Illumina HiSeq 1000 http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer HiSeq 1000 A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. http://purl.obolibrary.org/obo/OBI_0002023 Human Genome U133 Plus 2.0 tiling array http://purl.obolibrary.org/obo/OBI_0001307 tiling microarray Affymetrix HT Human Genome U133 Plus 2 Array Plate Set A tiling array which is a comprehensive whole human genome expression array manufactured by the Affymetrix corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 47,000 transcripts and variants. http://purl.obolibrary.org/obo/OBI_0002024 SOLiD 4 System http://purl.obolibrary.org/obo/OBI_0000696 AB SOLiD System SOLiD 4 An AB SOLid System which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. http://purl.obolibrary.org/obo/OBI_0002025 Human Exon 1.0 ST tilling array http://purl.obolibrary.org/obo/OBI_0001307 tiling microarray Human Exon 1.0 ST Array A tiling microarray which is manufactured by the Affymetrix corporation. Built to analyze 3' DNA sequence copy number by comparative genomic hybridization for human DNA against 28,000 genes. It can be used for gene expression and alternative splicing assay http://purl.obolibrary.org/obo/OBI_0002026 Human Genome U133 tiling array http://purl.obolibrary.org/obo/OBI_0001307 tiling microarray HG-U133 array A tiling array which is manufactured by the Affymetrix corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 39,000 transcripts and variants. http://purl.obolibrary.org/obo/OBI_0002027 Genome Analyzer IIe http://purl.obolibrary.org/obo/OBI_0000703 Illumina Genome Analyzer II Illumina Genome Analyzer IIe An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIe makes industry-leading next-generation sequencing technology accessible to more laboratories. http://purl.obolibrary.org/obo/OBI_0002029 serial analysis of gene expression assay http://purl.obolibrary.org/obo/OBI_0000424 transcription profiling assay SAGE A transcription profiling assay that quantifies RNA through creating short signature tags of the messages and ligating them into a larger molecule than was sequenced. http://purl.obolibrary.org/obo/OBI_0002030 genotyping by tiling array assay http://purl.obolibrary.org/obo/OBI_0001274 genotyping by array assay DNA sequence variation detection by tiling array A genotyping by array assay that uses tiling array technology. http://purl.obolibrary.org/obo/OBI_0002031 genotyping by SNP array assay http://purl.obolibrary.org/obo/OBI_0001274 genotyping by array assay DNA sequence variation detection by snp array A genotyping by array assay that uses SNP array technology. http://purl.obolibrary.org/obo/OBI_0002032 parallel analysis of RNA structure assay http://purl.obolibrary.org/obo/OBI_0001014 single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing PARS A single-nucleotide-resolution nucleic acid structure mapping assay that performs simultaneous in vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution using enzymatic probing based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes http://purl.obolibrary.org/obo/OBI_0002033 translation-associated transcript leader sequencing assay http://purl.obolibrary.org/obo/OBI_0001271 RNA-seq assay TATL-seq An RNA-seq assay that combines TL-seq with polysome fractionation http://purl.obolibrary.org/obo/OBI_0002034 transcript leader sequencing assay http://purl.obolibrary.org/obo/OBI_0001271 RNA-seq assay TL-seq An RNA-seq assay that combines enzymatic capture of m(7)G-capped mRNA 5' ends with high-throughput sequencing. http://purl.obolibrary.org/obo/OBI_0002035 peptide mass fingerprinting assay http://purl.obolibrary.org/obo/OBI_0000470 mass spectrometry assay protein fingerprinting A mass spectrometry assay that measures the absolute mass of the cleaved peptides derived from an unknown protein of interest. These masses are then compared to values for known protein sequences to identify the unknown protein. http://purl.obolibrary.org/obo/OBI_0002038 ribosomal profiling by sequencing assay http://purl.obolibrary.org/obo/OBI_0001271 RNA-seq assay ribosomal profiling A RNA-seq assay that sequences only mRNA protected by the ribosome during translation. http://purl.obolibrary.org/obo/OBI_0002039 assay for transposase-accessible chromatin using sequencing http://purl.obolibrary.org/obo/OBI_0000070 assay ATAC-seq assay An assay to capture the location of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution by Tn5 transposase insertion. http://purl.obolibrary.org/obo/OBI_0002040 chromatin isolation by RNA purification sequencing assay http://purl.obolibrary.org/obo/OBI_0000874 detection of specific nucleic acid polymers with complementary probes Chromatin Isolation by RNA purification A detection of specific nucleic acids with complementary probes assay that measures regions of the genome which are bound by a specific RNA (or a by a ribonucleoprotein containing the RNA of interest) using high-throughput sequencing. http://purl.obolibrary.org/obo/OBI_0002041 self-transcribing active regulatory region sequencing assay http://purl.obolibrary.org/obo/OBI_0001271 RNA-seq assay STARR-seq assay An RNA-seq assay that identifies the sequences that act as transcriptional enhancers in a direct, quantitative, and genome-wide manner from sheared genomic DNA. http://purl.obolibrary.org/obo/OBI_0002042 carbon-copy chromosome conformation capture assay followed by sequencing assay http://purl.obolibrary.org/obo/OBI_0001919 Carbon-copy chromosome conformation capture assay Carbon-copy chromosome conformation capture assay followed by sequencing A carbon-copy chromosome conformation capture assay to analyze the organization of chromosomes in an unbiased, genome-wide manner using high throughput sequening following carbon-copy chromosome conformation capture. http://purl.obolibrary.org/obo/OBI_0002043 individual-nucleotide resolution cross-linking and immunoprecipitation sequencing assay http://purl.obolibrary.org/obo/OBI_0001858 cross-linking immunoprecipitation high-throughput sequencing assay iCLIP assay A cross-linking immunoprecipitation high-throughput sequencing assay that identifies protein-RNA interactions using UV light to covalently bind proteins and RNA molecules, allowing for a very stringent purification of the linked protein-RNA complexes. http://purl.obolibrary.org/obo/OBI_0002044 RNA Bind-n-Seq assay http://purl.obolibrary.org/obo/OBI_0001271 RNA-seq assay RNBS assay An RNA-seq assay that comprehensively characterizes sequence and structural specificity of RNA binding proteins (RBPs). http://purl.obolibrary.org/obo/OBI_0002045 polyA-site sequencing assay http://purl.obolibrary.org/obo/OBI_0001271 RNA-seq assay poly(A)-site sequencing assay A RNA-seq assay that quantitatively profiles RNA polyadenylation at the transcriptome level. http://purl.obolibrary.org/obo/OBI_0002046 surface plasmon resonance sensor chip http://purl.obolibrary.org/obo/OBI_0000968 device sensor chip A device that is used as a binding surface for ligand during a surface plasmon resonance assay, consisting of a glass plate to which a metal film is attached http://purl.obolibrary.org/obo/OBI_0002048 Illumina HiSeq 3000 http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer HiSeq 3000 A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. http://purl.obolibrary.org/obo/OBI_0002049 Illumina HiSeq 4000 http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer HiSeq 4000 A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. http://purl.obolibrary.org/obo/OBI_0002077 specimens derived from shared ancestor http://purl.obolibrary.org/obo/OBI_0002076 collection of specimens specimen family A collection of specimens derived from one common specimen via one or more material processing process(es). http://purl.obolibrary.org/obo/OBI_0002079 specimens collected in one encounter http://purl.obolibrary.org/obo/OBI_0002076 collection of specimens specimen set A collection of specimens that is collected from one source (e.g. one organism) during a time period which for the purpose of the study can be considered to be taken at the same sampling time. http://purl.obolibrary.org/obo/OBI_0002082 reporter gene assay http://purl.obolibrary.org/obo/OBI_0000070 assay reporter gene detection assay An assay that detects expression of a reporter gene that was inserted under the control of a regulatory sequence of interest. http://purl.obolibrary.org/obo/OBI_0002083 enhancer activity detection by reporter gene assay http://purl.obolibrary.org/obo/OBI_0002082 reporter gene assay enhancer reporter gene assay A reporter gene assay that detects expression of a reporter gene that was inserted under the control of an enhancer of interest. http://purl.obolibrary.org/obo/OBI_0002084 transcription cofactor activity region identification by ChIP-Seq assay http://purl.obolibrary.org/obo/OBI_0000716 ChIP-seq assay chromatin modifier binding site identification by ChIP-Seq assay A ChIP-seq assay that identifies regions of chromatin bound to a chromatin modifying protein, e.g. a histone acetyltransferase. http://purl.obolibrary.org/obo/OBI_0002085 transcript expression location detection by hybridization chain reaction assay http://purl.obolibrary.org/obo/OBI_0001686 in-situ hybridization assay transcript expression location detection by fluorescent HCR. An in situ hybridization assay in which the location (e.g. anatomical/tissue) of a transcript is detected by a multiplexed fluorescent in situ hybridization, based on orthogonal amplification with hybridization chain reactions (HCR). RNA probes complementary to mRNA targets trigger chain reactions in which fluorophore-labeled RNA hairpins self-assemble into tethered fluorescent amplification polymers. http://purl.obolibrary.org/obo/OBI_0002086 Tet-assisted bisulfite sequencing assay http://purl.obolibrary.org/obo/OBI_0000748 bisulfite sequencing assay Tet-assisted bisulfite sequencing A bisulfite sequencing assay that identifies genomic methylation patterns by using a bisulfite based protocol with the Tet enzyme to differentiate 5-hydroxylmethylcytosine (5hmC) from 5-methylcytosine (5mC) through a step-wise oxidative demethylation of 5mC, converting it to 5-carboxylcytosine (5caC) while keeping 5hmC protected. http://purl.obolibrary.org/obo/OBI_0002090 rapid amplification of cDNA ends http://purl.obolibrary.org/obo/OBI_0000552 reverse transcribed polymerase chain reaction RACE A reverse transcribed polymerase chain reaction that is used to amplify a mRNA sequence between a defined internal site and the 5' or 3' end of the mRNA. http://purl.obolibrary.org/obo/OBI_0002091 5' rapid amplification of cDNA ends http://purl.obolibrary.org/obo/OBI_0002090 rapid amplification of cDNA ends 5' RACE A rapid amplication of cDNA ends to amplify a mRNA sequence between a defined internal site and the 5' end of the mRNA. http://purl.obolibrary.org/obo/OBI_0002092 3' rapid amplification of cDNA ends http://purl.obolibrary.org/obo/OBI_0002090 rapid amplification of cDNA ends 3' RACE A rapid amplication of cDNA ends to amplify a mRNA sequence between a defined internal site and the 3' end of the mRNA. http://purl.obolibrary.org/obo/OBI_0002093 5' RNA ligase mediated rapid amplification of cDNA ends http://purl.obolibrary.org/obo/OBI_0002091 5' rapid amplification of cDNA ends 5' RLM RACE A 5' rapid amplification pf cDNA ends that uses RNA ligase to add an RNA adapter oligonucleotide to intact 5' mRNA ends, allowing the amplification of cDNA only from full-length, capped mRNA. http://purl.obolibrary.org/obo/OBI_0002094 MethylC-Capture sequencing assay http://purl.obolibrary.org/obo/OBI_0000748 bisulfite sequencing assay MethylC-Capture Sequencing A bisulfite sequencing assay in which a whole-genome sequencing library is prepared, bisulfite converted and amplified, followed by a capture enriching for targeted bisulfite-converted DNA fragments that are are subsequently identified by DNA sequencing. http://purl.obolibrary.org/obo/OBI_0002106 carboxyfluorescein succinimidyl ester staining assay http://purl.obolibrary.org/obo/OBI_0600017 assay detecting a molecular label CFSE assay a assay detecting a molecular label assay where the amount of carboxyfluorescein succinimidyl ester is measured using fluorescence detection. http://purl.obolibrary.org/obo/OBI_0002107 bio-layer interferometry assay http://purl.obolibrary.org/obo/OBI_0001146 binding assay biolayer interferometry, BLI A binding assay that detects a shift in the interference pattern reflected from a layer of immobilized material on the biosensor tip to measure binding to- or dissociating from the material on the biosensor. http://purl.obolibrary.org/obo/OBI_0002108 small-angle scattering assay http://purl.obolibrary.org/obo/OBI_0600045 3D structure determination assay SAXS A 3D structure determination assay in which the scattering pattern of a neutron or x-ray beam targeted at a material entity is recorded at small angles relative to the incident beam to determine the size, shape and structure of the material entity examined. http://purl.obolibrary.org/obo/OBI_0002109 Human 6x630K CGH Whole Genome Tiling Array http://purl.obolibrary.org/obo/OBI_0001307 tiling microarray NimbleGen Human 6x630K CGH Whole Genome Tiling Array A tiling array which is manufactured by the Nimblegen corporation to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 6x630,000 features. http://purl.obolibrary.org/obo/OBI_0002110 digital object identifier http://purl.obolibrary.org/obo/IAO_0000577 centrally registered identifier symbol DOI A centrally registered identifier symbol used to uniquely identify objects given by International DOI Foundation. The DOI system is particularly used for electronic documents such as journal articles. http://purl.obolibrary.org/obo/OBI_0002111 enhanced cross-linking immunoprecipitation high-throughput sequencing assay http://purl.obolibrary.org/obo/OBI_0002043 individual-nucleotide resolution cross-linking and immunoprecipitation sequencing assay eCLIP An iCLIP assay that is enhanced to robustly identify protein-RNA interactions with high efficiency through improvements in library preparation of RNA fragments. http://purl.obolibrary.org/obo/OBI_0002112 small RNA sequencing assay http://purl.obolibrary.org/obo/OBI_0001271 RNA-seq assay small RNA-seq An RNA-seq assay which is targeting small RNA (< 200 bp) sequences such as, but not exclusive to, miRNAs using, for example, small RNA library preparation kits. http://purl.obolibrary.org/obo/OBI_0002113 bromouridine labeling and sequencing assay http://purl.obolibrary.org/obo/OBI_0001271 RNA-seq assay Bru-seq An RNA-seq assay to identify spans of nascent transcription in the genome through isolation of recent bromouridine (Bru) labelled RNAs. http://purl.obolibrary.org/obo/OBI_0002114 bromouridine pulse-chase and sequencing assay http://purl.obolibrary.org/obo/OBI_0001271 RNA-seq assay BruChase-seq An RNA-seq assay to identify RNA populations of specific ages through isolation of RNAs first labelled with bromouridine (Bru) followed by chasing in uridine for different periods of time. http://purl.obolibrary.org/obo/OBI_0002115 cytometry time of flight assay http://purl.obolibrary.org/obo/OBI_0001977 cytometry assay CyTOF A cytometry assay in which the presence of molecules of interest on or in cells is indicated by binding of antibodies labeled with rare earth element tags which are detected by time-of-flight mass spectrometry. http://purl.obolibrary.org/obo/OBI_0002116 high performance liquid chromotography assay http://purl.obolibrary.org/obo/OBI_0001630 analytical chromatography HPLC An analytical chromatography assay that utilizes a high performance liquid chromatography instrument for separation of compounts in a solution. http://purl.obolibrary.org/obo/OBI_0002117 whole genome sequencing assay http://purl.obolibrary.org/obo/OBI_0000626 DNA sequencing assay WGS A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. http://purl.obolibrary.org/obo/OBI_0002118 exome sequencing assay http://purl.obolibrary.org/obo/OBI_0000626 DNA sequencing assay WES A DNA sequencing assay that intends to provide information about the sequence of the protein coding components of a genome (exons). http://purl.obolibrary.org/obo/OBI_0002120 mixed lymphocyte reaction assay http://purl.obolibrary.org/obo/OBI_0001977 cytometry assay MLR A cytometry assay where lymphocytes from two individuals are co-cultured with the lymphocytes from one of the allogeneic individuals (Responders) being labeled (with 3H Thymidine or BrdU) and the proliferation of the labeled cells is measured, which is thought to reflect recognition of histocompatibility antigens on the unlabeled cells (stimulators). http://purl.obolibrary.org/obo/OBI_0002121 killer cell immunoglobulin-like receptor typing assay http://purl.obolibrary.org/obo/OBI_0000435 genotyping assay KIR typing A genotyping assay in which the alleles of genes encoding for killer cell immunoglobulin-like receptors are determined. http://purl.obolibrary.org/obo/OBI_0002122 major histocompatibility typing assay http://purl.obolibrary.org/obo/OBI_0000435 genotyping assay MHC typing, HLA typing A genotyping assay in which the alleles of genes encoding for major histocompatibility complex molecules are determined. http://purl.obolibrary.org/obo/OBI_0002503 feces specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism stool specimen A specimen that is derived from feces. http://purl.obolibrary.org/obo/OBI_0002504 digestive system fluid or secretion specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism gastric fluid specimen A specimen that is derived from digestive system fluid or secretion. http://purl.obolibrary.org/obo/OBI_0002511 vitreous humor specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism vitreous fluid specimen A specimen that is derived from vireous humor. http://purl.obolibrary.org/obo/OBI_0002521 renal medulla specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism kidney medulla specimen A specimen that is derived from renal medulla. http://purl.obolibrary.org/obo/OBI_0002523 breast specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism mammary tissue specimen A specimen that is derived from breast. http://purl.obolibrary.org/obo/OBI_0002526 skin of body specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism skin specimen A specimen that is derived from skin. http://purl.obolibrary.org/obo/OBI_0002531 cortex of kidney specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism kidney cortex specimen A specimen that is derived from cortex of kidney. http://purl.obolibrary.org/obo/OBI_0002535 esophagus muscularis mucosa specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism esophagus muscularis specimen A specimen that is derived from esophagus muscularis mucosa. http://purl.obolibrary.org/obo/OBI_0002536 cerebral cortex specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism brain cortex specimen A specimen that is derived from cerebral cortex. http://purl.obolibrary.org/obo/OBI_0002538 cerebellum specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism brain cerebellum specimen A specimen that is derived from cerebellum. http://purl.obolibrary.org/obo/OBI_0100016 blood plasma specimen http://purl.obolibrary.org/obo/OBI_0000953 processed specimen plasma a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended. http://purl.obolibrary.org/obo/OBI_0100046 phosphate buffered saline solution http://purl.obolibrary.org/obo/OBI_0302729 chemical solution PBS buffer Phosphate buffered saline (abbreviated PBS) is a buffer solution commonly used in biochemistry. It is a salty solution containing sodium chloride, sodium phosphate and in some preparations potassium chloride and potassium phosphate. The buffer helps to maintain a constant pH. The concentration usually matches the human body (isotonic). http://purl.obolibrary.org/obo/OBI_0100056 obsolete_immortal cell line culture http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class immortal cell line sample|permanent cell line A cell line that is expected to be capable of indefinite propagation in an vitro culture. http://purl.obolibrary.org/obo/OBI_0100058 xenograft http://purl.obolibrary.org/obo/OBI_0000047 processed material xenotransplant A material entity which results from the transplantation of living cells, tissues or organs from on organism of one species to an organism of another species. http://purl.obolibrary.org/obo/OBI_0100060 cultured cell population http://purl.obolibrary.org/obo/OBI_0000047 processed material cell culture sample A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history. http://purl.obolibrary.org/obo/OBI_0100061 primary cultured cell population http://purl.obolibrary.org/obo/OBI_0100060 cultured cell population primary cell culture sample A cultured cell population comprised of cells expanded directly from living tissue prior to being passaged. http://purl.obolibrary.org/obo/OBI_0100062 obsolete_cell line http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class cell line sample A secondary cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (ie has been successively passaged together in culture). http://purl.obolibrary.org/obo/OBI_0100063 cultured clonal cell population http://purl.obolibrary.org/obo/OBI_0100060 cultured cell population clonal cell culture sample A cultured cell population comprised of cells which can all be traced back to a single ancestor cell, and which therefore can be treated as identical. http://purl.obolibrary.org/obo/OBI_0100067 bronchial alveolar lavage http://purl.obolibrary.org/obo/OBI_0100051 specimen BAL Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space. http://purl.obolibrary.org/obo/OBI_0100086 glucose in solution http://purl.obolibrary.org/obo/BFO_0000040 material entity glucose molecules A scattered aggregate of glucose molecules in a liquid http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://purl.obolibrary.org/obo/OBI_0000011 planned process data processing A planned process that produces output data from input data. http://purl.obolibrary.org/obo/OBI_0200022 variance stabilizing transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation variance stabilising transformation A variance stabilizing transformation is a data transformation, described in PMID 12169536, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (6) in this paper. One of the goals is to obtain an output matrix whose rows have equal variances. The method relies on various assumptions described in the paper. http://purl.obolibrary.org/obo/OBI_0200029 mean centering http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation mean centring A mean centering is a data transformation that takes as input an n-dimensional (real) vector, performs a mean calculation on its components, and subtracts the resulting mean from each component of the input. http://purl.obolibrary.org/obo/OBI_0200030 median centering http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation median centring A median centering is a data transformation that takes as input an n-dimensional (real) vector, performs a median calculation on its components, and subtracts the resulting median from each component of the input. http://purl.obolibrary.org/obo/OBI_0200034 jackknifing method http://purl.obolibrary.org/obo/OBI_0000792 statistical model validation jackknifing Jacknifing is a re-sampling data transformation process used to estimate the precision of sampling statistics and is a resampling method http://purl.obolibrary.org/obo/OBI_0200050 dimensionality reduction http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating data projection A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m. http://purl.obolibrary.org/obo/OBI_0200051 principal components analysis dimensionality reduction http://purl.obolibrary.org/obo/OBI_0200050 dimensionality reduction pca data reduction A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones. http://purl.obolibrary.org/obo/OBI_0200064 centroid mass spectrum http://purl.obolibrary.org/obo/OBI_0200085 mass spectrometry analysis centroiding A centroid mass spectrum is a data transformation in which many points are used to delineate a mass spectral peak, is converted into mass-centroided data by a data compression algorithm. The centroided mass peak is located at the weighted center of mass of the profile peak. The normalized area of the peak provides the mass intensity data. http://purl.obolibrary.org/obo/OBI_0200073 family wise error rate correction method http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating FWER correction A family wise error rate correction method is a multiple testing procedure that controls the probability of at least one false positive. http://purl.obolibrary.org/obo/OBI_0200080 network analysis http://purl.obolibrary.org/obo/OBI_0200000 data transformation network topology analysis A data transformation that takes as input data that describes biological networks in terms of the node (a.k.a. vertex) and edge graph elements and their characteristics and generates as output properties of the constituent nodes and edges, the sub-graphs, and the entire network. http://purl.obolibrary.org/obo/OBI_0200082 longitudinal data analysis http://purl.obolibrary.org/obo/OBI_0200000 data transformation longitudinal data analysis Longitudinal analysis is a data transformation used to perform repeated observations of the same items over long periods of time. http://purl.obolibrary.org/obo/OBI_0200083 survival analysis objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective survival analysis A data transformation objective which has the data transformation aims to model time to event data (where events are e.g. death and or disease recurrence); the purpose of survival analysis is to model the underlying distribution of event times and to assess the dependence of the event time on other explanatory variables http://purl.obolibrary.org/obo/OBI_0200089 multiple testing correction method http://purl.obolibrary.org/obo/OBI_0000668 error correction data transformation multiple testing procedure A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate http://purl.obolibrary.org/obo/OBI_0200091 inter-rater reliability objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective inter-rater agreement a data transformation objective of determining the concordance or agreement between human judges. http://purl.obolibrary.org/obo/OBI_0200092 Westfall and Young family wise error rate correction http://purl.obolibrary.org/obo/OBI_0200073 family wise error rate correction method Westfall and Young FWER correction Is a data transformation process in which the Westfall and Young method is applied with the aim of controlling for multiple testing http://purl.obolibrary.org/obo/OBI_0200098 soft independent modeling of class analogy analysis http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation SIMCA Soft independent modeling by class analogy (SIMCA) is a descriptive statistics method for supervised classification of data. The method requires a training data set consisting of samples (or objects) with a set of attributes and their class membership. The term soft refers to the fact the classifier can identify samples as belonging to multiple classes and not necessarily producing a classification of samples into non-overlapping classes. http://purl.obolibrary.org/obo/OBI_0200100 canonical variate analysis http://purl.obolibrary.org/obo/OBI_0200171 partitioning data transformation CVA canonical variate analysis is a form of discriminant analysis that takes several continuous predictor variables and uses the entire set to predict several criterion variables, each of which is also continuous. CVA simultaneously calculates a linear composite of all x variables and a linear composite of all y variables. Unlike other multivariate techniques, these weighted composites are derived in pairs. Each linear combination is called a canonical variate and takes the general linear form. http://purl.obolibrary.org/obo/OBI_0200105 partial least square regression analysis http://purl.obolibrary.org/obo/OBI_0200102 regression analysis method PLS-RA Partial least squares regression is an extension of the multiple linear regression model (see, e.g., Multiple Regression or General Stepwise Regression). In its simplest form, a linear model specifies the (linear) relationship between a dependent (response) variable Y, and a set of predictor variables, the X's, so that Y = b0 + b1X1 + b2X2 + ... + bpXp In this equation b0 is the regression coefficient for the intercept and the bi values are the regression coefficients (for variables 1 through p) computed from the data. http://purl.obolibrary.org/obo/OBI_0200107 partial least square discriminant analysis http://purl.obolibrary.org/obo/OBI_0200106 discriminant analysis PLS-DA PLS Discriminant Analysis (PLS-DA) is a discriminant analysis performed in order to sharpen the separation between groups of observations, by hopefully rotating PCA (Principal Components Analysis) components such that a maximum separation among classes is obtained, and to understand which variables carry the class separating information. http://purl.obolibrary.org/obo/OBI_0200111 data visualization http://purl.obolibrary.org/obo/OBI_0000011 planned process visualization An planned process that creates images, diagrams or animations from the input data. http://purl.obolibrary.org/obo/OBI_0200125 data combination http://purl.obolibrary.org/obo/OBI_0200000 data transformation data pooling A data transformation in which individual input data elements and values are merged together into a output set of data elements and values. http://purl.obolibrary.org/obo/OBI_0200141 log base http://purl.obolibrary.org/obo/OBI_0200140 mathematical feature logarithmic base The log base is a feature of a logarithmic function which is defined in http://en.wikipedia.org/wiki/Logarithm. Its value can be any positive real number different from 1. http://purl.obolibrary.org/obo/OBI_0200149 unit-variance scaling http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation autoscaling A unit-variance scaling is a data transformation that divides all measurements of a variable by the standard deviation of that variable. http://purl.obolibrary.org/obo/OBI_0200154 agglomerative hierarchical clustering http://purl.obolibrary.org/obo/OBI_0200042 hierarchical clustering bottom-up hierarchical clustering An agglomerative hierarchical clustering is a hierarchical clustering which starts with separate clusters and then successively combines these clusters until there is only one cluster remaining. http://purl.obolibrary.org/obo/OBI_0200155 divisive hierarchical clustering http://purl.obolibrary.org/obo/OBI_0200042 hierarchical clustering top-down hierarchical clustering A divisive hierarchical clustering is a hierarchical clustering which starts with a single cluster and then successively splits resulting clusters until only clusters of individual objects remain. http://purl.obolibrary.org/obo/OBI_0200160 generalized family wise error rate correction method http://purl.obolibrary.org/obo/OBI_0200089 multiple testing correction method gFWER correction A generalized FWER correction method is a multiple testing procedure that controls the probability of at least k+1 false positives, where k is a user-supplied integer. http://purl.obolibrary.org/obo/OBI_0200161 quantile number of false positives correction method http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating QNFP A quantile number of false positives correction method is a MTP that controls for the pth quantile of the distribution of the number of false positives out of the total number of tests performed' http://purl.obolibrary.org/obo/OBI_0200162 tail probability for the proportion of false positives correction method http://purl.obolibrary.org/obo/OBI_0200089 multiple testing correction method TPPFP correction method A TPPFP correction method is a MTP that controls the probability that the proportion of false positives among all rejected hypotheses is no greater than a constant q, where q is between 0 and 1. http://purl.obolibrary.org/obo/OBI_0200163 false discovery rate correction method http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating FDR correction method The false discovery rate is a data transformation used in multiple hypothesis testing to correct for multiple comparisons. It controls the expected proportion of incorrectly rejected null hypotheses (type I errors) in a list of rejected hypotheses. It is a less conservative comparison procedure with greater power than familywise error rate (FWER) control, at a cost of increasing the likelihood of obtaining type I errors. . http://purl.obolibrary.org/obo/OBI_0200164 proportion of expected false positives correction method http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating PEFP correction method A proportion of expected false positives correction method is a multiple testing procedure that controls the ratio of the expected value of the numbers of false positives to the expected value of the numbers of rejected hypotheses. http://purl.obolibrary.org/obo/OBI_0200165 quantile proportion of false positives correction method http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating QPFP correction method A quantile proportion of false positives correction method is a multiple testing procedure that controls the pth quantile of the distribution of the proportion of false positives among the rejected hypothesis (false discovery rate). http://purl.obolibrary.org/obo/OBI_0200175 class discovery data transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation unsupervised classification data transformation A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery. http://purl.obolibrary.org/obo/OBI_0200178 class discovery objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective unsupervised classification objective A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic. http://purl.obolibrary.org/obo/OBI_0200179 class prediction objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective supervised classification objective A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data. http://purl.obolibrary.org/obo/OBI_0200188 cross validation objective http://purl.obolibrary.org/obo/OBI_0200172 partitioning objective rotation estimation objective A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis. http://purl.obolibrary.org/obo/OBI_0200189 merging objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective combining objective A merging objective is a data transformation objective in which the data transformation has the aim of performing a union of two or more sets. http://purl.obolibrary.org/obo/OBI_0200195 proportional hazards model estimation http://purl.obolibrary.org/obo/OBI_0200194 survival analysis data transformation Cox proportional hazards model Proportional hazards model is a data transformation model to estimate the effects of different covariates influencing the times-to-failure of a system. http://purl.obolibrary.org/obo/OBI_0302714 obsolete_collection (of entities of organismal origin) http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class group a collection is a bfo:aggregate object, that is a set of material object of the same kind http://purl.obolibrary.org/obo/OBI_0302729 chemical solution http://purl.obolibrary.org/obo/BFO_0000040 material entity liquid chemical solution A material entity that is made up of at least 2 scattered molecular aggregates, one playing the role of solvent and the other one playing the role of solute. http://purl.obolibrary.org/obo/OBI_0302731 buffer role http://purl.obolibrary.org/obo/BFO_0000023 role buffer a role which inheres in some molecular entity realized during the process of buffering http://purl.obolibrary.org/obo/OBI_0302736 comet assay http://purl.obolibrary.org/obo/OBI_0001977 cytometry assay single cell gel electrophoresis assay An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis http://purl.obolibrary.org/obo/OBI_0302737 PCR-SSCP assay http://purl.obolibrary.org/obo/OBI_0002692 polymerase chain reaction assay polymerase chain reaction-single strand conformation polymorphism assay An assay that identifies DNA sequence variation (mutation, deletion, insertions) in target DNA sequences amplified using polymerase chain reaction using gel electrophoresis and denaturating conditions http://purl.obolibrary.org/obo/OBI_0302898 intentional overdosing http://purl.obolibrary.org/obo/OBI_0000919 animal euthanization lethal injection intentional overdosing is a process by which an excess dose of a chemical compound is given with the intent of causing death http://purl.obolibrary.org/obo/OBI_0302912 electroporation http://purl.obolibrary.org/obo/OBI_0600033 cell permeabilization electropermeabilization a process in which a significant increase in the electrical conductivity and permeability of the cell plasma membrane caused by an externally applied electrical field. It is usually used in molecular biology as a way of introducing some substance into a cell, such as loading it with a molecular probe, a drug that can change the cell's function, or a piece of coding DNA http://purl.obolibrary.org/obo/OBI_0400007 analog-to-digital converter http://purl.obolibrary.org/obo/OBI_0000968 device A-D An analog-to-digital_converter is an instrument that converts an infinite resolution analog signal to a finite resolution digital signal. http://purl.obolibrary.org/obo/OBI_0400043 flow cell http://purl.obolibrary.org/obo/OBI_0000967 container flow_cell Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell. http://purl.obolibrary.org/obo/OBI_0400050 Guava Personal Cell Analysis http://purl.obolibrary.org/obo/OBI_0400008 flow cytometer analyzer Guava_PCA A Guava_Personal_Cell_Analysis System is a flow_cytometer_analyser that includes a single 532 nm laser, and filters and PMTs to collect up to 2 fluorescent parameters. It includes a photodiode forward scatter collector. Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The PCA96 uses only tubes to introduce specimen. The Guava PCA cytometer is a small portable cytometer particularly useful for field measurement. http://purl.obolibrary.org/obo/OBI_0400051 Guava Personal Cell Analysis-96 http://purl.obolibrary.org/obo/OBI_0400008 flow cytometer analyzer Guava_PCA-96 The Guava_Personal_Cell_Analysis-96 Systems is a flow_cytometer_analyser that includes a single 532 nm laser, and filters and PMTs to collect up to 2 fluorescent parameters. It includes a photodiode forward scatter collector. Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The PCA96 uses either tubes or 96 well plates to introduce specimen. The Guava PCA -96 cytometer is a small portable cytometer particularly useful for field measurement. http://purl.obolibrary.org/obo/OBI_0400064 laser http://purl.obolibrary.org/obo/OBI_0400065 light source light amplification by the stimulated emission of radiation A laser (acronym for light amplification by the stimulated emission of radiation) is a light source that emits photons of the same characteristics in a coherent beam. A laser uses a solid, liquid or gaseous lasing medium, that contains molecules, of which some atoms have electrons that emit photons of the same frequency when falling back to their normal orbital after excitation (pumping) by external means A laser is the most common way to irradiate a cell in a flow cytometer. http://purl.obolibrary.org/obo/OBI_0400112 liquid handler http://purl.obolibrary.org/obo/OBI_0000968 device liquid_handling_instrument A device that is used for automated liquid transfer and handling. http://purl.obolibrary.org/obo/OBI_0400116 thermal cycler http://purl.obolibrary.org/obo/OBI_0002089 physical store Polymerase_Chain_Reaction_ machine An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. http://purl.obolibrary.org/obo/OBI_0400118 vortexer http://purl.obolibrary.org/obo/OBI_0001033 perturbation device vortex_mixer A vortexer is an instrument that mixes small vials of liquid by creating a rotation of the liquid around its own center. It consists of an electric motor with the drive shaft oriented vertically and attached to a cupped rubber piece mounted slightly off-center. As the motor runs the rubber piece oscillates rapidly in a circular motion. When a test tube or other appropriate container is pressed into the rubber cup (or touched to its edge) the motion is transmitted to the liquid inside and a vortex is created. http://purl.obolibrary.org/obo/OBI_0400121 molecular crosslinker http://purl.obolibrary.org/obo/OBI_0001034 environmental control device molecular crosslinker A device that is able to chemically join two or more molecules. http://purl.obolibrary.org/obo/OBI_0400140 gel tank http://purl.obolibrary.org/obo/OBI_0002089 physical store electrophoresis unit A device which holds a gel and running buffers to allow electrophoresis to be performed. A gel tank has the function to contain and to control the contained environment and transfer energy from an energy supply through the running buffers to the gel matrix and the material with charged molecules in an electric field across a porous matrix or medium with the objective to separate the charged molecules. http://purl.obolibrary.org/obo/OBI_0400142 power supply http://purl.obolibrary.org/obo/OBI_0000968 device power supply unit A power supply is an device or part of a device that permits the required application of a defined electrical charge to an instrument. The power supply may permit the defined application of a given amount of current for a defined length of time. http://purl.obolibrary.org/obo/OBI_0400146 multispectral imaging flow cytometer http://purl.obolibrary.org/obo/OBI_0000398 image creation device MIFC A multispectral_imaging_flow_cytometer is an instrument which combines quantitative image analysis and flow cytometry in a single platform. It measures the amount, location and movement of molecules on, in, or between cells, and the location and co-localization of multiple markers on or in cells. It can also quantitate morphologically distinct cell subpopulations. http://purl.obolibrary.org/obo/OBI_0400148 DNA microarray http://purl.obolibrary.org/obo/OBI_0400147 microarray DNA-array A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample. http://purl.obolibrary.org/obo/OBI_0400171 animal cage http://purl.obolibrary.org/obo/OBI_0000967 container laboratory cage A processed material which has the function to define a bounded habitat which is amenable to keeping animals. http://purl.obolibrary.org/obo/OBI_0500000 study design http://purl.obolibrary.org/obo/IAO_0000104 plan specification experimental design A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. http://purl.obolibrary.org/obo/OBI_0500006 parallel group design http://purl.obolibrary.org/obo/OBI_0500000 study design independent measure design A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design. Subjects of a treatment group receive a unique combination of independent variable values making up a treatment http://purl.obolibrary.org/obo/OBI_0500026 eligibility criterion http://purl.obolibrary.org/obo/OBI_0001755 selection criterion eligibility rule an eligibility criterion (rule) is_a selection criterion which defines and states the requirements (positive or negative) for an entity to be considered as suitable for a given task or participation in a process. http://purl.obolibrary.org/obo/OBI_0500027 inclusion criterion http://purl.obolibrary.org/obo/OBI_0500026 eligibility criterion inclusion rule an inclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity suitable for a given task or participation in a given process. For instance, in a study protocol, inclusion criteria indicate the conditions that prospective subjects MUST meet to be eligible for participation in a study. http://purl.obolibrary.org/obo/OBI_0600002 tumor grading http://purl.obolibrary.org/obo/OBI_0000070 assay grading of tumor An assay that determines the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus. http://purl.obolibrary.org/obo/OBI_0600003 performing a clinical assessment http://purl.obolibrary.org/obo/OBI_0000011 planned process clinical diagnosis A protocol application during which a series of tests are made of a patient leading to determination of disease state, or condition. http://purl.obolibrary.org/obo/OBI_0600006 killing http://purl.obolibrary.org/obo/OBI_0000094 material processing sacrifice A protocol application in which an organism is intentionally put to death http://purl.obolibrary.org/obo/OBI_0600010 material acquisition http://purl.obolibrary.org/obo/OBI_0600008 acquisition material procurement An acquisition in which possession of a material entity is gained. http://purl.obolibrary.org/obo/OBI_0600013 information acquisition http://purl.obolibrary.org/obo/OBI_0600008 acquisition data collection An acquisition in which possession of information is gained. http://purl.obolibrary.org/obo/OBI_0600015 group assignment http://purl.obolibrary.org/obo/OBI_0000011 planned process study assignment group assignment is a process which has an organism as specified input and during which a role is assigned http://purl.obolibrary.org/obo/OBI_0600016 pooling specimens http://purl.obolibrary.org/obo/OBI_0000652 material combination sample pooling physical combination of several instances of like material http://purl.obolibrary.org/obo/OBI_0600018 material portioning http://purl.obolibrary.org/obo/OBI_0600014 material component separation apportioning a material processing in which the input substance is partitioned into a number of portions that are similar in composition. http://purl.obolibrary.org/obo/OBI_0600020 histological assay http://purl.obolibrary.org/obo/OBI_0000070 assay histology An assay that uses visual examination of cells or tissue (or images of them) to make an assessment regarding a quality of the cells or tissue. This assay can include steps of staining, imaging, and judgement. http://purl.obolibrary.org/obo/OBI_0600031 enzyme-linked immunospot assay http://purl.obolibrary.org/obo/OBI_0001977 cytometry assay ELISPOT assay A cytometry assay in which cells are cultured on a surface coated with a capture antibody binding a secretory material of interest which subsequently gets stained resulting in a spot for each cell producing the secretory material of interest. http://purl.obolibrary.org/obo/OBI_0600037 cell culture splitting http://purl.obolibrary.org/obo/OBI_0600014 material component separation cell culture passaging The act of taking part of a homogeneous cell culture and creating one or more additional separate cultures of similar qualities. input: cell_culture, output cell_culture min cardinality 2. part of cell culturing http://purl.obolibrary.org/obo/OBI_0600038 addition of molecular label http://purl.obolibrary.org/obo/OBI_0000094 material processing labeling a material processing technique intended to add a molecular label to some input material entity, to allow detection of the molecular target of this label in a detection of molecular label assay http://purl.obolibrary.org/obo/OBI_0600040 synthesis http://purl.obolibrary.org/obo/OBI_0000094 material processing synthesize the construction of a biomaterial from simpler biomaterials http://purl.obolibrary.org/obo/OBI_0600043 genetic transformation http://purl.obolibrary.org/obo/OBI_0000094 material processing genetic modification the introduction. alteration or integration of genetic material into a cell or organism http://purl.obolibrary.org/obo/OBI_0600055 DNA restriction enzyme digestion http://purl.obolibrary.org/obo/OBI_0600050 specific enzymatic cleavage restriction enzyme assay A specific enzymatic cleavage of DNA molecules using endonucleases that cleave DNA molecules at specific sites based on the surrounding nucleotide sequence http://purl.obolibrary.org/obo/OBI_0600064 recombinant vector cloning http://purl.obolibrary.org/obo/OBI_0000094 material processing molecular cloning a planned process with the objective to insert genetic material into a cloning vector for future replication of the inserted material http://purl.obolibrary.org/obo/OBI_1000029 phage display library http://purl.obolibrary.org/obo/OBI_0000731 recombinant vector display library a phage display library is a collection of materials in which a mixture of genes or gene fragments is expressed and can be individually selected and amplified. http://purl.obolibrary.org/obo/OBI_1000036 cell lysate http://purl.obolibrary.org/obo/OBI_0000047 processed material lysed material a cell lysate is a material entity which is output of a cell lysis process http://purl.obolibrary.org/obo/OBI_1000049 whole mount tissue http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism whole mount sample A whole organism preparation resulting from a histological preparation known as whole mount preparation where the whole specimen is mounted or spread on the microscope (glass) slide http://purl.obolibrary.org/obo/OBI_1000207 assay bead http://purl.obolibrary.org/obo/OBI_0000047 processed material bead A globular or round particle of defined physicochemical properties and size which can be exploited as either the primary substance for detection or as a secondary solid platform for the attachment of bioactive molecules. http://purl.obolibrary.org/obo/OBI_1110010 disposition to cause an allergic reaction http://purl.obolibrary.org/obo/BFO_0000016 disposition allergenic disposition The role borne by a material entity that is realized when it is recognized by the immune system and results in the occurrence of an allergic disease. http://purl.obolibrary.org/obo/OBI_1110043 cultured adherent cell populaiton http://purl.obolibrary.org/obo/OBI_0100060 cultured cell population adherent cell culture sample A mixed cell population that is characterized by its ability to bind to tissue culture flasks or plates. This population typically contains macrophages and other cells capable of playing the antigen presenting cell role. http://purl.obolibrary.org/obo/OBI_1110044 cultured PBMC cell population http://purl.obolibrary.org/obo/OBI_0001875 cultured immune cell population PBMC cell culture sample A mixed cell population obtained by processing whole blood. The cells are characterized by having a similar density and are largely mononuclear cells (includes T cells, B cells, and other cell types). http://purl.obolibrary.org/obo/OBI_1110045 disposition to be bound by an adaptive immune receptor http://purl.obolibrary.org/obo/BFO_0000016 disposition epitope disposition Is the disposition borne by a material entity that is realized in a process of being bound by a adaptive immune receptor. http://purl.obolibrary.org/obo/OBI_1110047 cultured CD3+ T cell population http://purl.obolibrary.org/obo/OBI_0001875 cultured immune cell population CD3+ T cell culture sample A T cell population characterized by expressing the CD3 molecule on its surface. http://purl.obolibrary.org/obo/OBI_1110048 cultured CD3- T cell population http://purl.obolibrary.org/obo/OBI_0001875 cultured immune cell population CD3- T cell culture sample A T cell population characterized by not expressing the CD3 molecule on its surface. http://purl.obolibrary.org/obo/OBI_1110050 cultured CD4- T cell population http://purl.obolibrary.org/obo/OBI_0001875 cultured immune cell population CD4- T cell culture sample A T cell population characterized by not expressing the CD4 molecule on its surface. http://purl.obolibrary.org/obo/OBI_1110051 cultured CD8- T cell population http://purl.obolibrary.org/obo/OBI_0001875 cultured immune cell population CD8- T cell culture sample A T cell population characterized by not expressing the CD8 molecule on its surface. http://purl.obolibrary.org/obo/OBI_1110052 cultured CD4-/CD8- T cell population http://purl.obolibrary.org/obo/OBI_1110051 cultured CD8- T cell population CD4-/CD8- T cell culture sample A T cell population characterized by not expressing the CD4 nor the CD8 molecule on its surface. http://purl.obolibrary.org/obo/OBI_1110085 antigen presentation function http://purl.obolibrary.org/obo/BFO_0000034 function APC a function inhering in a cell that expresses MHC molecules which is realized in the process of antigen processing and presentation of antigen derived parts by MHC molecules on the cell surface. http://purl.obolibrary.org/obo/OBI_1110087 donor http://purl.obolibrary.org/obo/BFO_0000023 role donor role A role which inheres in an organism or part thereof from which any part including cell, organ or tissue is removed with the intention that the donated part will be placed into another organism and/or cultured in vitro. http://purl.obolibrary.org/obo/OBI_1110092 adjuvant role http://purl.obolibrary.org/obo/BFO_0000023 role adjuvent role Adjuvant role is a role that inheres in a material entity and which is realized through a process of modifying a biological response. http://purl.obolibrary.org/obo/OBI_1110106 cultured antigen presenting cell population http://purl.obolibrary.org/obo/OBI_0001875 cultured immune cell population antigen presenting cell culture sample a cell culture including cells that have an antigen presentation function http://purl.obolibrary.org/obo/OBI_1110107 cultured effector T cell population http://purl.obolibrary.org/obo/OBI_0001875 cultured immune cell population effector T cell culture sample A cell culture including cells that have an effector T cell function http://purl.obolibrary.org/obo/OBI_1110132 CD8 receptor http://purl.obolibrary.org/obo/PR_000000001 protein CD8 A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor. http://purl.obolibrary.org/obo/OBI_1110207 assay detecting IFN-gamma production http://purl.obolibrary.org/obo/OBI_0000070 assay IFNg release An assay that determines information about the production of the cytokine interferon gamma http://purl.obolibrary.org/obo/PATO_0001632 anterior to http://purl.obolibrary.org/obo/PATO_0000140 position frontal A spatial quality inhering in a bearer by virtue of the bearer's being located toward the front of an organism relative to another entity. http://purl.obolibrary.org/obo/PR_000023089 DNA ligase http://purl.obolibrary.org/obo/PR_000000001 protein ligase A protein that is a translation product of the Escherichia coli K-12 ligA gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/REO_0000171 obsolete molecular label role http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class molecular tracer role A reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay. http://purl.obolibrary.org/obo/REO_0000280 obsolete molecular label http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class molecular tracer A molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay http://purl.obolibrary.org/obo/SO_0000001 region http://purl.obolibrary.org/obo/BFO_0000031 generically dependent continuant sequence A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. http://purl.obolibrary.org/obo/SO_0000104 polypeptide http://purl.obolibrary.org/obo/SO_0000001 region polypeptide sequence A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation. http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating http://purl.obolibrary.org/obo/OBI_0000011 planned process dataset creation A planned process that has a data set as its specified output. http://purl.obolibrary.org/obo/OBI_0002457 precision nuclear run-on sequencing assay http://purl.obolibrary.org/obo/OBI_0002692 polymerase chain reaction assay precision nuclear run-on and sequencing assay An RNA-seq assay that maps the genome-wide distribution of transcriptionally-engaged Pol II at base-pair resolution by using biotin-labeled ribonucleotide triphosphate analogs (biotin-NTP) for nuclear run-on reactions, allowing the efficient affinity purification of nascent RNAs for high throughput sequencing from their 3' ends. http://purl.obolibrary.org/obo/OBI_0002458 chromosome conformation capture-on-chip assay http://purl.obolibrary.org/obo/OBI_0002692 polymerase chain reaction assay circularized chromosome conformation capture assay A nuclear ligation assay which uses cross-linking of proteins to proteins and DNA, followed by two rounds of digestion and ligation, inverse PCR, and characterization by microarray or DNA sequencing. This enables unbiased genome-wide screens for DNA contacts made by single genomic sites of interest. http://purl.obolibrary.org/obo/OBI_0002459 genotype phasing by Hi-C assay http://purl.obolibrary.org/obo/OBI_0000435 genotyping assay haplotype reconstruction by Hi-C assay A genotyping assay in which carbon-copy chromosome conformation is used to detect polymorphism in DNA samples. http://purl.obolibrary.org/obo/OBI_0002571 polyA-selected RNA sequencing assay http://purl.obolibrary.org/obo/OBI_0001271 RNA-seq assay mRNA-seq An RNA-seq assay to study transcriptomes through the enrichment of polyadenylated transcripts or removal of ribosomal RNA prior to high-throughput sequencing. http://purl.obolibrary.org/obo/OBI_0002572 polyA-depleted RNA sequencing assay http://purl.obolibrary.org/obo/OBI_0001271 RNA-seq assay polyA-depleted RNA-seq An RNA-seq assay to study non-polyadenylated transcripts, such as, but not exclusive to unspliced and circular isoforms, through the depletion of polyadenylated transcripts prior to high-throughput sequencing. http://purl.obolibrary.org/obo/OBI_0002575 isoform sequencing http://purl.obolibrary.org/obo/OBI_0001271 RNA-seq assay ISO-seq A method for sequencing isoforms by enriching a cDNA library for full-length reads spanning entire transcript isoforms. http://purl.obolibrary.org/obo/CHEBI_33839 macromolecule http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity polymer A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. http://purl.obolibrary.org/obo/OBI_0002930 light trap http://purl.obolibrary.org/obo/OBI_0002920 arthropod trap light trap catch An arthropod trap that uses light as an attractant. http://purl.obolibrary.org/obo/GO_0032991 protein-containing complex http://purl.obolibrary.org/obo/BFO_0000040 material entity protein complex A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. http://purl.obolibrary.org/obo/GO_0032640 tumor necrosis factor production http://purl.obolibrary.org/obo/GO_0071706 tumor necrosis factor superfamily cytokine production TNF alpha production The appearance of tumor necrosis factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032641 lymphotoxin A production http://purl.obolibrary.org/obo/GO_0071706 tumor necrosis factor superfamily cytokine production TNF beta production The chemical reactions and pathways resulting in the formation of the cytokine lymphotoxin A. http://purl.obolibrary.org/obo/GO_0042571 immunoglobulin complex, circulating http://purl.obolibrary.org/obo/GO_0019814 immunoglobulin complex antibody An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component. http://purl.obolibrary.org/obo/OBI_0002651 image guided biopsy http://purl.obolibrary.org/obo/OBI_0002654 needle biopsy imaging guided biopsy A biopsy which uses an imaging procedure to guide a needle biopsy. http://purl.obolibrary.org/obo/OBI_0002652 computed tomography assisted biopsy http://purl.obolibrary.org/obo/OBI_0002651 image guided biopsy Computed Tomography-Guided Needle Biopsy A needle biopsy guided by real-time computed tomography (CT) scan images. http://purl.obolibrary.org/obo/OBI_0002655 fine needle aspiration biopsy http://purl.obolibrary.org/obo/OBI_0002654 needle biopsy FNAB A biopsy that uses a thin needle to extract cells. http://purl.obolibrary.org/obo/OBI_0002656 core needle biopsy http://purl.obolibrary.org/obo/OBI_0002654 needle biopsy CNB A biopsy that uses a hollow tube to collect a core of tissue. http://purl.obolibrary.org/obo/OBI_0002657 surgical biopsy http://purl.obolibrary.org/obo/OBI_0002650 biopsy open biopsy A biopsy involving a surgical incision into an organism to access the biopsy material. http://purl.obolibrary.org/obo/OBI_0002660 abdominal wall fat pad biopsy http://purl.obolibrary.org/obo/OBI_0002650 biopsy abdominal wall biopsy A biopsy involving the collection of a small part of the abdominal wall fat pad. http://purl.obolibrary.org/obo/OBI_0002661 tail biopsy http://purl.obolibrary.org/obo/OBI_0002650 biopsy snip A biopsy involving the collection of the tip of a mamallian tail. http://purl.obolibrary.org/obo/OBI_0002663 skinpunch biopsy http://purl.obolibrary.org/obo/OBI_0002650 biopsy punch biopsy; skin biopsy A biopsy that involves the collection of a cylinder of skin (including epidermis, dermis and superficial fat) using a punch tool. http://purl.obolibrary.org/obo/OBI_0002745 vacuum-assisted biopsy http://purl.obolibrary.org/obo/OBI_0002654 needle biopsy VAB A biopsy performed with a needle augmented with a vacuum device. http://purl.obolibrary.org/obo/OBI_0002750 Oxford Nanopore MinION http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer ONT MinION, MinION A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. http://purl.obolibrary.org/obo/OBI_0002751 Oxford Nanopore GridION Mk1 http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer Oxford Nanopore GridION X5, GridION Mk1 A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individually. http://purl.obolibrary.org/obo/OBI_0002752 Oxford Nanopore PromethION http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer PromethION A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. http://purl.obolibrary.org/obo/OBI_0002753 PRO-cap http://purl.obolibrary.org/obo/OBI_0002692 polymerase chain reaction assay PRO-CAP Precision nuclear run-on and sequencing to detect Pol II initiation sites http://purl.obolibrary.org/obo/OBI_0002759 ribosomal RNA-depleted RNA sequencing assay http://purl.obolibrary.org/obo/OBI_0001271 RNA-seq assay rRNA-deleted RNA sequencing assay An RNA-seq assay in which highly abundant ribosomal RNAs are removed from total RNA before sequencing, resulting in more efficient transcript/gene detection. http://purl.obolibrary.org/obo/OBI_0002761 lipid profiling assay http://purl.obolibrary.org/obo/OBI_0000443 analyte assay lipidomic assay An analyte assay assay that detects and identifies lipids resulting from biochemical and cellular metabolism. http://purl.obolibrary.org/obo/OBI_0002762 single-nucleus ATAC-seq http://purl.obolibrary.org/obo/OBI_0002039 assay for transposase-accessible chromatin using sequencing snATAC-seq An ATAC-seq assay in which single nuclei are isolated from frozen tissue samples, through a protocol designed to maximally preserve nucleus integrity during sample processing and optimize transposase-mediated fragmentation of chromatin in individual nuclei. http://purl.obolibrary.org/obo/OBI_0002763 16s ribosomal gene sequencing assay http://purl.obolibrary.org/obo/OBI_0002767 amplicon sequencing assay 16S rRNA sequencing assay An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample. http://purl.obolibrary.org/obo/OBI_0002764 single-cell ATAC-seq http://purl.obolibrary.org/obo/OBI_0002039 assay for transposase-accessible chromatin using sequencing scATAC-seq An ATAC assay designed to robustly map the accessible genome of individual cells, using sequencing integrated into a programmable microfluidics platform, in order to provide insights into cell-to-cell variation in accessibility profiles. http://purl.obolibrary.org/obo/OBI_0002765 microbiome protein expression profiling assay http://purl.obolibrary.org/obo/OBI_0000615 protein expression profiling assay metaproteomic assay A protein expression profiling assay of microbial proteins extracted from a microbioal community of mixed species from a given microbiome. http://purl.obolibrary.org/obo/OBI_0002773 single-value binding of antibody with reporter to antigen assay http://purl.obolibrary.org/obo/OBI_0000070 assay immunoassay An assay that detects the linking of antigens and antibodies via special signaling mechanisms, such as EIA, ELISA, chemiluminescence, etc. that produces one measure (quantitative or qualitative) of the analyte of interest http://purl.obolibrary.org/obo/OBI_0002447 suppression subtractive hybridization http://purl.obolibrary.org/obo/OBI_0000253 artificially induced nucleic acid hybridization subtractive hybridization An artificially induced nucleic acid hybridization that is performed to compare gene expression in different cell or tissue types based on normalization and suppression, which creates a subtracted cDNA or genomic DNA library. http://purl.obolibrary.org/obo/OBI_0002448 differential screening hybridization http://purl.obolibrary.org/obo/OBI_0000253 artificially induced nucleic acid hybridization differential screening An artificially induced nucleic acid hybridization that is performed to identify differentially expressed genes through hybridization of cDNA probes. http://purl.obolibrary.org/obo/OBI_0002490 medication time value specification http://purl.obolibrary.org/obo/OBI_0001931 scalar value specification medication timepoint A scalar value specification that specifies the point in time that a human participant under investigation self-administers a medication material http://purl.obolibrary.org/obo/OBI_0002491 medication dose value specification http://purl.obolibrary.org/obo/OBI_0001931 scalar value specification medication dose A scalar value specification that specifies the value of the quantity of a material entity administered to an organism as a treatment http://purl.obolibrary.org/obo/OBI_0002621 reconstitution assay http://purl.obolibrary.org/obo/OBI_0000471 study design execution reconstitution experiment An assay in which a cellular process is replicated from the bottom-up using isolated components in order to observe how the components work together. http://purl.obolibrary.org/obo/OBI_0002623 whole metagenome sequencing assay http://purl.obolibrary.org/obo/OBI_0000626 DNA sequencing assay WMS A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample. http://purl.obolibrary.org/obo/OBI_0002625 gene knockdown http://purl.obolibrary.org/obo/OBI_0600043 genetic transformation gene knock-down A genetic transformation which reduces the expression of a specific gene or genes in an organism. http://purl.obolibrary.org/obo/OBI_0002626 RNAi gene knockdown http://purl.obolibrary.org/obo/OBI_0002625 gene knockdown RNA interference gene knockdown A gene knockdown that silences genes through artificially-induced RNA interference. This is accomplished by introducing small double-stranded interfering RNA complementary to the target mRNA to be silenced, which is then cleaved by a ribonuclease. http://purl.obolibrary.org/obo/OBI_0002628 RNAi knockdown assay http://purl.obolibrary.org/obo/OBI_0001672 gene knock-down assay RNAi gene knockdown assay A gene knockdown assay in which RNAi gene knockdown is used to disrupt gene transcripts. http://purl.obolibrary.org/obo/OBI_0002629 direct RNA sequencing assay http://purl.obolibrary.org/obo/OBI_0001271 RNA-seq assay direct RNA-seq An assay to study transcription through direct RNA sequence determination, without prior conversion of RNA molecules to cDNA. http://purl.obolibrary.org/obo/OBI_0002630 Illumina NovaSeq 6000 http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer NovaSeq 6000 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. http://purl.obolibrary.org/obo/IAO_0000707 graphical abstract http://purl.obolibrary.org/obo/IAO_0000315 abstract visual abstract An abstract that is pictorial summary of the main findings described in the document. http://purl.obolibrary.org/obo/IAO_0000606 abbreviations section http://purl.obolibrary.org/obo/IAO_0000314 document part nonstandard abbreviations and acronyms A part of a document where abbreviations and their long-forms used within the document are listed. http://purl.obolibrary.org/obo/IAO_0000607 author information section http://purl.obolibrary.org/obo/IAO_0000314 document part contributor information A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. http://purl.obolibrary.org/obo/IAO_0000609 author summary section http://purl.obolibrary.org/obo/IAO_0000314 document part synopsis A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers. http://purl.obolibrary.org/obo/IAO_0000611 availability section http://purl.obolibrary.org/obo/IAO_0000314 document part data sharing statement A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained. http://purl.obolibrary.org/obo/IAO_0000613 case report section http://purl.obolibrary.org/obo/IAO_0000314 document part case report A part of a document about the medical history of a specific patient as it relates to the topic of the document. http://purl.obolibrary.org/obo/IAO_0000615 conclusion section http://purl.obolibrary.org/obo/IAO_0000314 document part summary A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document. http://purl.obolibrary.org/obo/IAO_0000616 conflict of interest section http://purl.obolibrary.org/obo/IAO_0000314 document part authors' disclosures of potential conflicts of interest A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document. http://purl.obolibrary.org/obo/IAO_0000618 consent section http://purl.obolibrary.org/obo/IAO_0000314 document part consent A part of a document about the consent process that was used to enroll patients in a study. http://purl.obolibrary.org/obo/IAO_0000620 ethical approval section http://purl.obolibrary.org/obo/IAO_0000314 document part ethics statement A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis. http://purl.obolibrary.org/obo/IAO_0000622 figures section http://purl.obolibrary.org/obo/IAO_0000314 document part figures A part of a document that contains one or more figures. http://purl.obolibrary.org/obo/IAO_0000623 funding source declaration section http://purl.obolibrary.org/obo/IAO_0000314 document part study funding A part of a document used to detail information regarding the source of funding used in support of the generation of the document content. http://purl.obolibrary.org/obo/IAO_0000625 future directions section http://purl.obolibrary.org/obo/IAO_0000314 document part outlook A part of a document detailing extensions of the described work that may be implemented at some future point in time. http://purl.obolibrary.org/obo/IAO_0000627 genome announcement section http://purl.obolibrary.org/obo/IAO_0000314 document part genome announcement A document part announcing the publication of a novel draft genome sequence. http://purl.obolibrary.org/obo/IAO_0000630 keywords section http://purl.obolibrary.org/obo/IAO_0000314 document part keywords A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed. http://purl.obolibrary.org/obo/IAO_0000631 study limitations section http://purl.obolibrary.org/obo/IAO_0000314 document part study limitations A part of a document about biases or short comings related to the study design and execution. http://purl.obolibrary.org/obo/IAO_0000633 materials section http://purl.obolibrary.org/obo/IAO_0000314 document part materials A part of a document about the materials required to reproduce the content of the document. http://purl.obolibrary.org/obo/IAO_0000634 notes section http://purl.obolibrary.org/obo/IAO_0000314 document part notes A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc. http://purl.obolibrary.org/obo/IAO_0000637 pre-publication history section http://purl.obolibrary.org/obo/IAO_0000314 document part pre-publication history A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors. http://purl.obolibrary.org/obo/IAO_0000639 related work section http://purl.obolibrary.org/obo/IAO_0000314 document part related work A part of a document about work in other publications that is relevant to the content of the document. http://purl.obolibrary.org/obo/IAO_0000641 requirements section http://purl.obolibrary.org/obo/IAO_0000314 document part requirements A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource. http://purl.obolibrary.org/obo/IAO_0000644 statistical analysis section http://purl.obolibrary.org/obo/IAO_0000314 document part statistical analysis A part of the document used to describe the statistical methodologies employed in the work presented in the document. http://purl.obolibrary.org/obo/IAO_0000645 tables section http://purl.obolibrary.org/obo/IAO_0000314 document part tables A part of a document that contains one or more tables. http://purl.obolibrary.org/obo/IAO_0000650 database extract, transform, and load process http://purl.obolibrary.org/obo/OBI_0000011 planned process ETL A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second. http://purl.obolibrary.org/obo/IAO_8000002 editors ontology module http://purl.obolibrary.org/obo/IAO_8000000 ontology module source ontology module An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. http://purl.obolibrary.org/obo/IAO_8000005 import ontology module http://purl.obolibrary.org/obo/IAO_8000006 subset ontology module import file A subset ontology module that is intended to be imported from another ontology. http://purl.obolibrary.org/obo/IAO_8000009 single layer subset ontology module http://purl.obolibrary.org/obo/IAO_8000006 subset ontology module ribbon subset A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. http://purl.obolibrary.org/obo/IAO_8000010 exclusion subset ontology module http://purl.obolibrary.org/obo/IAO_8000006 subset ontology module antislim A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. http://purl.obolibrary.org/obo/IAO_8000011 external import ontology module http://purl.obolibrary.org/obo/IAO_8000005 import ontology module external import An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. http://purl.obolibrary.org/obo/IAO_8000012 species subset ontology module http://purl.obolibrary.org/obo/IAO_8000006 subset ontology module taxon subset A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. http://purl.obolibrary.org/obo/CHMO_0000087 fluorescence microscopy http://purl.obolibrary.org/obo/OBI_0002119 microscopy assay fluorescence microscopic imaging Any type of microscopy where the specimen can be made to fluoresce (emit energy as visible light) by illuminating it with light of specific wavelengths. These specimens are called fluorophores. http://purl.obolibrary.org/obo/CHMO_0000089 confocal fluorescence microscopy http://purl.obolibrary.org/obo/OBI_0002119 microscopy assay scanning confocal fluorescence microscopy Microscopy where the specimen can be made to fluoresce (emit energy as visible light) by scanning a gas (Ar or Kr) laser spot of specific wavelength over its surface and using a spatial pinhole to eliminate out-of-focus fluorescence. http://purl.obolibrary.org/obo/CHMO_0000102 light microscopy http://purl.obolibrary.org/obo/OBI_0002119 microscopy assay optical microscopy Microscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image. http://purl.obolibrary.org/obo/CHMO_0000701 liquid chromatography-tandem mass spectrometry http://purl.obolibrary.org/obo/OBI_0200198 tandem mass spectrometry liquid chromatography-tandem mass spectroscopy A method where a sample mixture is first separated by liquid chromatography before being ionised and characterised by mass-to-charge ratio and relative abundance using two mass spectrometers in series. http://purl.obolibrary.org/obo/OBI_0002598 inverse polymerase chain reaction http://purl.obolibrary.org/obo/OBI_0000415 polymerase chain reaction inverse PCR A polymerase chain reaction which amplifies DNA with only one known sequence from which primers may be designed. A series of restriction digestions and ligations result in a looped DNA fragment which can be primed for PCR. http://purl.obolibrary.org/obo/OBI_0002190 courier organization http://purl.obolibrary.org/obo/OBI_0000245 organization courier An organization that delivers messages, packages, and mail. http://purl.obolibrary.org/obo/OBI_0002198 molecular analysis facility organization http://purl.obolibrary.org/obo/OBI_0000245 organization MAF An organization that provides molecular analysis service. http://purl.obolibrary.org/obo/OBI_0002200 cannot be assessed determination http://purl.obolibrary.org/obo/OBI_0002199 reason for lack of data item cannot be assessed A reason for lack of data item that is the negative output of a determination if assay will provide reliable results. http://purl.obolibrary.org/obo/OBI_0002210 histologic grade according to the Fuhrman Nuclear Grading System http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification Histologic Grade (Fuhrman Nuclear Grading System) A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System. http://purl.obolibrary.org/obo/OBI_0002224 pathologic primary tumor stage for colon and rectum according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition) A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. http://purl.obolibrary.org/obo/OBI_0002232 pathologic primary tumor stage for lung according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification pT: Pathologic spread lung primary tumor (AJCC 7th Edition) A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. http://purl.obolibrary.org/obo/OBI_0002243 pathologic primary tumor stage for kidney according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification pT: Pathologic spread kidney primary tumor (AJCC 7th Edition) A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. http://purl.obolibrary.org/obo/OBI_0002256 pathologic primary tumor stage for ovary according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition) A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. http://purl.obolibrary.org/obo/OBI_0002270 pathologic lymph node stage for colon and rectum according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. http://purl.obolibrary.org/obo/OBI_0002279 pathologic lymph node stage for lung according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. http://purl.obolibrary.org/obo/OBI_0002284 pathologic lymph node stage for kidney according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition) A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. http://purl.obolibrary.org/obo/OBI_0002287 pathologic lymph node stage for ovary according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition) A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. http://purl.obolibrary.org/obo/OBI_0002290 pathologic distant metastases stage for colon according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification M: colon distant metastases (AJCC 7th Edition) A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. http://purl.obolibrary.org/obo/OBI_0002298 pathologic distant metastases stage for lung according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification M: lung distant metastases (AJCC 7th Edition) A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. http://purl.obolibrary.org/obo/OBI_0002306 pathologic distant metastases stage for kidney according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification M: kidney distant Metastases (AJCC 7th Edition) A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. http://purl.obolibrary.org/obo/OBI_0002310 pathologic distant metastases stage for ovary according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification M: ovarian distant metastases (AJCC 7th Edition) A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. http://purl.obolibrary.org/obo/OBI_0002314 clinical tumor stage group according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification Clinical tumor stage group (AJCC 7th Edition) A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems. http://purl.obolibrary.org/obo/OBI_0002326 International Federation of Gynecology and Obstetrics cervical cancer stage value specification http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification Clinical FIGO stage A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems. http://purl.obolibrary.org/obo/OBI_0002341 International Federation of Gynecology and Obstetrics ovarian cancer stage value specification http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification Pathologic Tumor Stage Grouping for ovarian cancer (FIGO) A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system. http://purl.obolibrary.org/obo/OBI_0002356 performance status value specification http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification Performance Status Scale A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life). http://purl.obolibrary.org/obo/OBI_0002357 Eastern Cooperative Oncology Group score value specification http://purl.obolibrary.org/obo/OBI_0002356 performance status value specification ECOG score A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient. http://purl.obolibrary.org/obo/OBI_0002363 Karnofsky score vaue specification http://purl.obolibrary.org/obo/OBI_0002356 performance status value specification Karnofsky Score A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment. http://purl.obolibrary.org/obo/OBI_0002369 clinical history devoid of cancer http://purl.obolibrary.org/obo/OGMS_0000015 clinical history clinical history of no cancer A clinical history in which there was no diagnosis of cancer. http://purl.obolibrary.org/obo/OBI_0002371 diagnosis of cancer http://purl.obolibrary.org/obo/OGMS_0000073 diagnosis cancer diagnosis A diagnosis that is an assertion that a patient who is the subject of a diagnostic process has cancer. http://purl.obolibrary.org/obo/OBI_0002372 family clinical history of cancer http://purl.obolibrary.org/obo/OGMS_0000015 clinical history family history of cancer A clinical history in which there is a diagnosis of cancer in a blood relative. http://purl.obolibrary.org/obo/OBI_0002406 delivery form for hormonal replacement therapy http://purl.obolibrary.org/obo/OBI_0000047 processed material form of hormone replacement therapy A processed material used for delivery of hormones in hormone replacement therapy. http://purl.obolibrary.org/obo/OBI_0002421 indicator of whether an inclusion criterion was met http://purl.obolibrary.org/obo/IAO_0000030 information content entity eligibility criterion met An information content entity that indicates whether or not an entity has met a specific requirement in order to take part in a given process. http://purl.obolibrary.org/obo/OBI_0002422 indicator of whether all inclusion criteria were met http://purl.obolibrary.org/obo/IAO_0000030 information content entity all eligibility criteria met An information content entity that indicates whether or not an entity has met all specific requirements in order to take part in a given process. http://purl.obolibrary.org/obo/OBI_0002437 widefield microscopy http://purl.obolibrary.org/obo/CHMO_0000087 fluorescence microscopy WFM A fluorescence microscopy technique where the specimen under investigation is fully bathed in light, as opposed to confocal microscopy in which only a small portion of the specimen is illuminated. http://purl.obolibrary.org/obo/OBI_0002439 chromosome conformation capture assay http://purl.obolibrary.org/obo/OBI_0002438 nuclear ligation assay 3C assay A nuclear ligation assay that detects chromosomal interactions between any two genomic loci. Chromatin segments are cross-linked, cut by restriction enzymes, ligated, and finally analyzed by PCR. http://purl.obolibrary.org/obo/OBI_0002443 methidiumpropyl-EDTA-iron(II) footprinting assay http://purl.obolibrary.org/obo/OBI_0002162 footprinting assay MPE-Fe(II) footprinting A footprinting assay that determines protein-binding sites on DNA by partial cleavage of ligand-protected DNA restriction fragments with methidium-propyl-EDTA (MPE). MPE-Fe(II) in the presence of oxygen efficiently catalyzes the non-specific clevage of DNA. http://purl.obolibrary.org/obo/OBI_0002631 single-cell RNA sequencing assay http://purl.obolibrary.org/obo/OBI_0001271 RNA-seq assay scRNA-seq An RNA sequencing assay that uses RNA extracts as input that can be traced to a single cell of origin. http://purl.obolibrary.org/obo/OBI_0002632 PacBio Sequel http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer Pacific BioSciences Sequel A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation http://purl.obolibrary.org/obo/OBI_0002633 PacBio Sequel II http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer Pacific BioSciences Sequel II A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate (""HiFi"") long reads, and which is manufactured by the Pacific Biosciences corporation. http://purl.obolibrary.org/obo/OBI_0002673 enrichment culture medium http://purl.obolibrary.org/obo/OBI_0000079 culture medium isolation medium A culture medium that is designed to favor the growth of a particular microorganism or cells over others, enriching a sample for the microorganism or cells of interest. http://purl.obolibrary.org/obo/OBI_0002675 massively parallel reporter assay http://purl.obolibrary.org/obo/OBI_0002082 reporter gene assay MPRA An assay in which multiplexing the construction and interrogation of larger libraries of reporter constructs allows measurement of the transcriptional regulatory activities of thousands to hundreds of thousands of DNA sequences. http://purl.obolibrary.org/obo/OBI_0002680 pseudovirus entry assay http://purl.obolibrary.org/obo/OBI_0001187 infectious agent detection assay pseudovirus cell entry An assay that measures the entry in target cells of reporter viral particles that express an envelope protein of a different virus of interest. http://purl.obolibrary.org/obo/OBI_0002683 short interspersed nuclear elements polymerase chain reaction http://purl.obolibrary.org/obo/OBI_0000415 polymerase chain reaction short interspersed elements PCR A polymerase chain reaction that amplifies short interspersed nuclear elements (SINEs). http://purl.obolibrary.org/obo/OBI_0002684 nested polymerase chain reaction http://purl.obolibrary.org/obo/OBI_0000415 polymerase chain reaction nested PCR A polymerase chain reaction with modification intended to reduce non-specific binding in products due to the amplification of unexpected primer binding sites. The nested polymerase chain reaction (PCR) involves the use of two primer sets and two successive PCR reactions. The first set of primers are designed to anneal to sequences upstream from the second set of primers and are used in an initial PCR reaction. http://purl.obolibrary.org/obo/OBI_0002685 immunoelectrophoresis http://purl.obolibrary.org/obo/OBI_0600053 electrophoresis IEP An electrophoresis that separates and characterize proteins based on reaction with antibodies. http://purl.obolibrary.org/obo/OBI_0002687 ligase detection reaction http://purl.obolibrary.org/obo/OBI_0001494 linear amplification LDR A linear amplification that uses a thermostable ligase to amplify a piece of DNA. Because the enzyme retains activity after multiple thermal cycles, the ligations may be repeated to linearly increase product. http://purl.obolibrary.org/obo/OBI_0002688 loop-mediated isothermal amplification http://purl.obolibrary.org/obo/OBI_0600058 enzymatic amplification LAMP An enzymatic amplification in which a piece of DNA is amplified at a constant temperature of 60 - 65 degree C using either two or three sets of primers and a polymerase with high strand displacement activity in addition to a replication activity. This amplification does not need thermal cyclers and may be a low cost alternative to PCR. http://purl.obolibrary.org/obo/OBI_0002691 arthropod meal of blood specimen http://purl.obolibrary.org/obo/OBI_0100051 specimen blood meal A specimen of the blood ingested by an arthropod. http://purl.obolibrary.org/obo/OBI_0002693 restriction fragment length polymorphism assay http://purl.obolibrary.org/obo/OBI_0000070 assay restriction fragment length polymorphism An assay that uses digestion of DNA with specific restriction enzymes followed by gel electropheresis to detect differences in the sizes of the generated fragments that are due to genetic differences (polymorphisms) in homologous sequences. http://purl.obolibrary.org/obo/OBI_0002694 DNA fingerprinting assay http://purl.obolibrary.org/obo/OBI_0000070 assay DNA profiling An assay to identify a specific individual organism from a DNA specimen by looking at unique patterns in their DNA. http://purl.obolibrary.org/obo/OBI_0002695 insecticide resistance assay http://purl.obolibrary.org/obo/OBI_0000070 assay resistance identification/monitoring An assay that aims to detect the presence and/or frequency of resistance to insecticides in an organism or organism population. http://purl.obolibrary.org/obo/OBI_0002696 insecticide resistance by monitoring known mutations assay http://purl.obolibrary.org/obo/OBI_0002695 insecticide resistance assay monitoring known mutations An insecticide resistance assay that detects, in a population, presence and frequency of mutant alleles for previously characterized mutations with insecticide resistance phenotypes. http://purl.obolibrary.org/obo/OBI_0002697 insecticide resistance by detecting enzyme activity assay http://purl.obolibrary.org/obo/OBI_0002695 insecticide resistance assay metabolic resistance assay An insecticide resistance assay that is based on determination the catalytic activity of an enzyme associated with insecticide resistance phenotypes. http://purl.obolibrary.org/obo/OBI_0002698 insecticide resistance bioassay http://purl.obolibrary.org/obo/OBI_0002695 insecticide resistance assay bioassay An insecticide resistance assay that is typically conducted to measure the effects of a substance on a living organism. http://purl.obolibrary.org/obo/OBI_0002699 insecticide resistance by detecting alpha esterase activity assay http://purl.obolibrary.org/obo/OBI_0002697 insecticide resistance by detecting enzyme activity assay alpha esterase activity assay An insecticide resistance by detecting enzyme activity assay that measures activity of alpha esterase. http://purl.obolibrary.org/obo/OBI_0002700 insecticide resistance by detecting beta esterase activity assay http://purl.obolibrary.org/obo/OBI_0002697 insecticide resistance by detecting enzyme activity assay beta esterase activity assay An insecticide resistance by detecting enzyme activity assay that measures activity of beta esterase. http://purl.obolibrary.org/obo/OBI_0002701 insecticide resistance by detecting acetylcholinesterase activity assay http://purl.obolibrary.org/obo/OBI_0002697 insecticide resistance by detecting enzyme activity assay acetylcholinesterase assay An insecticide resistance by detecting enzyme activity assay that measures activity of acetylcholinesterase. http://purl.obolibrary.org/obo/OBI_0002702 insecticide resistance by detecting glutathione S-transferase activity assay http://purl.obolibrary.org/obo/OBI_0002697 insecticide resistance by detecting enzyme activity assay GST related assay An insecticide resistance by detecting enzyme activity assay that measures activity of glutathione S-transferase (GST). http://purl.obolibrary.org/obo/OBI_0002703 insecticide resistance by detecting carboxylic ester hydrolase activity assay http://purl.obolibrary.org/obo/OBI_0002697 insecticide resistance by detecting enzyme activity assay pNPA assay An insecticide resistance by detecting enzyme activity assay that measures activity of carboxylic ester hydrolase using p-nitrophenyl acetate as a substrate. http://purl.obolibrary.org/obo/OBI_0002704 insecticide resistance by detecting mixed-function oxidase assay http://purl.obolibrary.org/obo/OBI_0002697 insecticide resistance by detecting enzyme activity assay mixed-function oxidase assay An insecticide resistance by detecting enzyme activity assay that measures whether mixed-function oxidase activity present. http://purl.obolibrary.org/obo/OBI_0002705 direct insecticide resistance bioassay http://purl.obolibrary.org/obo/OBI_0002698 insecticide resistance bioassay direct bioassay An insecticide resistance bioassay without the use of any synergist. http://purl.obolibrary.org/obo/OBI_0002706 topical application insecticide resistance bioassay http://purl.obolibrary.org/obo/OBI_0002698 insecticide resistance bioassay topical application assay An insecticide resistance bioassay by adding insecticide directly to the thorax of the insect. http://purl.obolibrary.org/obo/OBI_0002707 direct insecticide resistance diagnostic assay http://purl.obolibrary.org/obo/OBI_0002705 direct insecticide resistance bioassay diagnostic test A direct insecticide resistance assay that at preset insecticide dosage scoring mortality to determine resistance of a population. http://purl.obolibrary.org/obo/OBI_0002708 insecticide resistance dose response assay http://purl.obolibrary.org/obo/OBI_0002705 direct insecticide resistance bioassay dose response test A direct insecticide resistance assay in which an insect population is exposed to a range of insecticide dosage scoring mortality to determine resistance. http://purl.obolibrary.org/obo/OBI_0002709 insecticide resistance time response assay http://purl.obolibrary.org/obo/OBI_0002705 direct insecticide resistance bioassay time response test A direct insecticide resistance assay to determine resistance as a consequence of the time of exposure to insecticide. http://purl.obolibrary.org/obo/OBI_0002710 Centre for Disease Control and Prevention bottle bioassay http://purl.obolibrary.org/obo/OBI_0002707 direct insecticide resistance diagnostic assay CDC bottle bioassay A direct insecticide resistance diagnostic assay performs in a glass bottle coated with insecticides for detecting resistance to insecticides in vector populations. http://purl.obolibrary.org/obo/OBI_0002711 WHO cone kit diagnostic assay http://purl.obolibrary.org/obo/OBI_0002707 direct insecticide resistance diagnostic assay cone DT A direct insecticide resistance diagnostic assay uses WHO cone kit. http://purl.obolibrary.org/obo/OBI_0002712 WHO paper kit diagnostic assay http://purl.obolibrary.org/obo/OBI_0002707 direct insecticide resistance diagnostic assay WHO paper kit DT A direct insecticide resistance diagnostic assay uses WHO paper kit. http://purl.obolibrary.org/obo/OBI_0002713 WHO larvicide diagnostic assay http://purl.obolibrary.org/obo/OBI_0002707 direct insecticide resistance diagnostic assay WHO larvicide DT A direct insecticide resistance diagnostic assay tests survival of larvae in a medium supplemented with insecticide. http://purl.obolibrary.org/obo/OBI_0002714 insecticide resistance dose response by bottle assay http://purl.obolibrary.org/obo/OBI_0002708 insecticide resistance dose response assay bottle bioassay DR test An insecticide resistance dose response assay that performs in a glass bottle coated with insecticides. http://purl.obolibrary.org/obo/OBI_0002715 insecticide resistance dose response by survival of larvae assay http://purl.obolibrary.org/obo/OBI_0002708 insecticide resistance dose response assay WHO larvicide DR test An insecticide resistance dose response assay that tests survival of larvae in a medium supplemented with insecticide. http://purl.obolibrary.org/obo/OBI_0002716 insecticide resistance dose response by WHO paper kit assay http://purl.obolibrary.org/obo/OBI_0002708 insecticide resistance dose response assay WHO paper kit DR test An insecticide resistance dose response assay using WHO paper kit. http://purl.obolibrary.org/obo/OBI_0002717 insecticide resistance time response by bottle assay http://purl.obolibrary.org/obo/OBI_0002709 insecticide resistance time response assay bottle bioassay TR test An insecticide resistance time response assay that is performed in a glass bottle coated with insecticides, with the presence of a synergist. http://purl.obolibrary.org/obo/OBI_0002718 insecticide resistance time response by WHO paper kit assay http://purl.obolibrary.org/obo/OBI_0002709 insecticide resistance time response assay WHO paper kit TR test An insecticide resistance time response assay using WHO paper kit, with the presence of a synergist. http://purl.obolibrary.org/obo/OBI_0002719 insecticide resistance by amplification refractory mutation system assay http://purl.obolibrary.org/obo/OBI_0002696 insecticide resistance by monitoring known mutations assay Amplification Refractory Mutation System An insecticide resistance by monitoring known mutations assay that detects any mutation involving single base changes or small deletions using amplification refractory mutation system (ARMS). The ARMS is based on the use of sequence-specific PCR primers that allow amplification of test DNA only when the target allele is contained within the sample. Following an ARMS reaction the presence or absence of a PCR product is diagnostic for the presence or absence of the target allele. It can be used to analyze human genomic DNA for one or more mutations. http://purl.obolibrary.org/obo/OBI_0002720 insecticide resistance by primer introduced restriction analysis PCR assay http://purl.obolibrary.org/obo/OBI_0002696 insecticide resistance by monitoring known mutations assay polymerase chain reaction-primer-introduced restriction analysis An insecticide resistance by monitoring known mutations assay that detects Single Nucleotide Polymorphisms (SNPs) using PCR technique and mismatched primers that is close to the mutation of interest and digested the PCR productions using restriction enzymes. http://purl.obolibrary.org/obo/OBI_0002721 insecticide resistance by nested polymerase chain reaction assay http://purl.obolibrary.org/obo/OBI_0002696 insecticide resistance by monitoring known mutations assay gene mutation detection by nested PCR An insecticide resistance by monitoring known mutations assay that detects gene mutation based on nested polymerase chain reaction technique. http://purl.obolibrary.org/obo/OBI_0002723 insecticide resistance by ligase detection reaction-fluorescent microsphere assay http://purl.obolibrary.org/obo/OBI_0002722 insecticide resistance by ligase detection reaction assay ligase detection reaction-fluorescent microsphere assay An insecticide resistance by ligase detection reaction assay that uses fluorescently labeled conserved probes in ligase detection reaction. http://purl.obolibrary.org/obo/OBI_0002724 insecticide resistance by PCR amplification of specific alleles assay http://purl.obolibrary.org/obo/OBI_0002696 insecticide resistance by monitoring known mutations assay allele-specific amplification and amplification refractory mutation system An insecticide resistance assay that is based on monitoring known mutations by PCR amplification of specific alleles to detect polymorphic or mutant alleles. http://purl.obolibrary.org/obo/OBI_0002726 insecticide resistance by PCR-RELP assay http://purl.obolibrary.org/obo/OBI_0002696 insecticide resistance by monitoring known mutations assay PCR-RFLP An insecticide resistance by monitoring known mutations assay based on restriction fragment length polymorphism assay. http://purl.obolibrary.org/obo/OBI_0002727 insecticide resistance by short interspersed elements PCR assay http://purl.obolibrary.org/obo/OBI_0002696 insecticide resistance by monitoring known mutations assay Short Interspersed Elements PCR An insecticide resistance assay that is based on monitoring known mutations by PCR amplification of short interspersed elements (SINEs). http://purl.obolibrary.org/obo/OBI_0002728 pathogen detection assay http://purl.obolibrary.org/obo/OBI_0000070 assay pathogen detection method An assay that aims to detect pathogens. http://purl.obolibrary.org/obo/OBI_0002729 VectorTest assay http://purl.obolibrary.org/obo/OBI_0002728 pathogen detection assay VectorTest A pathogen detection assay that identifies the presence or absence of specific peptide epitopes of circumsporozoite (CS) protein of the most important Plasmodium falciparum and two strains (variants 210 and 247) of the more widespread Plasmodium vivax using a dipstick wicking test strip. http://purl.obolibrary.org/obo/OBI_0002730 pathogen detection by Rapid Analyte Measurement Platform assay http://purl.obolibrary.org/obo/OBI_0002728 pathogen detection assay Rapid Analyte Measurement Platform A pathogen detection assay that is based on Rapid Analyte Measurement Platform (RAMP) technology to quantify immunologically active substances. http://purl.obolibrary.org/obo/OBI_0002731 pathogen detection by loop-mediated isothermal amplification assay http://purl.obolibrary.org/obo/OBI_0002728 pathogen detection assay Loop-mediated isothermal amplification A pathogen detection assay that is based on loop-mediated isothermal amplification. http://purl.obolibrary.org/obo/OBI_0002732 blood meal assay http://purl.obolibrary.org/obo/OBI_0000070 assay blood meal analysis An assay that analyzes the specimen taken from blood meal fed organism, such as insect. http://purl.obolibrary.org/obo/OBI_0002733 blood meal by counter current immunoelectrophoresis assay http://purl.obolibrary.org/obo/OBI_0002732 blood meal assay countercurrent immunoelectrophoresis A blood meal assay that uses a counter current immunoelectrophoresis technique. http://purl.obolibrary.org/obo/OBI_0002734 DNA based blood meal finger printing assay http://purl.obolibrary.org/obo/OBI_0002732 blood meal assay DNA based blood meal finger printing A DNA fingerprinting assay that uses DNA extracted from blood meal fed organism, such as insect. http://purl.obolibrary.org/obo/OBI_0002735 organism identification by size assay http://purl.obolibrary.org/obo/OBI_0001624 organism identification assay by size An organism identification assay that is based on the size of organism. http://purl.obolibrary.org/obo/OBI_0002736 organism identification by cross mating assay http://purl.obolibrary.org/obo/OBI_0001624 organism identification assay cross mating experiment An organism identification assay that is based on genetic crossings between specimens collected in the field to determine whether fertile progeny is produced. http://purl.obolibrary.org/obo/OBI_0002737 organism identification by cytological chromosome examination assay http://purl.obolibrary.org/obo/OBI_0001624 organism identification assay cytological chromosome examination An organism identification assay that is based on analysis of polytene chromosomes through cytological examination of the banding pattern of the species. http://purl.obolibrary.org/obo/OBI_0002738 organism identification by isoenzyme electrophoresis assay http://purl.obolibrary.org/obo/OBI_0001624 organism identification assay isoenzyme electrophoresis An organism identification assay that is based on electrophoresis to determine the isozymes that are present in a specific population to determine the species. http://purl.obolibrary.org/obo/OBI_0002739 organism identification by morphological examination assay http://purl.obolibrary.org/obo/OBI_0001624 organism identification assay morphological examination An organism identification assay that is based on examination of morphology and the use of specific "taxonomic keys" to determine the species of the specimen. http://purl.obolibrary.org/obo/OBI_0002740 organism identification by PCR assay http://purl.obolibrary.org/obo/OBI_0002692 polymerase chain reaction assay PCR-based species identification An organism identification assay that is based on PCR. http://purl.obolibrary.org/obo/OBI_0002741 organism identification by specific DNA hybridization assay http://purl.obolibrary.org/obo/OBI_0001624 organism identification assay species specific DNA hybridization An organism identification assay that is based on DNA hybrdization. http://purl.obolibrary.org/obo/OBI_0002742 organism identification by salinity tolerance assay http://purl.obolibrary.org/obo/OBI_0001624 organism identification assay salinity tolerance tests An organism identification assay of mosquito species that is on the basis of mosquito survival depending on the salt concentration in the water used to lay their eggs to differentiate between morphologically very similar species. http://purl.obolibrary.org/obo/OBI_0002743 molecular label role http://purl.obolibrary.org/obo/OBI_0000086 reagent role molecular tracer role A reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay. http://purl.obolibrary.org/obo/OBI_0002744 molecular label http://purl.obolibrary.org/obo/OBI_0001879 reagent molecular tracer A molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay http://purl.obolibrary.org/obo/OBI_0002126 IHC-stained fixed tissue slide specimen http://purl.obolibrary.org/obo/OMIABIS_0000052 fixed tissue slide specimen immunohistochemistry slide specimen A fixed tissue slide specimen that is the output of immunohistochemistry slide staining. http://purl.obolibrary.org/obo/OBI_0002128 Illumina Genome Analyzer http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer Illumina Genome Analyzer I A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. http://purl.obolibrary.org/obo/OBI_0002129 Illumina HiSeq X Ten http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer HiSeq X Ten A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. http://purl.obolibrary.org/obo/OBI_0002132 pulse stable isotope labeling by amino acids in cell culture http://purl.obolibrary.org/obo/OBI_0000070 assay pulsed SILAC An assay that detects differences in protein abundance using samples that have been metabolically labeled in vivo with a stable non-radioactive heavy isotope containing amino acid for a short period of time. After diluting the pulsed cells into growth media without label, high resolution mass spectrometry-based proteomics is used to analyze the time-dependent decay and determine protein stability. http://purl.obolibrary.org/obo/OBI_0002594 direct interaction identification design http://purl.obolibrary.org/obo/OBI_0002590 molecular interaction identification design molecular binding identification design A molecular interaction identification design that investigates the influence of molecules, which are in direct contact, on one another. http://purl.obolibrary.org/obo/OBI_0002597 chromosome conformation capture sequencing assay http://purl.obolibrary.org/obo/OBI_0002458 chromosome conformation capture-on-chip assay 3C-seq assay A chromosome conformation capture-on-chip assay quantitates the products with multiplexed high-throughput sequencing. http://purl.obolibrary.org/obo/OBI_0002612 fecal swab specimen http://purl.obolibrary.org/obo/OBI_0002599 swab specimen stool swab specimen A specimen that is collected with a swab from the surface of a feces. http://purl.obolibrary.org/obo/OBI_1200000 FFPE specimen http://purl.obolibrary.org/obo/OBI_0000950 paraffin specimen formalin-fixed paraffin-embeded specimen A specimen that has been fixed in formalin and embedded in paraffin. http://purl.obolibrary.org/obo/OBI_0002489 differential medium assay http://purl.obolibrary.org/obo/OBI_0001624 organism identification assay bacteriological assay an organism identification assay that uses a differential medium to achieve its objective http://purl.obolibrary.org/obo/OBI_0002778 tracheal aspirate specimen http://purl.obolibrary.org/obo/OBI_0002599 swab specimen tracheal wash specimen A specimen that is collected with a suctioning tube from the trachea. http://purl.obolibrary.org/obo/OBI_0002780 nasal aspirate specimen http://purl.obolibrary.org/obo/OBI_0002599 swab specimen nasal wash specimen|nasopharyngeal aspirate A specimen that is collected with a suctioning tube from the nasal cavity. http://purl.obolibrary.org/obo/OBI_0002781 lower respiratory tract aspirate specimen http://purl.obolibrary.org/obo/OBI_0002599 swab specimen lower respiratory tract wash specimen A specimen that is collected with a suctioning tube from the lower respiratory tract. http://purl.obolibrary.org/obo/OBI_0002785 aspiration specimen collection http://purl.obolibrary.org/obo/OBI_0000659 specimen collection process aspiration procedure Procedure using suction, usually with a thin needle and syringe, to remove bodily fluid or tissue. http://purl.obolibrary.org/obo/OBI_0002898 cluster study group role http://purl.obolibrary.org/obo/OBI_0000174 study group role cluster study arm A study group role that is the result of the allocation of a cluster of study-defined groupings of people in a clinical trial to receive a specific intervention/treatment, or no intervention, according to the trial's protocol. http://purl.obolibrary.org/obo/OBI_0002899 compound study group role http://purl.obolibrary.org/obo/OBI_0000174 study group role compound study arm A study group role that is the result of the allocation of a compound of geographically-proximate households with a shared component in a clinical trial to receive a specific intervention/treatment, or no intervention, according to the trial's protocol. http://purl.obolibrary.org/obo/OBI_0002900 ultraviolet light source http://purl.obolibrary.org/obo/OBI_0400065 light source UV light source A light source that provides ultraviolet (UV) light for use in a distant area using a delivery system. http://purl.obolibrary.org/obo/OBI_0002904 adult arthropod specimen collection process http://purl.obolibrary.org/obo/OBI_0002919 live arthropod specimen collection process collection of adults A live arthropod specimen collection process in which the arthropods are in the adult stage. http://purl.obolibrary.org/obo/OBI_0002905 animal-biting arthropod specimen collection by aspiration http://purl.obolibrary.org/obo/OBI_0002912 arthropod specimen collection by aspiration animal biting catch An arthropod specimen collection by aspiration that occurs while the arthropod is biting an animal. http://purl.obolibrary.org/obo/OBI_0002906 animal-biting outdoor arthropod specimen collection by aspiration http://purl.obolibrary.org/obo/OBI_0002905 animal-biting arthropod specimen collection by aspiration animal biting catch - outdoors An animal-biting arthropod specimen collection by aspiration that occurs outside a building. http://purl.obolibrary.org/obo/OBI_0002907 aquatic arthropod specimen collection process http://purl.obolibrary.org/obo/OBI_0002913 arthropod specimen collection process aquatic environment catch An arthropod specimen collection process that has the objective of collecting mosquitoes from an aquatic environment. http://purl.obolibrary.org/obo/OBI_0002908 arthropod resting in animal house specimen collection by aspiration http://purl.obolibrary.org/obo/OBI_0002912 arthropod specimen collection by aspiration animal shed resting catch An arthropod specimen collection by aspiration that catches specimens resting inside an animal house. http://purl.obolibrary.org/obo/OBI_0002909 arthropod resting outdoors on artificial support specimen collection by aspiration http://purl.obolibrary.org/obo/OBI_0002911 arthropod resting outdoors specimen collection by aspiration outdoors shelter catch - artificial An arthropod resting outdoors specimen collection by aspiration that occurs while the arthropod rests on a processed material such as a wall or furniture. http://purl.obolibrary.org/obo/OBI_0002910 arthropod resting outdoors on natural support specimen collection by aspiration http://purl.obolibrary.org/obo/OBI_0002911 arthropod resting outdoors specimen collection by aspiration outdoors shelter catch - natural An arthropod resting outdoors specimen collection by aspiration that occurs while the arthropod rests on an unprocessed material such as a plant. http://purl.obolibrary.org/obo/OBI_0002911 arthropod resting outdoors specimen collection by aspiration http://purl.obolibrary.org/obo/OBI_0002905 animal-biting arthropod specimen collection by aspiration outdoors shelter catch An animal-biting arthropod specimen collection by aspiration that occurs while the arthropod is resting outside a building during a period of inactivity. http://purl.obolibrary.org/obo/OBI_0002912 arthropod specimen collection by aspiration http://purl.obolibrary.org/obo/OBI_0002904 adult arthropod specimen collection process catch by aspiration A live arthropod specimen collection process that involves the use of an aspirator, a device which draws an arthropod by suction into a container. http://purl.obolibrary.org/obo/OBI_0002913 arthropod specimen collection process http://purl.obolibrary.org/obo/OBI_0000659 specimen collection process collection of arthropods A specimen collection process that has the objective of collecting arthropods as specimens. http://purl.obolibrary.org/obo/OBI_0002914 human-biting arthropod specimen collection by aspiration http://purl.obolibrary.org/obo/OBI_0002912 arthropod specimen collection by aspiration man biting catch An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human. http://purl.obolibrary.org/obo/OBI_0002915 human-biting indoor arthropod specimen collection by aspiration http://purl.obolibrary.org/obo/OBI_0002914 human-biting arthropod specimen collection by aspiration man biting catch - indoors An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human inside a building. http://purl.obolibrary.org/obo/OBI_0002916 human-biting outdoor arthropod specimen collection by aspiration http://purl.obolibrary.org/obo/OBI_0002914 human-biting arthropod specimen collection by aspiration man biting catch - outdoors An arthropod specimen collection by aspiration designed to catch specimens that are in the process of biting a human outside a building. http://purl.obolibrary.org/obo/OBI_0002917 knockdown arthropod specimen collection by pyrethrum spray http://purl.obolibrary.org/obo/OBI_0002918 knockdown arthropod specimen collection process pyrethrum spray catch A knockdown arthropod specimen collection process in which the pesticide is pyrethrum. http://purl.obolibrary.org/obo/OBI_0002918 knockdown arthropod specimen collection process http://purl.obolibrary.org/obo/OBI_0002919 live arthropod specimen collection process knockdown collection An arthropod specimen collection process that involves exposing arthropods to pesticide, then collecting them once they become dead or immobilized. http://purl.obolibrary.org/obo/OBI_0002919 live arthropod specimen collection process http://purl.obolibrary.org/obo/OBI_0002913 arthropod specimen collection process catch of live specimens An arthropod specimen collection process meant to collect live specimens. http://purl.obolibrary.org/obo/OBI_0002920 arthropod trap http://purl.obolibrary.org/obo/OBI_0000968 device trap catch A device designed to catch arthropods. http://purl.obolibrary.org/obo/OBI_0002923 barrier trap http://purl.obolibrary.org/obo/OBI_0002920 arthropod trap barrier catch An arthropod trap consisting of a static physical barrier designed to funnel arthropods in flight into a container. http://purl.obolibrary.org/obo/OBI_0002924 BG-Counter http://purl.obolibrary.org/obo/OBI_0000968 device BG-Counter trap catch A device manufactured by BioGents that is designed to count mosquitoes passing through the device, differentiating the mosquitoes from other arthropods. http://purl.obolibrary.org/obo/OBI_0002925 BG-Sentinel trap http://purl.obolibrary.org/obo/OBI_0002920 arthropod trap BG-Sentinel trap catch An arthropod trap that is manufactured by Biogents and is designed to attract arthropods through the use of a motorized fan to mimic convection currents produced by a human. The current also pulls arthropods into the trap, where a layer of gauze prevents the arthropods from escaping along with the air current. http://purl.obolibrary.org/obo/OBI_0002926 Centers for Disease Control and Prevention light trap http://purl.obolibrary.org/obo/OBI_0002930 light trap CDC light trap catch A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the light attractant. This trap is also designed to be lightweight and operate in environments in which electricity may be scarce. http://purl.obolibrary.org/obo/OBI_0002927 dipper for arthropod immatures http://purl.obolibrary.org/obo/OBI_0000968 device dipper for immatures A device that is designed for the collection of arthropod larvae or pupae from water and has the shape of a ladle or a pan. http://purl.obolibrary.org/obo/OBI_0002928 encephalitis virus surveillance trap http://purl.obolibrary.org/obo/OBI_0002930 light trap EVS trap catch A light trap that uses carbon dioxide as attractant. The trap consists of a container of dry ice with holes in the bottom to allow the carbon dioxide to flow downward into a separate container, in which a motorized fan creates suction to collect arthropods. http://purl.obolibrary.org/obo/OBI_0002929 gravid trap http://purl.obolibrary.org/obo/OBI_0002920 arthropod trap gravid trap catch An arthropod trap that is designed to collect gravid female arthropods or their eggs. http://purl.obolibrary.org/obo/OBI_0002931 light trap for indoor use http://purl.obolibrary.org/obo/OBI_0002930 light trap indoor light trap catch A light trap designed to be placed inside a building. http://purl.obolibrary.org/obo/OBI_0002932 light trap for outdoor use http://purl.obolibrary.org/obo/OBI_0002930 light trap outdoor light trap catch A light trap designed to be placed outside a building. http://purl.obolibrary.org/obo/OBI_0002933 Mosquito Magnet trap http://purl.obolibrary.org/obo/OBI_0002920 arthropod trap mosquito magnet pro catch An arthropod trap that is powered by propane and is designed to emit a combination of carbon dioxide, heat, water, and oct-1-en-3-ol attractants while simultaneously using suction to trap arthropods. http://purl.obolibrary.org/obo/OBI_0002935 New Jersey light trap http://purl.obolibrary.org/obo/OBI_0002930 light trap new jersey trap catch A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the light attractant. http://purl.obolibrary.org/obo/OBI_0002936 Onderstepoort Veterinary Institute light-suction trap http://purl.obolibrary.org/obo/OBI_0002920 arthropod trap OVI light-suction trap A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the attractant. The light is supplied by an 8 watt tube, and the fan providing the suction has an 11-centimeter diameter. http://purl.obolibrary.org/obo/OBI_0002937 outlet window trap http://purl.obolibrary.org/obo/OBI_0002920 arthropod trap outlet window trap catch An arthropod trap that is positioned adjacent to a window of a building and is designed to collect arthropods flying out of the building. http://purl.obolibrary.org/obo/OBI_0002938 ovitrap http://purl.obolibrary.org/obo/OBI_0002920 arthropod trap oviposition trap An arthropod trap that consists of a container holding a mesh layer above water and is designed to trap arthropods hatched from eggs dropped over the water by gravid females. http://purl.obolibrary.org/obo/OBI_0002940 resting box trap http://purl.obolibrary.org/obo/OBI_0002939 resting arthropod trap resting box catch An arthropod trap that consists of a box that is open on one end. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity. http://purl.obolibrary.org/obo/OBI_0002941 resting bucket http://purl.obolibrary.org/obo/OBI_0002939 resting arthropod trap resting bucket catch An arthropod trap that consists of a bucket, which is lined with fabric and placed on its side, and a wet cloth inside the bucket. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity (not actively seeking a host). http://purl.obolibrary.org/obo/OBI_0002942 Shannon trap http://purl.obolibrary.org/obo/OBI_0002920 arthropod trap shannon trap catch An arthropod trap that is made of cloth and netting and is designed to be suspended from above (e.g. from a tree). It is also designed so that the arthropod enters the trap from beneath, being attracted to some bait, and is prevented from escaping upward by the suspended cloth, which allows them to be collected from the upper interior of the trap. http://purl.obolibrary.org/obo/OBI_0002943 sticky resting bucket http://purl.obolibrary.org/obo/OBI_0002939 resting arthropod trap sticky resting bucket catch An arthropod trap that consists of a bucket, which is lined with adhesive and placed on its side, and a wet cloth inside the bucket. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity. The trap is designed for arthropods to become caught in the adhesive so that they can be collected. http://purl.obolibrary.org/obo/OBI_0002944 sticky trap http://purl.obolibrary.org/obo/OBI_0002939 resting arthropod trap sticky trap catch An arthropod trap that is designed to capture arthropods resting on a surface by coating the surface with adhesive. http://purl.obolibrary.org/obo/OBI_0002543 atrial appendage specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from the atrium auricular region. http://purl.obolibrary.org/obo/OBI_0002550 sigmoid colon specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from sigmoid colon. http://purl.obolibrary.org/obo/OBI_0002466 alignment counting algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm An algorithm used to assign aligned sequence reads, resulting from a reference genome transcriptome alignment algorithm, to sequence features (e.g. genes or transcripts). http://purl.obolibrary.org/obo/OBI_0002467 alignment counting application http://purl.obolibrary.org/obo/IAO_0000594 software application A software application that implements an alignment counting algorithm, used to count the overlap of aligned sequencing reads with genes. http://purl.obolibrary.org/obo/OBI_0002468 base calling algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm An algorithm that assigns nucleotides to temporal or spatial peaks generated by a detector, such as peaks of light intensities generated by a DNA sequencer http://purl.obolibrary.org/obo/OBI_0002469 base calling application http://purl.obolibrary.org/obo/IAO_0000594 software application A base-calling application that implments a base-calling algorithm to convert BCL (binary base call) files, (e.g., those generated by Illumina sequencing systems) to standard FASTQ file formats for downstream analysis. http://purl.obolibrary.org/obo/OBI_0002461 BCL format http://purl.obolibrary.org/obo/IAO_0000098 data format specification A data format specification that is a binary file containing base calling data. These files are created by sequencing machines during the act of sequencing, and contain data about each of the nucleotide clusters on a sequencing flow cell. http://purl.obolibrary.org/obo/OBI_0002470 bcl2fastq software application http://purl.obolibrary.org/obo/OBI_0002469 base calling application A base calling application that implments a base calling algorithm to convert BCL (binary base call) files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis. http://purl.obolibrary.org/obo/OBI_0002471 date process started http://purl.obolibrary.org/obo/IAO_0000027 data item A data item that is the date when a process was initiated. http://purl.obolibrary.org/obo/OBI_0002462 ERCC RNA spike-in http://purl.obolibrary.org/obo/OBI_0000047 processed material A processed material developed by the External RNA Controls Consortium (ERCC) that consists of 92 transcripts, derived and traceable from NIST-certified DNA plasmids. http://purl.obolibrary.org/obo/OBI_0002473 material amplification role http://purl.obolibrary.org/obo/OBI_0000116 worker role A worker role played by the person who runs the enzymatic amplifying process. http://purl.obolibrary.org/obo/OBI_0002474 material sequencing library preparation role http://purl.obolibrary.org/obo/OBI_0000116 worker role A worker role played by the person who performs the library preparation process to generate a sequencing library for a sample to be sequenced. http://purl.obolibrary.org/obo/OBI_0002487 microraft http://purl.obolibrary.org/obo/OBI_0000932 material separation device A material separation device also commerically known as Isoraft, that is used to isolate single cells. http://purl.obolibrary.org/obo/OBI_0002476 number of rounds of amplification http://purl.obolibrary.org/obo/IAO_0000027 data item A data item that is the number of times an amplification reaction happened. http://purl.obolibrary.org/obo/OBI_0002488 pipette http://purl.obolibrary.org/obo/OBI_0000968 device A device that is a laboratory tool commonly used in chemistry, biology and medicine to transport a measured volume of liquid, often as a media dispenser. http://purl.obolibrary.org/obo/OBI_0002477 reference genome role http://purl.obolibrary.org/obo/OBI_0000025 reference substance role A reference substance role that is played by a reference genome when used during sequence alignment. http://purl.obolibrary.org/obo/OBI_0002478 reference genome-transcriptome alignment algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm An algorithm that attempts to align a nucleic acid sequence to a reference genome and transcriptome. http://purl.obolibrary.org/obo/OBI_0002481 single-end library http://purl.obolibrary.org/obo/OBI_0002754 cDNA library A cDNA library that is a collection of short tags from only one end of DNA fragments. http://purl.obolibrary.org/obo/OBI_0002463 SIRV RNA spike-in http://purl.obolibrary.org/obo/OBI_0000047 processed material A processed material that consists of transcript isoforms of 7 spike-in RNA variant (SIRV) genes and possibly the 92 External RNA Controls Consortium (ERCC) RNA spike-in genes. http://purl.obolibrary.org/obo/OBI_0002483 spike-in dilution factor http://purl.obolibrary.org/obo/IAO_0000027 data item A data item that indicates the dilution of spike-in added to a specimen. http://purl.obolibrary.org/obo/OBI_0002484 star algorithm http://purl.obolibrary.org/obo/OBI_0002478 reference genome-transcriptome alignment algorithm A reference genome transcriptome alignment algorithm that is a standalone RNA-seq alignment algorithm that uses uncompressed suffix arrays and a mapping algorithm similar to those used in large-scale genome alignment tools to align RNA-seq reads to a genomic reference. http://purl.obolibrary.org/obo/OBI_0002486 verse algorithm http://purl.obolibrary.org/obo/OBI_0002466 alignment counting algorithm An alignment counting algorithm that assigns gene features to genomic alignments using a hierarchical assignment scheme, which allows simultaneous quantification of multiple feature types or annotation levels without repeatedly assigning reads. http://purl.obolibrary.org/obo/ONS_0000070 Cohort Study http://purl.obolibrary.org/obo/OBI_0500000 study design Data are obtained from groups who have been exposed, or not exposed, to the new technology or factor of interest (eg from databases). No allocation of exposure is made by the researcher. Best for study the effect of predictive risk factors on an outcome. http://purl.obolibrary.org/obo/ONS_0000071 Case-Control Studies http://purl.obolibrary.org/obo/OBI_0500000 study design Patients with a certain outcome or disease and an appropriate group of controls without the outcome or disease are selected (usually with careful consideration of appropriate choice of controls, matching, etc) and then information is obtained on whether the subjects have been exposed to the factor under investigation. http://purl.obolibrary.org/obo/ONS_0000072 Cross-Sectional Survey http://purl.obolibrary.org/obo/OBI_0500000 study design A study that examines the relationship between diseases (or other health-related characteristics) and other variables of interest as they exist in a defined population at one particular time (ie exposure and outcomes are both measured at the same time). Best for quantifying the prevalence of a disease or risk factor, and for quantifying the accuracy of a diagnostic test. http://purl.obolibrary.org/obo/CHEBI_31624 fluorescein http://purl.obolibrary.org/obo/OBI_0002744 molecular label A xanthene dye that is highly fluorescent, detectable even when present in minute quantities. Used forensically to detect traces of blood, in analytical chemistry as an indicator in silver nitrate titrations and in microscopy. http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity http://purl.obolibrary.org/obo/BFO_0000040 material entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. http://purl.obolibrary.org/obo/CHEBI_23995 N-ethyl-N-nitrosourea http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity A member of the class of N-nitrosoureas that is urea in which one of the nitrogens is substituted by ethyl and nitroso groups. http://purl.obolibrary.org/obo/CHEBI_24636 proton http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u. http://purl.obolibrary.org/obo/CHEBI_26710 sodium chloride http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity An inorganic chloride salt having sodium(1+) as the counterion. http://purl.obolibrary.org/obo/CHEBI_28619 acrylamide http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia. http://purl.obolibrary.org/obo/CHEBI_33250 atom http://purl.obolibrary.org/obo/BFO_0000040 material entity A chemical entity constituting the smallest component of an element having the chemical properties of the element. http://purl.obolibrary.org/obo/CHEBI_37972 phosphorus-32 atom http://purl.obolibrary.org/obo/OBI_0001879 reagent The radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days. http://purl.obolibrary.org/obo/CHEBI_37973 phosphorus-33 atom http://purl.obolibrary.org/obo/OBI_0001879 reagent The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2. http://purl.obolibrary.org/obo/CHEBI_42098 digoxigenin http://purl.obolibrary.org/obo/OBI_0002744 molecular label A hydroxy steroid that consists of 5beta-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3beta-, 12beta- and 14beta-positions. It has been isolated from the plant species of the genus Digitalis. http://purl.obolibrary.org/obo/CHEBI_59050 dimethyl sulfate http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity The dimethyl ester of sulfuric acid. http://purl.obolibrary.org/obo/CHEBI_9754 tris http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity A primary amino compound that is tert-butylamine in which one hydrogen attached to each methyl group is replaced by a hydroxy group. A compound widely used as a biological buffer substance in the pH range 7--9; pKa = 8.3 at 20 degreeC; pKa = 7.82 at 37 degreeC. http://purl.obolibrary.org/obo/CHEBI_50076 chromium-51 http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival. http://purl.obolibrary.org/obo/APOLLO_SV_00000008 software development http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process that has specified output a software product and that involves the creation of source code. http://purl.obolibrary.org/obo/OBI_0002140 temperature measurement assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay to determine the temperature of an evaluant. http://purl.obolibrary.org/obo/OBI_0002566 file merge http://purl.obolibrary.org/obo/OBI_0200000 data transformation A data transformation in which data contained in 2 or more files are merged into a single file. http://purl.obolibrary.org/obo/OBI_0002567 sequence alignment http://purl.obolibrary.org/obo/OBI_0200187 sequence analysis data transformation A data transformation in which one or more sequences (reads) are positioned on a reference sequence template (often a reference set of genes), according to the genetic base-pairing paradigm. http://purl.obolibrary.org/obo/OBI_0002568 sequence data feature count tabulation http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating The counting of features (typically, genes) within aligned sequence data, and organization of these counts into one or more tables. http://purl.obolibrary.org/obo/OBI_0002569 trimmed sequence data http://purl.obolibrary.org/obo/OBI_0000973 sequence data The results of a data transformation of sequence data in which (e.g., low quality) read bases are removed, to achieve some specific objective. http://purl.obolibrary.org/obo/OBI_0002578 adapter sequence data http://purl.obolibrary.org/obo/OBI_0000973 sequence data Nucleotide sequences of molecules that are ligated to assay samples prior to sequencing of these samples; these sequences are provided by assay kit manufacturers and typically used to combine sequencing of multiple samples in one assay run. http://purl.obolibrary.org/obo/OBI_0002579 adapter-trimmed sequence data http://purl.obolibrary.org/obo/OBI_0000973 sequence data The results of a data transformation of sequence data in which reference subsequences corresponding to ligated library adapters are removed. http://purl.obolibrary.org/obo/OBI_0002580 aligned sequence data http://purl.obolibrary.org/obo/OBI_0000973 sequence data The results of a sequence alignment. http://purl.obolibrary.org/obo/OBI_0002581 merged aligned sequence data http://purl.obolibrary.org/obo/OBI_0000973 sequence data The results of a data transformation of sequence data in which files containing aligned sequence data are merged together http://purl.obolibrary.org/obo/OBI_0002582 sequence library feature count data http://purl.obolibrary.org/obo/IAO_0000100 data set The results of a sequence data feature count tabulation. http://purl.obolibrary.org/obo/OBI_0002583 DNA methylation profiling data http://purl.obolibrary.org/obo/OBI_0000973 sequence data The results of a DNA methylation profiling assay http://purl.obolibrary.org/obo/OBI_0002584 differential expression analysis data http://purl.obolibrary.org/obo/IAO_0000100 data set The results of a differential expression analysis. http://purl.obolibrary.org/obo/OBI_0002585 sequence trimming http://purl.obolibrary.org/obo/OBI_0200000 data transformation A data transformation in which subsequences of a molecular sequence are cut (removed). http://purl.obolibrary.org/obo/OBI_0002587 machine learning http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process in which statistical techniques are used to give computers the ability to learn about patterns in data, without being explicitly programmed. Learning is defined in this case as progressively improving performance on a specific task. http://purl.obolibrary.org/obo/OBI_0002588 supervised machine learning http://purl.obolibrary.org/obo/OBI_0002587 machine learning A machine learning process using a function that maps an input to an output based on example input-output pairs. It infers a function from labeled training data consisting of a set of training examples. http://purl.obolibrary.org/obo/IAO_0000646 postal code http://purl.obolibrary.org/obo/IAO_0020000 identifier An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail. http://purl.obolibrary.org/obo/IAO_0000647 Postal delivery route http://purl.obolibrary.org/obo/IAO_0000104 plan specification A plan specification that if realized, is realized by the delivery of mail to some facility or mailbox within some geographical region. http://purl.obolibrary.org/obo/ONE_0000001 dietary survey method http://purl.obolibrary.org/obo/OBI_0000070 assay An investigation of food and nutrient intake and dietary pattern of an individual or individuals. http://purl.obolibrary.org/obo/ONE_0000002 retrospective dietary survey method http://purl.obolibrary.org/obo/ONE_0000001 dietary survey method A type of dietary survey method that is based on a recall of food or drink intake that have already been consumed. http://purl.obolibrary.org/obo/ONE_0000003 prospective dietary survey method http://purl.obolibrary.org/obo/ONE_0000001 dietary survey method A type of dietary survey method that involves recording the diet when the foods or drinks are being consumed. http://purl.obolibrary.org/obo/ONE_0000005 24-hour dietary recall method http://purl.obolibrary.org/obo/ONE_0000002 retrospective dietary survey method A type of retrospective dietary survey method where respondents are asked, by a nutritionist or dietitian who has been trained in interviewing techniques, to recall and report all foods and beverages consumed over the preceding 24 hours. http://purl.obolibrary.org/obo/ONE_0000006 dietary history method http://purl.obolibrary.org/obo/ONE_0000002 retrospective dietary survey method A type of retrospective dietary survey method that is a detailed assessment to describe usual food intake and its variation over a long period of time. http://purl.obolibrary.org/obo/ONE_0000008 duplicate diet method http://purl.obolibrary.org/obo/ONE_0000003 prospective dietary survey method A type of prospective dietary survey method that involves setting aside duplicate portions of all foods and beverages consumed throughout a specific time period. These duplicate portions are set aside, weighed, either by the respondent or fieldworker, and then sent to a laboratory for chemical analysis to determine content. http://purl.obolibrary.org/obo/ONE_0000009 dietary records method http://purl.obolibrary.org/obo/ONE_0000003 prospective dietary survey method A type of prospective dietary survey method collecting data about the foods and beverages consumed over a previously specified period of time. http://purl.obolibrary.org/obo/ONE_0000010 retrospective method for assessing dietary diversity of infant and yong child http://purl.obolibrary.org/obo/ONE_0000004 retrospective method for assessing dietary diversity A retrospective method for assessing dietary diversity with the "Infant and Young Child Dietary Diversity Score" (IYCDDS, defined as the Proportion of children 6–23 months of age who receive foods from four or more predefined food groups. http://purl.obolibrary.org/obo/ONE_0000011 retrospective method for assessing dietary diversity of women http://purl.obolibrary.org/obo/ONE_0000004 retrospective method for assessing dietary diversity A retrospective method for assessing dietary diversity in women. Minimum Dietary Diversity-Women is a dichotomous indicator of whether or not women of 15–49 years of age have consumed at least five out of ten predefined food groups during the previous 24 hours. http://purl.obolibrary.org/obo/ONE_0000012 screener method http://purl.obolibrary.org/obo/ONE_0000007 Food Frequency Questionnaire method A retrospective dietary survey method that uses modified versions of longer Food Frequency Questionnaires varying in length, frequency categories and number of foods listed. http://purl.obolibrary.org/obo/ONE_0000013 non-quantitative FFQ method http://purl.obolibrary.org/obo/ONE_0000007 Food Frequency Questionnaire method A type of Food Frequency Questionnaire method that collects only frequency of food or drink intake. http://purl.obolibrary.org/obo/ONE_0000014 semi-quantitative FFQ method http://purl.obolibrary.org/obo/ONE_0000007 Food Frequency Questionnaire method A type of Food Frequency Questionnaire method that includes information about both the frequency and quantity of food or drink intake. http://purl.obolibrary.org/obo/ONE_0000015 weighed food records method http://purl.obolibrary.org/obo/ONE_0000009 dietary records method A type of dietary records method that adopts the same methodological principles as the estimated food record method. However, in this method respondents are asked to weigh foods or drinks using weighing scales. http://purl.obolibrary.org/obo/ONE_0000016 estimated food records method http://purl.obolibrary.org/obo/ONE_0000009 dietary records method A type of dietary records method that instructions respondents to document all foods and beverages consumed during a predefined period. http://purl.obolibrary.org/obo/ONE_0001001 quality indicator of a dietary survey http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity that specifies the quality of a dietary survey. http://purl.obolibrary.org/obo/ONE_0001002 quality indicator of a diet recall method http://purl.obolibrary.org/obo/ONE_0001001 quality indicator of a dietary survey : An indicator that specifies the quality of a diet recall method. http://purl.obolibrary.org/obo/ONE_0001003 quality indicator of a diet survey questionnaire http://purl.obolibrary.org/obo/ONE_0001001 quality indicator of a dietary survey An indicator that specifies the quality of dietary survey questionnaires that includes a predetermined set of questions used to collect diet intake information. http://purl.obolibrary.org/obo/ONE_0001004 representativeness of days as a quality indicator of a dietary survey http://purl.obolibrary.org/obo/ONE_0001001 quality indicator of a dietary survey An indicator that specifies the representativeness of days of a dietary survey. http://purl.obolibrary.org/obo/ONE_0001005 quality indicator of a food quantification method http://purl.obolibrary.org/obo/ONE_0001001 quality indicator of a dietary survey An indicator that specifies the accuracy of a food quantification process (i.e. a process that helps express food intake into units of weights or volume.). http://purl.obolibrary.org/obo/ONE_0001006 administration type of a diet recall method http://purl.obolibrary.org/obo/ONE_0001002 quality indicator of a diet recall method An indicator that specifies the administration type of a diet recall method. A diet recall method can be proxy administered, self-administered or interview administered. http://purl.obolibrary.org/obo/ONE_0001007 time of dietary record http://purl.obolibrary.org/obo/ONE_0001002 quality indicator of a diet recall method An indicator that specifies when the dietary intake was recorded. (e.g. during eating occasion, immediately after eating occasion, or later). http://purl.obolibrary.org/obo/ONE_0001008 origin of a diet survey questionnaire http://purl.obolibrary.org/obo/ONE_0001003 quality indicator of a diet survey questionnaire An indicator that specifies how the questionnaire was developed (e.g. de novo self-developed questionnaire, standardized questionnaire, questionnaire adapted from another questionnaires, etc.). http://purl.obolibrary.org/obo/ONE_0001009 content validity of a diet survey questionnaire http://purl.obolibrary.org/obo/ONE_0001003 quality indicator of a diet survey questionnaire An indicator that specifies the content validity of a diet survey questionnaire in another comparable population in terms of both age and dietary habits. The reference, the type of the validation, and validation estimates are important pieces of information. http://purl.obolibrary.org/obo/ONE_0001013 representativeness of seasons of a dietary survey http://purl.obolibrary.org/obo/ONE_0001004 representativeness of days as a quality indicator of a dietary survey An indicator that specifies if data collection was seasonality representative. http://purl.obolibrary.org/obo/ONE_0001014 representativeness of week/weekend days of a dietary survey http://purl.obolibrary.org/obo/ONE_0001004 representativeness of days as a quality indicator of a dietary survey An indicator that specifies the representativeness of week/weekend days when conducting a dietary survey. http://purl.obolibrary.org/obo/ONE_0001015 number of days of a dietary survey http://purl.obolibrary.org/obo/ONE_0001004 representativeness of days as a quality indicator of a dietary survey An indicator that specifies the number of days of a dietary recall/measurement per individual. http://purl.obolibrary.org/obo/ONE_0001016 selection of recall/measurement days of a dietary survey http://purl.obolibrary.org/obo/ONE_0001004 representativeness of days as a quality indicator of a dietary survey An indicator that specifies how the recall/measurement days of a dietary survey were selected. http://purl.obolibrary.org/obo/ONE_0001017 quantification of a food portion size http://purl.obolibrary.org/obo/ONE_0001005 quality indicator of a food quantification method An indicator that specifies how the quantity of the portion sizes is estimated. http://purl.obolibrary.org/obo/ONE_0001018 quantification of food intake data http://purl.obolibrary.org/obo/ONE_0001005 quality indicator of a food quantification method An indicator that specifies how food intake data are expressed into units of weights or volume. http://purl.obolibrary.org/obo/ONE_0001019 geographically specific food quantification http://purl.obolibrary.org/obo/ONE_0001005 quality indicator of a food quantification method An indicator for food quantification method that indicates whether a food quantification method is geography matched to the area where the food is estimated. http://purl.obolibrary.org/obo/ONE_0001020 customized food quantification http://purl.obolibrary.org/obo/ONE_0001005 quality indicator of a food quantification method An indicator for food quantification method that indicates whether a food quantification method is tailored to the characteristics of the assessed population. http://purl.obolibrary.org/obo/ONE_0001021 referred food composition data for quantification http://purl.obolibrary.org/obo/ONE_0001005 quality indicator of a food quantification method An indicator that indicates how the measured food intake data are matched to food composition data. http://purl.obolibrary.org/obo/ONE_0002001 abstract of a published study based on dietary survey(s) http://purl.obolibrary.org/obo/IAO_0000315 abstract An abstract which states the dietary/nutritional assessment method(s) used in the research (STROBE-nut-1). http://purl.obolibrary.org/obo/ONE_0002002 participants result section http://purl.obolibrary.org/obo/ONE_0002004 results section of a published study based on dietary survey(s) A results section that reports the number of individuals excluded based on missing, incomplete or implausible dietary/nutritional data. http://purl.obolibrary.org/obo/ONE_0002003 methods of a published study based on dietary survey(s) http://purl.obolibrary.org/obo/IAO_0000317 methods section a methods section that includes a few sections to describe particular characterisitics of study methods based on dietary surveys. http://purl.obolibrary.org/obo/ONE_0002004 results section of a published study based on dietary survey(s) http://purl.obolibrary.org/obo/IAO_0000318 results section A results section that includes a few sections to describe particular characterisitics of research results of a study based on dietary surveys. http://purl.obolibrary.org/obo/ONE_0002005 discussion of a published study based on dietary survey(s) http://purl.obolibrary.org/obo/IAO_0000319 discussion section of a publication about an investigation A discussion section that interprets particular characterisitics of a study based on dietary surveys. http://purl.obolibrary.org/obo/ONE_0002006 ethics of a published study based on dietary survey(s) http://purl.obolibrary.org/obo/IAO_0000620 ethical approval section an ethical approval section that describes the procedure for consent and study approval from ethics committee(s). http://purl.obolibrary.org/obo/ONE_0002007 limitation section http://purl.obolibrary.org/obo/ONE_0002005 discussion of a published study based on dietary survey(s) A discussion section that describes the main limitations of the data sources and assessment methods used and implications for the interpretation of the findings. http://purl.obolibrary.org/obo/ONE_0002008 supplementary material of a published study based on dietary survey(s) http://purl.obolibrary.org/obo/IAO_0000326 supplementary material to a document a supplementary (online) material that provides data collection tools and data as online material or explain how they can be accessed. http://purl.obolibrary.org/obo/ONE_0002009 settings section http://purl.obolibrary.org/obo/ONE_0002003 methods of a published study based on dietary survey(s) A methods section that describes any characteristics of the study settings that might affect the dietary intake or nutritional status of the participants, if applicable. http://purl.obolibrary.org/obo/ONE_0002010 participants section http://purl.obolibrary.org/obo/ONE_0002003 methods of a published study based on dietary survey(s) A methods section that reports particular dietary, physiological or nutritional characteristics that were considered when selecting the target population. http://purl.obolibrary.org/obo/ONE_0002011 variables section http://purl.obolibrary.org/obo/ONE_0002003 methods of a published study based on dietary survey(s) A methods section that a) clearly defines foods, food groups, nutrients, or other food components.b) when using dietary patterns or indices, describes the methods to obtain them and their nutritional properties. http://purl.obolibrary.org/obo/ONE_0002012 data measurements section http://purl.obolibrary.org/obo/ONE_0002003 methods of a published study based on dietary survey(s) A methods section that includes 6 elements for the description of data measurements of a study based on dietary survey(s). http://purl.obolibrary.org/obo/ONE_0002013 bias section http://purl.obolibrary.org/obo/ONE_0002003 methods of a published study based on dietary survey(s) A method section that reports how bias in dietary or nutritional assessment was addressed, e.g., misreporting, changes in habits as a result of being measured, or data imputation from other sources http://purl.obolibrary.org/obo/ONE_0002014 quantitative variables section http://purl.obolibrary.org/obo/ONE_0002003 methods of a published study based on dietary survey(s) A methods section that explains categorization of dietary/nutritional data (e.g., use of N-tiles and handling of nonconsumers) and the choice of reference category, if applicable. http://purl.obolibrary.org/obo/ONE_0002015 statistical analysis section of a published study based on dietary survey(s) http://purl.obolibrary.org/obo/IAO_0000644 statistical analysis section A statistical analysis section that a) describes any statistical method used to combine dietary or nutritional data, if applicable; b) describes and justifies the method for energy adjustments, intake modeling, and use of weighting factors, if applicable; c) reports any adjustments for measurement error, i.e,. from a validity or calibration study. http://purl.obolibrary.org/obo/ONE_0002016 dietary assessment method(s) section http://purl.obolibrary.org/obo/ONE_0002012 data measurements section A data measurements section that describes the dietary assessment method(s), e.g., portion size estimation, number of days and items recorded, how it was developed and administered, and how quality was assured, and report if and how supplement intake was assessed. http://purl.obolibrary.org/obo/ONE_0002017 food composition data section http://purl.obolibrary.org/obo/ONE_0002012 data measurements section A data measurements section that describes and justifies food composition data used. (e.g. explain the procedure to match food composition with consumption data and describe the use of conversion factors, if applicable.) http://purl.obolibrary.org/obo/ONE_0002018 dietary reference values section http://purl.obolibrary.org/obo/ONE_0002012 data measurements section A data measurements section that describes the nutrient requirements, recommendations, or dietary guidelines and the evaluation approach used to compare intake with the dietary reference values, if applicable. http://purl.obolibrary.org/obo/ONE_0002019 biomarkers section http://purl.obolibrary.org/obo/ONE_0002012 data measurements section A data measurements section that reports the type of biomarkers used and their usefulness as dietary exposure markers. When using nutritional biomarkers, additionally use the STROBE Extension for Molecular Epidemiology (STROBE-ME). http://purl.obolibrary.org/obo/ONE_0002020 nondietary data section http://purl.obolibrary.org/obo/ONE_0002012 data measurements section A data measurements section that describes the assessment of nondietary data (e.g., nutritional status and influencing factors) and timing of the assessment of these variables in relation to dietary assessment. http://purl.obolibrary.org/obo/ONE_0002021 study validation section http://purl.obolibrary.org/obo/ONE_0002012 data measurements section A data measurements section that reports on the validity of the dietary or nutritional assessment methods and any internal or external validation used in the study, if applicable. http://purl.obolibrary.org/obo/ONE_0002022 descriptive data section http://purl.obolibrary.org/obo/ONE_0002004 results section of a published study based on dietary survey(s) A results section that gives the distribution of participant characteristics across the exposure variables if applicable, specifies if food consumption of total population or consumers only were used to obtain results. http://purl.obolibrary.org/obo/ONE_0002023 main results section http://purl.obolibrary.org/obo/ONE_0002004 results section of a published study based on dietary survey(s) A result section that specifies if nutrient intakes are reported with or without inclusion of dietary supplement intake, if applicable. http://purl.obolibrary.org/obo/ONE_0002024 other analyses section http://purl.obolibrary.org/obo/ONE_0002004 results section of a published study based on dietary survey(s) A results section that reports any sensitivity analysis (e.g., exclusion of misreporters or outliers) and data imputation, if applicable. http://purl.obolibrary.org/obo/ONE_0002025 interpretation section http://purl.obolibrary.org/obo/ONE_0002005 discussion of a published study based on dietary survey(s) A discussion section that reports the nutritional relevance of the findings, given the complexity of diet or nutrition as an exposure. http://purl.obolibrary.org/obo/UBERON_0000310 breast http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity The upper ventral region of the torso of an organism. http://purl.obolibrary.org/obo/PATO_0000025 composition http://purl.obolibrary.org/obo/PATO_0000141 structure A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts. http://purl.obolibrary.org/obo/PATO_0000033 concentration of http://purl.obolibrary.org/obo/PATO_0002182 molecular quality A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance. http://purl.obolibrary.org/obo/PATO_0000051 morphology http://purl.obolibrary.org/obo/PATO_0001241 physical object quality A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. http://purl.obolibrary.org/obo/PATO_0000117 size http://purl.obolibrary.org/obo/PATO_0000051 morphology A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. http://purl.obolibrary.org/obo/PATO_0000140 position http://purl.obolibrary.org/obo/PATO_0001018 physical quality A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity. http://purl.obolibrary.org/obo/PATO_0000141 structure http://purl.obolibrary.org/obo/PATO_0000051 morphology A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. http://purl.obolibrary.org/obo/PATO_0000165 time http://purl.obolibrary.org/obo/PATO_0001018 physical quality A quality in which events occur in sequence. http://purl.obolibrary.org/obo/PATO_0000169 viability http://purl.obolibrary.org/obo/PATO_0001995 organismal quality An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population. http://purl.obolibrary.org/obo/PATO_0001018 physical quality http://purl.obolibrary.org/obo/PATO_0001241 physical object quality A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. http://purl.obolibrary.org/obo/PATO_0001020 damage http://purl.obolibrary.org/obo/PATO_0000141 structure A structural quality inhering in a bearer by virtue of whether the bearer has been harmed or injured or spoiled. http://purl.obolibrary.org/obo/PATO_0001241 physical object quality http://purl.obolibrary.org/obo/BFO_0000019 quality A quality which inheres in a continuant. http://purl.obolibrary.org/obo/PATO_0001291 electromagnetic (EM) radiation quality http://purl.obolibrary.org/obo/PATO_0001739 radiation quality A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation. http://purl.obolibrary.org/obo/PATO_0001296 luminous flux http://purl.obolibrary.org/obo/PATO_0001300 optical quality A scalar optical quality which obtains by the magnitude of the light emitted by the bearer. http://purl.obolibrary.org/obo/PATO_0001300 optical quality http://purl.obolibrary.org/obo/PATO_0001291 electromagnetic (EM) radiation quality An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. http://purl.obolibrary.org/obo/PATO_0001335 bacterial mating type http://purl.obolibrary.org/obo/PATO_0001895 mating type A mating type that indicates whether the F plasmid has integrated into the chromosome. http://purl.obolibrary.org/obo/PATO_0001337 yeast mating type http://purl.obolibrary.org/obo/PATO_0001895 mating type A yeast mating type. http://purl.obolibrary.org/obo/PATO_0001342 Saccharomyces cerevisiae mating type http://purl.obolibrary.org/obo/PATO_0001337 yeast mating type A S. cerevisiae mating type. http://purl.obolibrary.org/obo/PATO_0001343 Schizosaccharomyces pombe mating type http://purl.obolibrary.org/obo/PATO_0001337 yeast mating type A S. pombe mating type determined by the gene configuration on the mat1 locus. http://purl.obolibrary.org/obo/PATO_0001393 euploid http://purl.obolibrary.org/obo/PATO_0001374 ploidy A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes. http://purl.obolibrary.org/obo/PATO_0001574 flow rate http://purl.obolibrary.org/obo/PATO_0001906 movement quality A physical quality inhering in a bearer by virtue of the bearer's motion characteristic. http://purl.obolibrary.org/obo/PATO_0001710 3-D extent http://purl.obolibrary.org/obo/PATO_0000117 size A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions. http://purl.obolibrary.org/obo/PATO_0001739 radiation quality http://purl.obolibrary.org/obo/PATO_0001018 physical quality A quality that inheres in an bearer by virtue of how that bearer interacts with radiation. http://purl.obolibrary.org/obo/PATO_0001740 activity (of a radionuclide) http://purl.obolibrary.org/obo/PATO_0001739 radiation quality A radiation quality inhering in a radioactive substance by virtue of its transformation (disintegration) rate. http://purl.obolibrary.org/obo/PATO_0001894 phenotypic sex http://purl.obolibrary.org/obo/PATO_0000047 biological sex An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics. http://purl.obolibrary.org/obo/PATO_0001895 mating type http://purl.obolibrary.org/obo/PATO_0000047 biological sex A biological sex quality inhering in an individual or a population that undergo sexual reproduction. http://purl.obolibrary.org/obo/PATO_0001906 movement quality http://purl.obolibrary.org/obo/PATO_0001018 physical quality A physical quality inhering in a bearer by virtue of the bearer's participation in movement. http://purl.obolibrary.org/obo/PATO_0002003 population quality http://purl.obolibrary.org/obo/PATO_0001241 physical object quality A quality that inheres in an entire population or part of a population. http://purl.obolibrary.org/obo/PATO_0002182 molecular quality http://purl.obolibrary.org/obo/PATO_0001241 physical object quality A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc. http://purl.obolibrary.org/obo/PATO_0002198 quality of a substance http://purl.obolibrary.org/obo/PATO_0001018 physical quality A quality inhering in a bearer by virtue of its constitution. http://purl.obolibrary.org/obo/UBERON_0036149 suprapubic skin http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity Area of skin in the hypoastric region of the abdomen. http://purl.obolibrary.org/obo/OBI_0002134 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 20 production by T cells. http://purl.obolibrary.org/obo/OBI_0002138 temperature value specification http://purl.obolibrary.org/obo/OBI_0001933 value specification A value specification that specifies the temperature of some thing. http://purl.obolibrary.org/obo/OBI_0002139 volume value specification http://purl.obolibrary.org/obo/OBI_0001933 value specification A value specification that specifies the volume of some thing. http://purl.obolibrary.org/obo/OBI_0002141 volume measurement assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay to determine the volume of an evaluant. http://purl.obolibrary.org/obo/OBI_0002162 footprinting assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that measures ligand binding and conformational changes by the solvent accessibility of the backbone, bases, or side-chain structures of macromolecules through their sensitivity to chemical or enzymatic cleavage or modification reactions. http://purl.obolibrary.org/obo/OBI_0002163 DNAse footprinting assay http://purl.obolibrary.org/obo/OBI_0002162 footprinting assay An enzymatic footprinting assay that determines protein-binding sites on DNA by identifying bound fragments that are protected from DNAse I-catalyzed hydrolysis http://purl.obolibrary.org/obo/OBI_0002164 mammalian 2-hybrid assay http://purl.obolibrary.org/obo/OBI_0001146 binding assay A binding assay that increases the expression of a reporter gene in mammalian cells by proteins of interest attached to two portions of the transcriptional activator, bringing those portions closer together. http://purl.obolibrary.org/obo/OBI_0002165 protein localization assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that determines the specific location of a protein. Subcellular localization is distinguished from tissue-based localization based on the type of microscopy applied. http://purl.obolibrary.org/obo/OBI_0002166 tissue-based protein localization assay http://purl.obolibrary.org/obo/OBI_0002165 protein localization assay A protein localization assay that determines the specific location of a protein in a living tissue sample. http://purl.obolibrary.org/obo/OBI_0002167 subcellular protein localization assay http://purl.obolibrary.org/obo/OBI_0002165 protein localization assay A protein localization assay that determines the specific subcellular location of a protein. The location is visualized through electron microscopy. http://purl.obolibrary.org/obo/OBI_0002168 subcellular protein immunohistochemistry assay http://purl.obolibrary.org/obo/OBI_0001986 immunohistochemistry An immunohistochemistry assay that uses antibodies to display the specific subcellular location of proteins. http://purl.obolibrary.org/obo/OBI_0002169 ChIP-qPCR assay http://purl.obolibrary.org/obo/OBI_0002692 polymerase chain reaction assay A ChIP assay that uses quantitative PCR to determine levels of specific DNA in immunoprecipitated samples. http://purl.obolibrary.org/obo/OBI_0002170 genomic SELEX http://purl.obolibrary.org/obo/OBI_0002161 systematic evolution of ligands by exponential enrichment assay A systematic evolution of ligands by exponential enrichment assay that starts with a library derived from genomic DNA instead of synthetically derived random DNA molecules. http://purl.obolibrary.org/obo/OBI_0002173 Southwestern blot assay http://purl.obolibrary.org/obo/OBI_0001591 direct binding assay A direct binding assay that detects interactions of labeled DNA with immobilized protein on a membrane. http://purl.obolibrary.org/obo/OBI_0002174 immunocytochemistry http://purl.obolibrary.org/obo/OBI_0001977 cytometry assay An immuno staining assay in which samples of intact cells are examined that have had most, if not all, of their surrounding extracellular matrix removed http://purl.obolibrary.org/obo/OBI_0002176 electrophysiology assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that measures the electrical properties of biological cells or tissues. Typically, this assay will generate measurements of voltage changes or electric current (or other associated variables such as impedence or capacitance). http://purl.obolibrary.org/obo/OBI_0002177 patch clamp assay http://purl.obolibrary.org/obo/OBI_0000447 intra cellular electrophysiology recording assay An intracellular electrophysiology assay where a glass micropipette is sealed to the surface of the cell membrane as a recording electrode to study ion channel activity. The key distinction of this technique is the electrical resistance of the seal between the cell membrane and the pipette is of the order 10-100 gigaohms, permitting high-resolution current measurements over the cell membrane in several different standard configurations. http://purl.obolibrary.org/obo/OBI_0002178 whole-cell patch clamp assay http://purl.obolibrary.org/obo/OBI_0002177 patch clamp assay A patch-clamp assay where the electrode is left in place on the cell, as in cell-attached recordings, but the membrane patch has been perforated, providing access from the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell. http://purl.obolibrary.org/obo/OBI_0002179 cell-attached patch clamp assay http://purl.obolibrary.org/obo/OBI_0002177 patch clamp assay A patch-clamp assay where the electrode is left in place on the cell, and the membrane patch has been left intact been perforated. This maintains the separation of the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell. http://purl.obolibrary.org/obo/OBI_0002180 inside-out patch clamp assay http://purl.obolibrary.org/obo/OBI_0002177 patch clamp assay A patch-clamp assay where a patch of the membrane is attached to the patch pipette, detached from the rest of the cell, and the cytosolic surface of the membrane is exposed to the external media, or bath. This provides the experimenter has access to the intracellular surface of the membrane via the bath and can manipulate the environment at the intracellular surface of single ion channels. For example, channels that are activated by intracellular ligands can then be studied through a range of ligand concentrations. http://purl.obolibrary.org/obo/OBI_0002181 outside-out patch clamp assay http://purl.obolibrary.org/obo/OBI_0002177 patch clamp assay A patch-clamp assay where a patch of the membrane is attached to the patch pipette. In this configuration, the external surface of the cell membrane is exposed as the outside of the membrane patch relative to the patch electrode. An outside-out patch starts with a gigaohm seal in a whole-cell recording configuration. The electrode is slowly withdrawn from the cell, until a fragment of membrane bulges away from the cell, which detaches and reforms as a convex membrane on the end of the electrode, with the original external surface of the membrane facing outward from the electrode. This provides the experimenter with access to the extracellular surface of the membrane via the bath and can manipulate the environment at the extracellular surface of single ion channels. http://purl.obolibrary.org/obo/OBI_0002182 voltage clamp assay http://purl.obolibrary.org/obo/OBI_0000447 intra cellular electrophysiology recording assay An cellular electrophysiology assay where the membrane potential of a cell is controlled by the experimentalist. This is accomplished through a feedback mechanism where any change in membrane potential is countered by permitting electrical current to flow into or out of the cell. http://purl.obolibrary.org/obo/OBI_0002185 current clamp assay http://purl.obolibrary.org/obo/OBI_0000447 intra cellular electrophysiology recording assay The current clamp technique records the membrane potential by injecting current into a cell through the recording electrode. Unlike in the voltage clamp mode, where the membrane potential is held at a level determined by the experimenter, in "current clamp" mode the membrane potential is free to vary, and the amplifier records whatever voltage the cell generates on its own or as a result of stimulation. This technique is used to study how a cell responds when electric current enters a cell; this is important for instance for understanding how neurons respond to neurotransmitters that act by opening membrane ion channels. http://purl.obolibrary.org/obo/OBI_0002187 single-unit recording http://purl.obolibrary.org/obo/OBI_0001977 cytometry assay An extracellular electrophysiology assay where a single microelectrode is placed in close proximity to a single neuron to measure voltage and current changes over time. This is the technicque used by Hubel and Wiesel to measure firing properties of primary visual cortex neurons in the 1950s in their original Nobel-prize winning study. A classic, old technique. http://purl.obolibrary.org/obo/OBI_0002188 multi-unit recording http://purl.obolibrary.org/obo/OBI_0000454 extracellular electrophysiology recording assay An extracellular electrophysiology assay where a collection of microelectrodes (often in an 'array' configuration) is placed into neural tissue to measure the distribution of voltage and current changes for a population of cells over time. http://purl.obolibrary.org/obo/OBI_0002189 local field potential recording http://purl.obolibrary.org/obo/OBI_0000454 extracellular electrophysiology recording assay An extracellular electrophysiology assay where a microelectrode is placed in the extracellular space of brain tissue to measure action potential and compared to an electrode either outside or inside that tissue. http://purl.obolibrary.org/obo/OBI_0002544 esophagogastric junction specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from the esophagogastric junction. http://purl.obolibrary.org/obo/OBI_0002545 ileum specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from ileum. http://purl.obolibrary.org/obo/OBI_0002546 liver specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from liver. http://purl.obolibrary.org/obo/OBI_0002547 minor salivary gland specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from minor salivary gland. http://purl.obolibrary.org/obo/OBI_0002548 omentum specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from omentum. http://purl.obolibrary.org/obo/OBI_0002549 ovary specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from female gonad. http://purl.obolibrary.org/obo/OBI_0002551 suprapubic skin specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from suprapubic skin. http://purl.obolibrary.org/obo/OBI_0002552 testis specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from testis. http://purl.obolibrary.org/obo/OBI_0002553 uterus specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from uterus. http://purl.obolibrary.org/obo/OBI_0002555 age group inclusion criterion http://purl.obolibrary.org/obo/OBI_0500027 inclusion criterion An inclusion criterion that defines and states an age bracket which, if met, makes an entity suitable for a given task or participation in a given process. http://purl.obolibrary.org/obo/OBI_0002556 minimum age value specification http://purl.obolibrary.org/obo/OBI_0001933 value specification A value specifcation that specifies the youngest age when specifying an age range. http://purl.obolibrary.org/obo/OBI_0002557 maximum age value specification http://purl.obolibrary.org/obo/OBI_0001933 value specification A value specifcation that specifies the oldest age when specifying an age range. http://purl.obolibrary.org/obo/OBI_0002558 use of medication inclusion criterion http://purl.obolibrary.org/obo/OBI_0500027 inclusion criterion An inclusion criterion that defines and states a a set of medications, which, if used by an entity, makes that entity suitable for a given task or participation in a given process. http://purl.obolibrary.org/obo/OBI_0002559 hospital patient inclusion criterion http://purl.obolibrary.org/obo/OBI_0500027 inclusion criterion An inclusion criterion defines that a human being has to be a hospital patient to be suitable for a given task or participation in a given process. http://purl.obolibrary.org/obo/OBI_0002560 family status inclusion criterion http://purl.obolibrary.org/obo/OBI_0500027 inclusion criterion An inclusion criterion that defines and states one or more family statuses, which, if met, makes a human being suitable for a given task or participation in a given process. http://purl.obolibrary.org/obo/OBI_0002561 sex inclusion criterion http://purl.obolibrary.org/obo/OBI_0500027 inclusion criterion An inclusion criterion that defines and states one or more sexes which, if met, makes an entity suitable for a given task or participation in a given process. http://purl.obolibrary.org/obo/OBI_0002562 country of residence inclusion criteria http://purl.obolibrary.org/obo/OBI_0500027 inclusion criterion An inclusion criterion that defines and states one or more countries of residence which, if met, makes a human being suitable for a given task or participation in a given process. http://purl.obolibrary.org/obo/OBI_0002563 ethnicity inclusion criterion http://purl.obolibrary.org/obo/OBI_0500027 inclusion criterion An inclusion criteria that defines and states one or more ethnicities which, if met, makes an entity suitable for a given task or participation in a given process. http://purl.obolibrary.org/obo/OBI_0002564 histopathology assay http://purl.obolibrary.org/obo/OBI_0600020 histological assay A histological assay that is intended to check for the presence or level of a specific disease. http://purl.obolibrary.org/obo/HP_0000855 Insulin resistance http://purl.obolibrary.org/obo/BFO_0000016 disposition Increased resistance towards insulin, that is, diminished effectiveness of insulin in reducing blood glucose levels. http://purl.obolibrary.org/obo/UBERON_0000002 uterine cervix http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity Lower, narrow portion of the uterus where it joins with the top end of the vagina. http://purl.obolibrary.org/obo/UBERON_0000057 urethra http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity the fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening http://purl.obolibrary.org/obo/UBERON_0000473 testis http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity A gonad of a male animal. A gonad produces and releases sperm. http://purl.obolibrary.org/obo/UBERON_0000947 aorta http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation http://purl.obolibrary.org/obo/UBERON_0001037 strand of hair http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity A filament, mostly protein, that grows from follicles found in the dermis[WP]. http://purl.obolibrary.org/obo/UBERON_0001264 pancreas http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]. http://purl.obolibrary.org/obo/UBERON_0001557 upper respiratory tract http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea. http://purl.obolibrary.org/obo/UBERON_0001621 coronary artery http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity An artery that supplies the myocardium. http://purl.obolibrary.org/obo/UBERON_0001638 vein http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity Any of the tubular branching vessels that carry blood from the capillaries toward the heart. http://purl.obolibrary.org/obo/UBERON_0001728 nasopharynx http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity the section of the pharynx that lies above the soft palate http://purl.obolibrary.org/obo/UBERON_0001729 oropharynx http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity the portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis http://purl.obolibrary.org/obo/UBERON_0001797 vitreous humor http://purl.obolibrary.org/obo/UBERON_0000463 organism substance A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina http://purl.obolibrary.org/obo/UBERON_0001987 placenta http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell. http://purl.obolibrary.org/obo/UBERON_0002037 cerebellum http://purl.obolibrary.org/obo/UBERON_0000481 multi-tissue structure Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA]. http://purl.obolibrary.org/obo/UBERON_0002067 dermis http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]. http://purl.obolibrary.org/obo/UBERON_0002369 adrenal gland http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. http://purl.obolibrary.org/obo/UBERON_0002371 bone marrow http://purl.obolibrary.org/obo/UBERON_0000479 tissue the soft tissue that fills the cavities of bones http://purl.obolibrary.org/obo/UBERON_0007650 esophagogastric junction http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity The junction between the esophagus and the stomach epithelium http://purl.obolibrary.org/obo/BFO_0000002 continuant http://purl.obolibrary.org/obo/BFO_0000001 entity An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. http://purl.obolibrary.org/obo/BFO_0000003 occurrent http://purl.obolibrary.org/obo/BFO_0000001 entity An entity that has temporal parts and that happens, unfolds or develops through time. http://purl.obolibrary.org/obo/BFO_0000004 independent continuant http://purl.obolibrary.org/obo/BFO_0000002 continuant A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. http://purl.obolibrary.org/obo/BFO_0000005 obsolete dependent continuant http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. http://purl.obolibrary.org/obo/BFO_0000015 process http://purl.obolibrary.org/obo/BFO_0000003 occurrent An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. http://purl.obolibrary.org/obo/BFO_0000017 realizable entity http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant http://purl.obolibrary.org/obo/BFO_0000002 continuant b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) http://purl.obolibrary.org/obo/BFO_0000023 role http://purl.obolibrary.org/obo/BFO_0000017 realizable entity A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. http://purl.obolibrary.org/obo/BFO_0000031 generically dependent continuant http://purl.obolibrary.org/obo/BFO_0000002 continuant A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. http://purl.obolibrary.org/obo/BFO_0000035 process boundary http://purl.obolibrary.org/obo/BFO_0000003 occurrent p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) http://purl.obolibrary.org/obo/BFO_0000040 material entity http://purl.obolibrary.org/obo/BFO_0000004 independent continuant An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. http://purl.obolibrary.org/obo/BFO_0000140 continuant fiat boundary http://purl.obolibrary.org/obo/BFO_0000141 immaterial entity b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) http://purl.obolibrary.org/obo/BFO_0000144 process profile http://purl.obolibrary.org/obo/BFO_0000015 process b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) http://purl.obolibrary.org/obo/BFO_0000145 relational quality http://purl.obolibrary.org/obo/BFO_0000019 quality b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) http://purl.obolibrary.org/obo/CLO_0000001 cell line cell http://purl.obolibrary.org/obo/OBI_0001866 secondary cultured cell A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture http://purl.obolibrary.org/obo/CLO_0000018 mortal cell line cell http://purl.obolibrary.org/obo/CLO_0000001 cell line cell A cell line cell that is capable of replicating a limited number of times in culture before undergoing senescence. http://purl.obolibrary.org/obo/CLO_0000019 immortal cell line cell http://purl.obolibrary.org/obo/CLO_0000001 cell line cell A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line. http://purl.obolibrary.org/obo/CLO_0000031 cell line http://purl.obolibrary.org/obo/OBI_0001905 secondary cultured cell population A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). http://purl.obolibrary.org/obo/CLO_0009828 immortal cell line http://purl.obolibrary.org/obo/CLO_0000031 cell line A cell line that is expected to be capable of indefinite propagation in an vitro culture. http://purl.obolibrary.org/obo/CLO_0009829 mortal cell line http://purl.obolibrary.org/obo/CLO_0000031 cell line A cell line is able to support only a limited number of passages in vitro. http://purl.obolibrary.org/obo/ENVO_00001998 soil http://purl.obolibrary.org/obo/BFO_0000040 material entity Soil is an environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, gases, liquids, and a broad range of resident micro- and macroorganisms. http://purl.obolibrary.org/obo/ENVO_00002257 podzol http://purl.obolibrary.org/obo/ENVO_00001998 soil Podzols are soils with a typically ash-grey upper subsurface horizon, bleached by loss of organic matter and iron oxides, on top of a dark accumulation horizon with brown, reddish or black illuviated humus and/or reddish Fe compounds. Podzols occur in humid areas in the boreal and temperate zones and locally also in the tropics. http://purl.obolibrary.org/obo/ENVO_00010483 environmental material http://purl.obolibrary.org/obo/BFO_0000040 material entity A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system. http://purl.obolibrary.org/obo/GAZ_00000448 geographic location http://purl.obolibrary.org/obo/BFO_0000029 site A reference to a place on the Earth, by its name or by its geographical location. http://purl.obolibrary.org/obo/IAO_0000001 conditional specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity A directive information entity that specifies what should happen if the trigger condition is fulfilled. http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label http://purl.obolibrary.org/obo/IAO_0000009 datum label A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. http://purl.obolibrary.org/obo/IAO_0000006 narrative object http://purl.obolibrary.org/obo/IAO_0000030 information content entity A narrative object is an information content entity that is a set of propositions. http://purl.obolibrary.org/obo/IAO_0000007 action specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity A directive information entity that describes an action the bearer will take. http://purl.obolibrary.org/obo/IAO_0000009 datum label http://purl.obolibrary.org/obo/IAO_0000030 information content entity A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label http://purl.obolibrary.org/obo/IAO_0000010 software http://purl.obolibrary.org/obo/IAO_0000104 plan specification Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. http://purl.obolibrary.org/obo/IAO_0000012 obsolete2_digital entity http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical. http://purl.obolibrary.org/obo/IAO_0000013 journal article http://purl.obolibrary.org/obo/IAO_0000311 publication A report that is published in a journal. http://purl.obolibrary.org/obo/IAO_0000015 information carrier http://purl.obolibrary.org/obo/BFO_0000019 quality A quality of an information bearer that imparts the information content http://purl.obolibrary.org/obo/IAO_0000017 model number http://purl.obolibrary.org/obo/IAO_0000028 symbol A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. http://purl.obolibrary.org/obo/IAO_0000019 obsolete2_binary digital entity http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters. http://purl.obolibrary.org/obo/IAO_0000024 obsolete_unit of measure http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class a unit of measure is the quality of some material entity compared to which another quality is some multiple of. http://purl.obolibrary.org/obo/IAO_0000025 programming language http://purl.obolibrary.org/obo/IAO_0000104 plan specification A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it. http://purl.obolibrary.org/obo/IAO_0000028 symbol http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. http://purl.obolibrary.org/obo/IAO_0000029 numeral http://purl.obolibrary.org/obo/IAO_0000028 symbol A symbol that denotes a number. http://purl.obolibrary.org/obo/IAO_0000030 information content entity http://purl.obolibrary.org/obo/BFO_0000031 generically dependent continuant A generically dependent continuant that is about some thing. http://purl.obolibrary.org/obo/IAO_0000031 integer numeral http://purl.obolibrary.org/obo/IAO_0000029 numeral A numeral that denotes an integer http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. http://purl.obolibrary.org/obo/IAO_0000033 directive information entity http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity whose concretizations indicate to their bearer how to realize them in a process. http://purl.obolibrary.org/obo/IAO_0000037 dot plot http://purl.obolibrary.org/obo/IAO_0000038 graph A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. http://purl.obolibrary.org/obo/IAO_0000038 graph http://purl.obolibrary.org/obo/IAO_0000309 diagram A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. http://purl.obolibrary.org/obo/IAO_0000047 obsolete2_text based digital entity http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class A text based digital entity is a digital entity that is encoded so that it only contains text characters. http://purl.obolibrary.org/obo/IAO_0000055 rule http://purl.obolibrary.org/obo/IAO_0000001 conditional specification A rule is an executable which guides, defines, restricts actions. http://purl.obolibrary.org/obo/IAO_0000059 obsolete2_report figure http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://purl.obolibrary.org/obo/IAO_0000104 plan specification A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. http://purl.obolibrary.org/obo/IAO_0000065 software interpreter http://purl.obolibrary.org/obo/IAO_0000064 algorithm A software interpreter is a software application that executes some specified input software. http://purl.obolibrary.org/obo/IAO_0000078 curation status specification http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. http://purl.obolibrary.org/obo/IAO_0000079 density plot http://purl.obolibrary.org/obo/IAO_0000038 graph A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel. http://purl.obolibrary.org/obo/IAO_0000088 report http://purl.obolibrary.org/obo/IAO_0000310 document A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record). http://purl.obolibrary.org/obo/IAO_0000091 obsolete_report element http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page). http://purl.obolibrary.org/obo/IAO_0000093 obsolete2_binary executable http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007) http://purl.obolibrary.org/obo/IAO_0000096 source code module http://purl.obolibrary.org/obo/IAO_0000033 directive information entity A source code module is a directive information entity that specifies, using a programming language, some algorithm. http://purl.obolibrary.org/obo/IAO_0000097 obsolete_report table http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content http://purl.obolibrary.org/obo/IAO_0000098 data format specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file http://purl.obolibrary.org/obo/IAO_0000100 data set http://purl.obolibrary.org/obo/IAO_0000027 data item A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. http://purl.obolibrary.org/obo/IAO_0000101 image http://purl.obolibrary.org/obo/IAO_0000308 figure An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part http://purl.obolibrary.org/obo/IAO_0000027 data item Data about an ontology part is a data item about a part of an ontology, for example a term http://purl.obolibrary.org/obo/IAO_0000104 plan specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. http://purl.obolibrary.org/obo/IAO_0000105 obsolete2_digital document http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file. http://purl.obolibrary.org/obo/IAO_0000109 measurement datum http://purl.obolibrary.org/obo/IAO_0000027 data item A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. http://purl.obolibrary.org/obo/IAO_0000129 version number http://purl.obolibrary.org/obo/IAO_0000028 symbol A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. http://purl.obolibrary.org/obo/IAO_0000131 serial number http://purl.obolibrary.org/obo/IAO_0000028 symbol A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. http://purl.obolibrary.org/obo/IAO_0000140 setting datum http://purl.obolibrary.org/obo/IAO_0000027 data item A settings datum is a datum that denotes some configuration of an instrument. http://purl.obolibrary.org/obo/IAO_0000144 conclusion textual entity http://purl.obolibrary.org/obo/OBI_0001909 conclusion based on data A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. http://purl.obolibrary.org/obo/IAO_0000178 material information bearer http://purl.obolibrary.org/obo/BFO_0000040 material entity A material entity in which a concretization of an information content entity inheres. http://purl.obolibrary.org/obo/IAO_0000179 histogram http://purl.obolibrary.org/obo/IAO_0000038 graph A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes. http://purl.obolibrary.org/obo/IAO_0000180 heatmap http://purl.obolibrary.org/obo/IAO_0000038 graph A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map. http://purl.obolibrary.org/obo/IAO_0000181 Venn diagram http://purl.obolibrary.org/obo/IAO_0000038 graph A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets. http://purl.obolibrary.org/obo/IAO_0000182 obsolete_survival curve http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time. http://purl.obolibrary.org/obo/IAO_0000183 dendrogram http://purl.obolibrary.org/obo/IAO_0000038 graph A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm. http://purl.obolibrary.org/obo/IAO_0000185 photograph http://purl.obolibrary.org/obo/IAO_0000101 image A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc. http://purl.obolibrary.org/obo/IAO_0000186 photographic print http://purl.obolibrary.org/obo/IAO_0000178 material information bearer A photographic print is a material entity upon which a photograph generically depends. http://purl.obolibrary.org/obo/IAO_0000225 obsolescence reason specification http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. http://purl.obolibrary.org/obo/IAO_0000301 citation http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity intended to identify a particular publication. http://purl.obolibrary.org/obo/IAO_0000302 author identification http://purl.obolibrary.org/obo/IAO_0000590 written name A textual entity intended to identify a particular author http://purl.obolibrary.org/obo/IAO_0000303 institutional identification http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity intended to identify a particular institution http://purl.obolibrary.org/obo/IAO_0000304 caption http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that describes a figure http://purl.obolibrary.org/obo/IAO_0000305 document title http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that names a document http://purl.obolibrary.org/obo/IAO_0000306 table http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions http://purl.obolibrary.org/obo/IAO_0000307 table of abbreviations http://purl.obolibrary.org/obo/IAO_0000306 table A table where the constituent texts are abbreviations and their expansions http://purl.obolibrary.org/obo/IAO_0000308 figure http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. http://purl.obolibrary.org/obo/IAO_0000309 diagram http://purl.obolibrary.org/obo/IAO_0000308 figure A figure that expresses one or more propositions http://purl.obolibrary.org/obo/IAO_0000310 document http://purl.obolibrary.org/obo/IAO_0000030 information content entity A collection of information content entities intended to be understood together as a whole http://purl.obolibrary.org/obo/IAO_0000313 patent http://purl.obolibrary.org/obo/IAO_0000310 document A document that has been accepted by a patent authority http://purl.obolibrary.org/obo/IAO_0000314 document part http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity that is part of a document. http://purl.obolibrary.org/obo/IAO_0000321 author list http://purl.obolibrary.org/obo/IAO_0000314 document part A part of a document that enumerates the authors of the document http://purl.obolibrary.org/obo/IAO_0000322 institution list http://purl.obolibrary.org/obo/IAO_0000314 document part A part of a document that has parts that are institution identifications associated with the authors of the document http://purl.obolibrary.org/obo/IAO_0000327 table of contents http://purl.obolibrary.org/obo/IAO_0000306 table A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred). http://purl.obolibrary.org/obo/IAO_0000328 table of figures http://purl.obolibrary.org/obo/IAO_0000306 table A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred). http://purl.obolibrary.org/obo/IAO_0000329 running title http://purl.obolibrary.org/obo/IAO_0000305 document title A shorter version of a document title http://purl.obolibrary.org/obo/IAO_0000330 copyright section http://purl.obolibrary.org/obo/IAO_0000314 document part A document part that describes legal restrictions on making or distributing copies of the document http://purl.obolibrary.org/obo/IAO_0000400 cartesian spatial coordinate datum http://purl.obolibrary.org/obo/IAO_0000027 data item A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude http://purl.obolibrary.org/obo/IAO_0000401 one dimensional cartesian spatial coordinate datum http://purl.obolibrary.org/obo/IAO_0000400 cartesian spatial coordinate datum A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region http://purl.obolibrary.org/obo/IAO_0000402 two dimensional cartesian spatial coordinate datum http://purl.obolibrary.org/obo/IAO_0000400 cartesian spatial coordinate datum A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region http://purl.obolibrary.org/obo/IAO_0000403 three dimensional cartesian spatial coordinate datum http://purl.obolibrary.org/obo/IAO_0000400 cartesian spatial coordinate datum A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region http://purl.obolibrary.org/obo/IAO_0000408 length measurement datum http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum A scalar measurement datum that is the result of measurement of length quality http://purl.obolibrary.org/obo/IAO_0000409 denotator type http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part A denotator type indicates how a term should be interpreted from an ontological perspective. http://purl.obolibrary.org/obo/IAO_0000414 mass measurement datum http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum A scalar measurement datum that is the result of measurement of mass quality http://purl.obolibrary.org/obo/IAO_0000415 hypothesis textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that expresses an assertion that is intended to be tested. http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum A scalar measurement datum that is the result of measuring a temporal interval http://purl.obolibrary.org/obo/IAO_0000422 postal address http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that is used as directive to deliver something to a person, or organization http://purl.obolibrary.org/obo/IAO_0000442 author role http://purl.obolibrary.org/obo/BFO_0000023 role A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name. http://purl.obolibrary.org/obo/IAO_0000443 data item extraction from journal article http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing http://purl.obolibrary.org/obo/IAO_0000572 documenting http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process in which a document is created or added to by including the specified input in it. http://purl.obolibrary.org/obo/IAO_0000576 obsolete_establishing a CRID registry http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID. http://purl.obolibrary.org/obo/IAO_0000590 written name http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that denotes a particular in reality. http://purl.obolibrary.org/obo/IAO_0000591 software method http://purl.obolibrary.org/obo/IAO_0000010 software A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task. http://purl.obolibrary.org/obo/IAO_0000592 software module http://purl.obolibrary.org/obo/IAO_0000010 software A software module is software composed of a collection of software methods. http://purl.obolibrary.org/obo/IAO_0000593 software library http://purl.obolibrary.org/obo/IAO_0000010 software A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application. http://purl.obolibrary.org/obo/IAO_0000594 software application http://purl.obolibrary.org/obo/IAO_0000010 software A software application is software that can be directly executed by some processing unit. http://purl.obolibrary.org/obo/IAO_0000595 software script http://purl.obolibrary.org/obo/IAO_0000010 software A software script is software whose instructions can be executed using a software interpreter. http://purl.obolibrary.org/obo/IDO_0000586 infection http://purl.obolibrary.org/obo/BFO_0000040 material entity A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population. http://purl.obolibrary.org/obo/IDO_0000666 human pathogenicity disposition http://purl.obolibrary.org/obo/IDO_0000450 pathogenic disposition A disposition to initiate processes that result in a disorder in a human organism. http://purl.obolibrary.org/obo/OBI_0000006 role of being consumer safety officer http://purl.obolibrary.org/obo/OBI_0000273 role of regulator of consumables and medical devices the role of a human being that is realized by enforcing regulations to ensure consumer safety http://purl.obolibrary.org/obo/OBI_0000010 fluorescent reporter intensity http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter. http://purl.obolibrary.org/obo/OBI_0000011 planned process http://purl.obolibrary.org/obo/BFO_0000015 process A process that realizes a plan which is the concretization of a plan specification. http://purl.obolibrary.org/obo/OBI_0000015 biological feature identification objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature. http://purl.obolibrary.org/obo/OBI_0000016 regulation-assigned role http://purl.obolibrary.org/obo/OBI_0000017 regulatory role Regulation-assigned role is a regulatory role defined by legislation or governmental orders http://purl.obolibrary.org/obo/OBI_0000017 regulatory role http://purl.obolibrary.org/obo/BFO_0000023 role a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body. http://purl.obolibrary.org/obo/OBI_0000021 list-mode data file http://purl.obolibrary.org/obo/IAO_0000030 information content entity A list-mode data file is a binary digital entity where events are stored sequentially, parameter by parameter. http://purl.obolibrary.org/obo/OBI_0000029 centrifuge pellet role http://purl.obolibrary.org/obo/BFO_0000023 role pellet role is a role which inheres in a material entity and is realized by a material separation process using gravitational force generated by a centrifuge in which the material bearing the pellet role is the heavier or heaviest component of the output material.. http://purl.obolibrary.org/obo/OBI_0000034 supernatant role http://purl.obolibrary.org/obo/BFO_0000023 role supernatant role is a role which inheres in a material entity and is realized by a material separation process using gravitational force in which the material bearing the supernatant role is the liquid component of the output material. http://purl.obolibrary.org/obo/OBI_0000038 chromatography column http://purl.obolibrary.org/obo/OBI_0000932 material separation device Chromatography column in chemistry is a tube and contents (typically glass) used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms. http://purl.obolibrary.org/obo/OBI_0000041 pump valve switch http://purl.obolibrary.org/obo/OBI_0000968 device A pump valve switch is a cardinal part of a liquid chromatography instrument that controls the flow. http://purl.obolibrary.org/obo/OBI_0000043 xenotransplantation http://purl.obolibrary.org/obo/OBI_0000105 transplantation is the transplantation of living cells, tissues or \norgans from one species to another such as from pigs to humans http://purl.obolibrary.org/obo/OBI_0000044 physical document http://purl.obolibrary.org/obo/OBI_0000047 processed material A physical document is an object serving as a record of information by means of symbolic marks. http://purl.obolibrary.org/obo/OBI_0000045 waiting http://purl.obolibrary.org/obo/OBI_0600009 exposure of material to environment not actively doing anything to a material for a duration of time. http://purl.obolibrary.org/obo/OBI_0000047 processed material http://purl.obolibrary.org/obo/BFO_0000040 material entity Is a material entity that is created or changed during material processing. http://purl.obolibrary.org/obo/OBI_0000049 mass spectrometer http://purl.obolibrary.org/obo/OBI_0000832 measurement device A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum http://purl.obolibrary.org/obo/OBI_0000050 obsolete_platform http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class A platform is an object_aggregate that is the set of instruments and software needed to perform a process. definition_source: OBI. http://purl.obolibrary.org/obo/OBI_0000051 liquid chromatography mass spectrometry platform http://purl.obolibrary.org/obo/OBI_0000932 material separation device A liquid chromatography mass spectrometry platform is a platform that is the collection of instrument, software and reagents needed to perform a liquid chromatography mass spectrometry protocol. definition_source: OBI. http://purl.obolibrary.org/obo/OBI_0000052 microarray platform http://purl.obolibrary.org/obo/OBI_0001034 environmental control device A microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI. http://purl.obolibrary.org/obo/OBI_0000054 ratio of collected to emitted light http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement datum measuring the amount of light collected s compared to the total amount of emitted light in the detector component of a flow cytometer instrument. The datum has a qualitative role http://purl.obolibrary.org/obo/OBI_0000055 software optimization objective http://purl.obolibrary.org/obo/OBI_0000242 software testing objective Software_optimization is a software_testing_objective role describing a study designed to identify the best software or parameters of the software. http://purl.obolibrary.org/obo/OBI_0000057 allotransplantation http://purl.obolibrary.org/obo/OBI_0000105 transplantation is the transplantation of organs between members of the same species. http://purl.obolibrary.org/obo/OBI_0000059 gamma counter http://purl.obolibrary.org/obo/OBI_0000832 measurement device A processed material which measures gamma radiation http://purl.obolibrary.org/obo/OBI_0000065 polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity triton X100 is a chemical entity which belongs to the group of The pluronics which are triblock copolymers of ethylene oxide and propylene oxide. Triton x-100 is_used_as detergent due to its non-ionic surfactant properties http://purl.obolibrary.org/obo/OBI_0000066 investigation http://purl.obolibrary.org/obo/OBI_0000011 planned process a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). http://purl.obolibrary.org/obo/OBI_0000067 evaluant role http://purl.obolibrary.org/obo/BFO_0000023 role a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role http://purl.obolibrary.org/obo/OBI_0000071 quantitative confidence value http://purl.obolibrary.org/obo/IAO_0000027 data item A data item which is used to indicate the degree of uncertainty about a measurement. http://purl.obolibrary.org/obo/OBI_0000075 diagnosis textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity diagnosis is an assessment of a disease or injury, its likely prognosis and treatment. http://purl.obolibrary.org/obo/OBI_0000076 unplanned occurrence effecting an investigation http://purl.obolibrary.org/obo/BFO_0000015 process a process which is external in origin to the investigation that has an impact on the outcome. http://purl.obolibrary.org/obo/OBI_0000078 eMedical record http://purl.obolibrary.org/obo/IAO_0000030 information content entity An eMedical record is a digital document derived from a computer system used primarily for patient care in a clinical setting. Not required to be compliant with requirements of 21 CFR Part 11. http://purl.obolibrary.org/obo/OBI_0000079 culture medium http://purl.obolibrary.org/obo/OBI_0000047 processed material a processed material that provides the needed nourishment for microorganisms or cells grown in vitro. http://purl.obolibrary.org/obo/OBI_0000083 electronic case report tabulation http://purl.obolibrary.org/obo/IAO_0000030 information content entity An electronic case report tabulation is a digital document containing tabular data about multiple trial participants which is part of a clinical regulatory submission. An eCRT has the property that it can be audited and compliant with requirements of 21 CFR Part 11 and has format suited to review by regulators. http://purl.obolibrary.org/obo/OBI_0000084 polystyrene tube http://purl.obolibrary.org/obo/OBI_0000836 test tube A polystyrene tube is a test tube made of polystyrene http://purl.obolibrary.org/obo/OBI_0000091 detector reagent role http://purl.obolibrary.org/obo/BFO_0000023 role a role which inheres in a molecular entity and is realized by the process of recording or registering a stimulus. http://purl.obolibrary.org/obo/OBI_0000096 protocol testing objective http://purl.obolibrary.org/obo/OBI_0000208 methodology testing objective Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols. http://purl.obolibrary.org/obo/OBI_0000097 participant under investigation role http://purl.obolibrary.org/obo/BFO_0000023 role A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected. http://purl.obolibrary.org/obo/OBI_0000100 obsolete_role of being first subject treated http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class First subject treated role is a study subject role borne by the subject realized in the application of the process specified in intervention study design with no previous study subject realizing the role prior in the study http://purl.obolibrary.org/obo/OBI_0000101 measured expression level http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement datum that is the outcome of the quantification of an assay for the activity of a gene, or the number of RNA transcripts. http://purl.obolibrary.org/obo/OBI_0000105 transplantation http://purl.obolibrary.org/obo/OBI_0000094 material processing a protocol application to replace an organ or tissue of an organism http://purl.obolibrary.org/obo/OBI_0000109 biological vector role http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class a biological vector role is a material to be added role that is realized by the process of transmitting material to the organism that is the target of the transmission. http://purl.obolibrary.org/obo/OBI_0000112 specimen role http://purl.obolibrary.org/obo/BFO_0000023 role a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation http://purl.obolibrary.org/obo/OBI_0000113 sequence feature identification objective http://purl.obolibrary.org/obo/OBI_0000015 biological feature identification objective Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide. http://purl.obolibrary.org/obo/OBI_0000115 intervention design http://purl.obolibrary.org/obo/OBI_0500000 study design An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays. http://purl.obolibrary.org/obo/OBI_0000117 Bernoulli trial http://purl.obolibrary.org/obo/OBI_0000070 assay An assay where the output data is a datum with one of two values denoting success and failure. http://purl.obolibrary.org/obo/OBI_0000118 gene list http://purl.obolibrary.org/obo/IAO_0000100 data set A data set of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis. http://purl.obolibrary.org/obo/OBI_0000119 number of particles in subset http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement datum measuring the number of subjects in a defined subset in a flow cytometer instrument. The datum has a qualitative role http://purl.obolibrary.org/obo/OBI_0000125 number of lost events electronic http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement datum measuring the number of analysis events lost due to errors in data acquisition electronic coincidence in a flow cytometer instrument. The datum has a qualitative role. http://purl.obolibrary.org/obo/OBI_0000129 calibration substance role http://purl.obolibrary.org/obo/OBI_0000025 reference substance role A reference substance role that is realized when characteristics or responses elicited by the bearer are used to ensure an instrument is within protocol specification of accuracy or performance http://purl.obolibrary.org/obo/OBI_0000131 molecular feature identification objective http://purl.obolibrary.org/obo/OBI_0000015 biological feature identification objective Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications. http://purl.obolibrary.org/obo/OBI_0000134 hardware testing objective http://purl.obolibrary.org/obo/OBI_0000208 methodology testing objective Hardware_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different hardware, e.g. scanner. http://purl.obolibrary.org/obo/OBI_0000136 incubator http://purl.obolibrary.org/obo/OBI_0001034 environmental control device A device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled http://purl.obolibrary.org/obo/OBI_0000146 supernatant collection system harvesting frame http://purl.obolibrary.org/obo/OBI_0000967 container A device that is designed for collecting 90% of the supernatant in a microplate well and separating the living cell with no stress, eliminating centrifugation and other similar techniques. It can be used in a variety of release assays with different radioactive isotopes, such as Cr51 or I125. http://purl.obolibrary.org/obo/OBI_0000151 filter paper http://purl.obolibrary.org/obo/OBI_0000932 material separation device A device manufacture with the intent to provide a porous unsized paper used for filtering. http://purl.obolibrary.org/obo/OBI_0000153 cell co-culturing http://purl.obolibrary.org/obo/OBI_0000094 material processing A material combination in which cell cultures of two or more different types are are combined and allowed to culture as one. http://purl.obolibrary.org/obo/OBI_0000158 eSource document http://purl.obolibrary.org/obo/IAO_0000030 information content entity an eSource document is a digital document consisting of a logical collection of Source data and other eSource documents that can be presented in an ordered way and capture the time of completion, change, and any signatures http://purl.obolibrary.org/obo/OBI_0000164 clonal cDNA library http://purl.obolibrary.org/obo/OBI_0000731 recombinant vector Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process. ALT DEF (PRS):: a cDNA library is a collection of host cells, typically E.Coli cells but not exclusively. modified by transfer of plasmid DNA molecule used as vector containing a fragment or totality of cDNA molecule (the insert) . cDNA library may have an array of role and applications. http://purl.obolibrary.org/obo/OBI_0000167 electronic case report form http://purl.obolibrary.org/obo/IAO_0000030 information content entity An electronic case report form is a digital document used to record all of the protocol required information to be reported for each trial subject. An eCRF has the property that it can be audited and compliant with requirements of 21 CFR Part 11. http://purl.obolibrary.org/obo/OBI_0000171 autotransplantation http://purl.obolibrary.org/obo/OBI_0000105 transplantation is the transplantation of tissue from one part of \nthe body to another in the same individual. ) http://purl.obolibrary.org/obo/OBI_0000172 parameter threshold http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement datum measuring the minimal signal that must be detected to generate an electrical event, as compared to the maximal detected signal in a flow cytometer instrument. The datum has a qualitative role http://purl.obolibrary.org/obo/OBI_0000175 p-value http://purl.obolibrary.org/obo/OBI_0000071 quantitative confidence value A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone. http://purl.obolibrary.org/obo/OBI_0000181 population http://purl.obolibrary.org/obo/BFO_0000040 material entity a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area http://purl.obolibrary.org/obo/OBI_0000182 nuclear magnetic resonance 3D structure determination assay http://purl.obolibrary.org/obo/OBI_0600045 3D structure determination assay A 3D structure determination assay that uses magnetic properties of atomic nuclei to determine the 3D structure and dynamics of molecules in the input sample. http://purl.obolibrary.org/obo/OBI_0000185 imaging assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that produces a picture of an entity. http://purl.obolibrary.org/obo/OBI_0000186 protocol optimization objective http://purl.obolibrary.org/obo/OBI_0000096 protocol testing objective Protocol_optimization is a protocol_testing_objective role describing a study designed to identify the best protocol. This may be carried out by comparing different protocols or by modifying the parameters used within a single protocol. http://purl.obolibrary.org/obo/OBI_0000201 radioactivity detection http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that measures the amount of radiation in the radioactive spectrum (alpha, beta or gamma rays) emitted from an input material. http://purl.obolibrary.org/obo/OBI_0000205 obsolete_dropout role http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class Dropout is a study subject role borne by an entity realized by a process of leaving the study earlier than the protocol specified and where the bearer of the dropout role had been borne study subject role prior to bearing dropout role. http://purl.obolibrary.org/obo/OBI_0000208 methodology testing objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification Methodology_testing_objective is an objective role carried out by a proposition defining the aim of the study is to examine the effect of using different methodologies. http://purl.obolibrary.org/obo/OBI_0000210 analytical cytology data file http://purl.obolibrary.org/obo/IAO_0000030 information content entity A digital entity intended to capture data in analytical cytology domain. http://purl.obolibrary.org/obo/OBI_0000213 fluorescence compensation matrix http://purl.obolibrary.org/obo/IAO_0000030 information content entity A fluorescence compensation matrix is a square matrix which is used as the left multiplier of the vector of fluorescence values while performing digital fluorescence compensation. Also, fluorescence compensation matrix is the inverse of the fluorescence spillover matrix. http://purl.obolibrary.org/obo/OBI_0000218 investigation results report http://purl.obolibrary.org/obo/IAO_0000088 report An investigation report is a report on the results of an investigation. http://purl.obolibrary.org/obo/OBI_0000219 cellular feature identification objective http://purl.obolibrary.org/obo/OBI_0000015 biological feature identification objective Cellular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the cellular level, e.g. stage of cell cycle, stage of differentiation. http://purl.obolibrary.org/obo/OBI_0000223 obsolete_blinded medication role http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class Is a role which inheres in a material entity which is manufactured to be similar in appearance to a test material entity in e.g. a clinical trial to prevent participants from detecting which is the active and inactive substance http://purl.obolibrary.org/obo/OBI_0000227 data encoding http://purl.obolibrary.org/obo/IAO_0000572 documenting a documenting process to encode an information entity into a digital document http://purl.obolibrary.org/obo/OBI_0000231 enzymatic cleavage http://purl.obolibrary.org/obo/OBI_0000094 material processing a material processing that digests the fraction of input material that is susceptible to that enzyme http://purl.obolibrary.org/obo/OBI_0000232 hardware optimization objective http://purl.obolibrary.org/obo/OBI_0000134 hardware testing objective Hardware_optimization is a hardware_testing_objective describing a study designed to identify the best hardware. http://purl.obolibrary.org/obo/OBI_0000233 obsolete_defined_material http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class Place holder class, Utility class to gather the defined classes http://purl.obolibrary.org/obo/OBI_0000235 standard error http://purl.obolibrary.org/obo/OBI_0000071 quantitative confidence value A quantitative confidence value which is the standard deviations of the sample in a frequency distribution, obtained by dividing the standard deviation by the total number of cases in the frequency distribution. http://purl.obolibrary.org/obo/OBI_0000237 antigen role http://purl.obolibrary.org/obo/BFO_0000023 role Antigen is a role played by material which when introduced into an immune-competent organism causes an immune response http://purl.obolibrary.org/obo/OBI_0000242 software testing objective http://purl.obolibrary.org/obo/OBI_0000208 methodology testing objective Software_testing_objective is a hardware_optimization role describing a study designed to examine the effects of using different software or software parameters, e.g. data processing software. http://purl.obolibrary.org/obo/OBI_0000245 organization http://purl.obolibrary.org/obo/BFO_0000040 material entity An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. http://purl.obolibrary.org/obo/OBI_0000251 cluster http://purl.obolibrary.org/obo/IAO_0000100 data set A data set which is a subset of data that are a similar to each other in some way. http://purl.obolibrary.org/obo/OBI_0000252 cohort role http://purl.obolibrary.org/obo/OBI_0000198 biological replicate role a cohort role is a biological replicate role played by a group of study participants who share a common characteristic of interest to the study. http://purl.obolibrary.org/obo/OBI_0000253 artificially induced nucleic acid hybridization http://purl.obolibrary.org/obo/OBI_0000094 material processing Is a material transformation in which strands of nucleic acids that are (somewhat) complementary form a double-stranded molecule. Has input at least two single stranded molecules of nucleic acid molecules. http://purl.obolibrary.org/obo/OBI_0000257 DNA extraction http://purl.obolibrary.org/obo/OBI_0666667 nucleic acid extraction A DNA extraction is a nucleic acid extraction where the desired output material is DNA. http://purl.obolibrary.org/obo/OBI_0000260 plan http://purl.obolibrary.org/obo/BFO_0000017 realizable entity A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. http://purl.obolibrary.org/obo/OBI_0000268 organism feature identification objective http://purl.obolibrary.org/obo/OBI_0000015 biological feature identification objective Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle. http://purl.obolibrary.org/obo/OBI_0000269 number of lost events computer http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement datum recording the number of measurement events lost due to overloading of the analysis chip in a flow cytometer instrument. The datum has a qualitative role http://purl.obolibrary.org/obo/OBI_0000272 protocol http://purl.obolibrary.org/obo/IAO_0000104 plan specification A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. http://purl.obolibrary.org/obo/OBI_0000274 adding a material entity into a target http://purl.obolibrary.org/obo/OBI_0000652 material combination is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'. http://purl.obolibrary.org/obo/OBI_0000275 analyte role http://purl.obolibrary.org/obo/OBI_0002444 measurand role A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role. http://purl.obolibrary.org/obo/OBI_0000278 disease stage http://purl.obolibrary.org/obo/GO_0008150 biological_process a part of an occurrence of a disease process which is associated with position in the normal progression of the disease http://purl.obolibrary.org/obo/OBI_0000281 intraperitoneal injection http://purl.obolibrary.org/obo/OBI_0000429 intraperitoneal administration is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe http://purl.obolibrary.org/obo/OBI_0000288 protein-protein interaction detection assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that determines interactions between proteins, such as protein-protein binding. http://purl.obolibrary.org/obo/OBI_0000296 obsolete_enrollment http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class enrollment is a process of identifying a set of objects for further use in an investigation based on a set of criteria or rules http://purl.obolibrary.org/obo/OBI_0000310 adverse event trigger http://purl.obolibrary.org/obo/IAO_0000001 conditional specification revisit? http://purl.obolibrary.org/obo/OBI_0000319 material to be added role http://purl.obolibrary.org/obo/BFO_0000023 role material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process http://purl.obolibrary.org/obo/OBI_0000323 obsolete_peritoneum http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class is the serous membrane that forms the lining of the abdominal cavity http://purl.obolibrary.org/obo/OBI_0000338 drawing a conclusion based on data http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion http://purl.obolibrary.org/obo/OBI_0000339 planning http://purl.obolibrary.org/obo/BFO_0000015 process a process of creating or modifying a plan specification http://purl.obolibrary.org/obo/OBI_0000341 histological sample preparation http://purl.obolibrary.org/obo/OBI_0000659 specimen collection process histological sample preparation is the preparation of an input tissue via slicing and labeling to make tissue microstructure of interest visible in a future histology assay http://purl.obolibrary.org/obo/OBI_0000343 inductive reasoning http://purl.obolibrary.org/obo/OBI_0000338 drawing a conclusion based on data a interpreting data that is used to ascribe properties or relations to types based on an observation instance (i.e., on a number of observations or experiences); or to formulate laws based on limited observations of recurring phenomenal patterns. http://purl.obolibrary.org/obo/OBI_0000345 mass analyzer http://purl.obolibrary.org/obo/OBI_0000932 material separation device A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields in vacuum where the two laws of Lorentz force law and Newton's second law of motion apply. http://purl.obolibrary.org/obo/OBI_0000355 hypothesis driven investigation http://purl.obolibrary.org/obo/OBI_0000066 investigation is an investigation with the goal to test one or more hypothesis http://purl.obolibrary.org/obo/OBI_0000356 hypothesis generating investigation http://purl.obolibrary.org/obo/OBI_0000066 investigation is an investigation in which data is generated and analyzed with the purpose of generating new hypothesis http://purl.obolibrary.org/obo/OBI_0000361 ion source http://purl.obolibrary.org/obo/OBI_0000968 device An ion source is a device that is part of a mass spectrometer that ionizes the material under analysis. The ions are then transported by magnetic or electric fields to the mass analyzer. Techniques for ionization have been key to determining what types of samples can be analyzed by mass spectrometry. Electron ionization and chemical ionization are used for gases and vapors. In chemical ionization sources, the material is ionized by chemical ion-molecule reactions during collisions in the source. Two techniques often used with liquid and solid biological samples include electrospray ionization (due to John Fenn PMID 2675315.) and matrix-assisted laser desorption/ionization (MALDI, due to M. Karas and F. Hillenkamp (Measuring Mass: From Positive Rays to Proteins by Michael A. Grayson (Editor) (ISBN 0-941901-31-9))). http://purl.obolibrary.org/obo/OBI_0000364 ion detector http://purl.obolibrary.org/obo/OBI_0000832 measurement device An ion detector is a device that measures and records the charge induced or current produced when an ion passes by or hits a surface. Example: In a scanning instrument the signal produced in the detector during the course of the scan versus where the instrument is in the scan (at what m/Q) will produce a mass spectrum, a record of ions as a function of m/Q. http://purl.obolibrary.org/obo/OBI_0000367 light emission function http://purl.obolibrary.org/obo/OBI_0000374 excitation function A light emission function is an excitation function to excite a material to a specific excitation state that it emits light. http://purl.obolibrary.org/obo/OBI_0000368 record function http://purl.obolibrary.org/obo/BFO_0000034 function A record function is a function that registers or collects information in a particular format on a particular recording medium. For example on paper or a digital representation http://purl.obolibrary.org/obo/OBI_0000369 magnify function http://purl.obolibrary.org/obo/BFO_0000034 function A magnify function is a function to increase the size of a transmitted object image through the precise arrangement of energy diffraction elements along an imaging path. http://purl.obolibrary.org/obo/OBI_0000370 contain function http://purl.obolibrary.org/obo/BFO_0000034 function A contain function is a function to constrain a material entities location in space http://purl.obolibrary.org/obo/OBI_0000371 heat function http://purl.obolibrary.org/obo/BFO_0000034 function A heat function is a function that increases the internal kinetic energy of a material http://purl.obolibrary.org/obo/OBI_0000372 material separation function http://purl.obolibrary.org/obo/BFO_0000034 function A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality. http://purl.obolibrary.org/obo/OBI_0000373 ionize process http://purl.obolibrary.org/obo/OBI_0000094 material processing a physical process of converting an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. This excludes chemical processes of dissociation. http://purl.obolibrary.org/obo/OBI_0000374 excitation function http://purl.obolibrary.org/obo/BFO_0000034 function A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons. http://purl.obolibrary.org/obo/OBI_0000375 freeze function http://purl.obolibrary.org/obo/BFO_0000034 function A freeze function is a function to decrease the internal kinetic energy of a material below the freezing point of that type of material. http://purl.obolibrary.org/obo/OBI_0000376 synthesizing function http://purl.obolibrary.org/obo/BFO_0000034 function A synthesizing function is a function to assemble new output materials from distinct input materials. The output materials typically consist of chemically distinct monomeric objects or object aggregate polymers. http://purl.obolibrary.org/obo/OBI_0000377 perturb function http://purl.obolibrary.org/obo/BFO_0000034 function A perturb function is a function that disrupts the normal function of a system induced through either internal or external means. External means of perturbation include: (1) displacement fields in the physical sense - e.g., temperature change, osmotic shock, pressure change; (2) application of small molecules such as drugs or toxins to perturb the function of specific pathways or application of surfactants to perturb the normal function of plasma membrane. Internal means of perturbation include: (1) manipulation of gene function via gene knockout or transcript knockdown via RNAi; (2) directed genetic mutation leading to minimal aa alterations that interfere with peptide function. http://purl.obolibrary.org/obo/OBI_0000378 filter function http://purl.obolibrary.org/obo/OBI_0000372 material separation function A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through http://purl.obolibrary.org/obo/OBI_0000379 mechanical function http://purl.obolibrary.org/obo/BFO_0000034 function A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force). http://purl.obolibrary.org/obo/OBI_0000380 gas filter function http://purl.obolibrary.org/obo/OBI_0000378 filter function A gas filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a gas-solid mixture http://purl.obolibrary.org/obo/OBI_0000381 liquid filter function http://purl.obolibrary.org/obo/OBI_0000378 filter function A liquid filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a liquid-solid mixture http://purl.obolibrary.org/obo/OBI_0000383 transfer function http://purl.obolibrary.org/obo/BFO_0000034 function A transfer function is a function to displace a material from one location to another. http://purl.obolibrary.org/obo/OBI_0000385 ionization function http://purl.obolibrary.org/obo/BFO_0000034 function An ionization function is a function to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. http://purl.obolibrary.org/obo/OBI_0000387 cool function http://purl.obolibrary.org/obo/BFO_0000034 function A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material. http://purl.obolibrary.org/obo/OBI_0000388 connection function http://purl.obolibrary.org/obo/BFO_0000034 function A connection function is a function to couple two or more flow channels so that material or signals can be transported from one set of channels to another. http://purl.obolibrary.org/obo/OBI_0000390 thermostatic circulator http://purl.obolibrary.org/obo/OBI_0002089 physical store A thermostatic circulator is a device which cools or heats a circulating liquid. It has the function to contain control the contained environment and transfer energy from or to the circulating liquid http://purl.obolibrary.org/obo/OBI_0000391 energy supply function http://purl.obolibrary.org/obo/BFO_0000034 function An energy supply function is a function to supply or transfer energy from an energy source to a consumer of the energy http://purl.obolibrary.org/obo/OBI_0000394 blot module http://purl.obolibrary.org/obo/OBI_0000968 device A blot module is a device which has the function to conatin and facilitate the material transfer process blotting to be realised http://purl.obolibrary.org/obo/OBI_0000395 signal amplification function http://purl.obolibrary.org/obo/OBI_0000393 signal conversion function A signal amplification function is a signal conversion function to inject energy into an input signal so as to produce an output signal with increased differential magnitude while also seeking to minimize increases in the signal to noise ratio. For example, to produce a 0.1 KW output signal from a 1 mW RMS input signal. http://purl.obolibrary.org/obo/OBI_0000397 image acquisition function http://purl.obolibrary.org/obo/OBI_0000453 measure function An image acquisition function is a function to acquire an image of a material http://purl.obolibrary.org/obo/OBI_0000399 solid support function http://purl.obolibrary.org/obo/BFO_0000034 function A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement http://purl.obolibrary.org/obo/OBI_0000400 display function http://purl.obolibrary.org/obo/OBI_0000392 information processor function A display function is a function to present information by translating that information through some lookup process into visual form. http://purl.obolibrary.org/obo/OBI_0000401 environment control function http://purl.obolibrary.org/obo/BFO_0000034 function An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature. http://purl.obolibrary.org/obo/OBI_0000403 sort function http://purl.obolibrary.org/obo/OBI_0000372 material separation function A sort function is a function to distinguish material components based on some associated physical quality or entity and to partition the separate components into distinct fractions according to a defined order. http://purl.obolibrary.org/obo/OBI_0000404 gel dryer http://purl.obolibrary.org/obo/OBI_0002089 physical store A gel dryer is a device which has the function to contain and to control the contained environment to facilitate the drying of gels http://purl.obolibrary.org/obo/OBI_0000405 primer role http://purl.obolibrary.org/obo/OBI_0000857 complementary nucleotide probe role a complementary nucleotide probe role which inheres in nucleic acid molecular entity and is realized by the use of the entity bearing the role to initiate chain elongation. http://purl.obolibrary.org/obo/OBI_0000406 PCR product http://purl.obolibrary.org/obo/CHEBI_4705 double-stranded DNA is double stranded DNA that is the specified output of a polymerase chain reaction http://purl.obolibrary.org/obo/OBI_0000407 viral RNA extraction http://purl.obolibrary.org/obo/OBI_0666666 RNA extraction The extraction of RNA from an input material that specifically isolates viral RNA http://purl.obolibrary.org/obo/OBI_0000409 nucleic acid template role http://purl.obolibrary.org/obo/OBI_0000025 reference substance role a reference substance role which inheres in nucleic acid material entity and is realized in the process of using the nucleic acid bearing the template role as a reference during synthesis of a reverse copy. http://purl.obolibrary.org/obo/OBI_0000410 recombinant plasmid http://purl.obolibrary.org/obo/OBI_0000731 recombinant vector a plasmid in which extraneous DNA has been inserted. http://purl.obolibrary.org/obo/OBI_0000411 cloning vector role http://purl.obolibrary.org/obo/OBI_0000319 material to be added role A material to be added role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning. http://purl.obolibrary.org/obo/OBI_0000413 cell cycle synchronization http://purl.obolibrary.org/obo/OBI_0000094 material processing a process with the objective to obtain a cell culture in which all cells are in the same stage of the cell cycle http://purl.obolibrary.org/obo/OBI_0000416 cloning insert role http://purl.obolibrary.org/obo/BFO_0000023 role cloning insert role is a role which inheres in DNA or RNA and is realized by the process of being inserted into a cloning vector in a cloning process. http://purl.obolibrary.org/obo/OBI_0000418 measuring glucose concentration in blood serum assay http://purl.obolibrary.org/obo/OBI_0000443 analyte assay An assay that determines the concentration of glucose molecules in a blood serum sample http://purl.obolibrary.org/obo/OBI_0000419 reverse transcriptase http://purl.obolibrary.org/obo/OBI_0000427 enzyme enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity) http://purl.obolibrary.org/obo/OBI_0000420 obsolete_trypsinized material http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class A material entity that has undergone a process of digestion with trypsin http://purl.obolibrary.org/obo/OBI_0000422 syringe http://purl.obolibrary.org/obo/OBI_0000968 device A processed material which is used to introduce or draw fluids from a material entity. A syringe is made of a piston and body. the movement of the piston in the body determines the amount/volume of fluid to inject or draw http://purl.obolibrary.org/obo/OBI_0000425 averaging objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation. http://purl.obolibrary.org/obo/OBI_0000426 injection http://purl.obolibrary.org/obo/OBI_0000274 adding a material entity into a target injection is process which aims at introducing a compound or a mixture into a material entity (either biological entity or instrument) by relying on devices such as syringe or injector connection, attached or forced into a vascular system (veins of an organism or tubes of a machine) or in a tissue. http://purl.obolibrary.org/obo/OBI_0000427 enzyme http://purl.obolibrary.org/obo/BFO_0000040 material entity (protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity) http://purl.obolibrary.org/obo/OBI_0000429 intraperitoneal administration http://purl.obolibrary.org/obo/OBI_0600007 administering substance in vivo The administration of a substance into the peritoneum of an organism http://purl.obolibrary.org/obo/OBI_0000430 plasmid http://purl.obolibrary.org/obo/CHEBI_4705 double-stranded DNA plasmid = DNA and has_quality circular and has_function (is_realized_as some gene expression) GO:0010467 http://purl.obolibrary.org/obo/OBI_0000431 injection into organ section http://purl.obolibrary.org/obo/OBI_0000426 injection A process in which an input substance is injected into a organ section. http://purl.obolibrary.org/obo/OBI_0000432 polyacrylamide gel http://purl.obolibrary.org/obo/OBI_0000047 processed material a material entity resulting from the polymerization of acrylamide with TEMED in some buffer solution http://purl.obolibrary.org/obo/OBI_0000433 DNA sequence feature detection assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay with the objective to determine a sequence feature of DNA http://purl.obolibrary.org/obo/OBI_0000434 adding material objective http://purl.obolibrary.org/obo/OBI_0000686 material combination objective is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity http://purl.obolibrary.org/obo/OBI_0000436 needle http://purl.obolibrary.org/obo/OBI_0000968 device A needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture. http://purl.obolibrary.org/obo/OBI_0000437 analyte measurement objective http://purl.obolibrary.org/obo/OBI_0000441 assay objective an assay objective to determine the presence or concentration of an analyte in the evaluant http://purl.obolibrary.org/obo/OBI_0000438 DNA sequence variation detection assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that measures changes (expansion, amplification, deletion, mutation) in the sequence of a DNA molecule. http://purl.obolibrary.org/obo/OBI_0000439 agarose gel http://purl.obolibrary.org/obo/OBI_0000047 processed material a material entity resulting from the polymerization of agarose after heating agarose suspended in some buffer solution http://purl.obolibrary.org/obo/OBI_0000441 assay objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role) http://purl.obolibrary.org/obo/OBI_0000442 obsolete_heart http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class The heart is a muscular organ found in all vertebrates that is responsible for pumping blood throughout the blood vessels by repeated, rhythmic contractions http://purl.obolibrary.org/obo/OBI_0000443 analyte assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. http://purl.obolibrary.org/obo/OBI_0000444 target of material addition role http://purl.obolibrary.org/obo/BFO_0000023 role target of material addition role is a role realized by an entity into which a material is added in a material addition process http://purl.obolibrary.org/obo/OBI_0000445 mass measurement assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that determines the mass of an evaluant http://purl.obolibrary.org/obo/OBI_0000446 obsolete_identification http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class a process by which the identity (what a thing is) of a material entity is established within a certain confidence interval http://purl.obolibrary.org/obo/OBI_0000447 intra cellular electrophysiology recording assay http://purl.obolibrary.org/obo/OBI_0000070 assay An electrophysiology recording assay where the recording location of the electrode is intracellular http://purl.obolibrary.org/obo/OBI_0000448 packed column http://purl.obolibrary.org/obo/OBI_0000038 chromatography column A packed column is a chromatography column where the particles of the solid stationary phase or the support coated with a liquid stationary phase may fill the whole inside volume of the tube. http://purl.obolibrary.org/obo/OBI_0000449 obsolete_defined_output http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class This is only a placeholder for defined classes, as are its siblings _defined_material and _defined protocol application. Its children should be defined classes constructed as output of a process. http://purl.obolibrary.org/obo/OBI_0000450 regulatory agency http://purl.obolibrary.org/obo/OBI_0000245 organization A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government. http://purl.obolibrary.org/obo/OBI_0000451 normalized data set http://purl.obolibrary.org/obo/IAO_0000100 data set A data set that is produced as the output of a normalization data transformation. http://purl.obolibrary.org/obo/OBI_0000453 measure function http://purl.obolibrary.org/obo/BFO_0000034 function Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference. http://purl.obolibrary.org/obo/OBI_0000454 extracellular electrophysiology recording assay http://purl.obolibrary.org/obo/OBI_0000070 assay An electrophysiology recording assay where the recording location of the electrode is extracellular http://purl.obolibrary.org/obo/OBI_0000455 consume data function http://purl.obolibrary.org/obo/BFO_0000034 function Process data function is a function that is borne by in a material entity by virtue of its structure. When realized the material entity consumes data. http://purl.obolibrary.org/obo/OBI_0000457 manufacturing http://purl.obolibrary.org/obo/OBI_0000094 material processing Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process http://purl.obolibrary.org/obo/OBI_0000458 manufacturing objective http://purl.obolibrary.org/obo/OBI_0000456 material transformation objective is the objective to manufacture a material of a certain function (device) http://purl.obolibrary.org/obo/OBI_0000463 column chromatography detector http://purl.obolibrary.org/obo/OBI_0000832 measurement device There is a wide range of detectors available for both GC and LC each having their own particular areas of application. In general the more catholic the response, the less sensitive the detector and the most sensitive detectors are those that have a specific response. The performance of all detectors should be properly specified so that the user can determine which is most suitable for a specific application. Such specifications are also essential to compare the performance of different detectors supplied by alternative instrument manufactures. Detector specifications should be presented in a standard form and in standard units, so that detectors can be compared that function on widely different principles. http://purl.obolibrary.org/obo/OBI_0000464 Bruker autosampler http://purl.obolibrary.org/obo/OBI_0000555 autosampler A Bruker autosampler is an autosampler made by Bruker. http://purl.obolibrary.org/obo/OBI_0000465 organic acid column http://purl.obolibrary.org/obo/OBI_0000038 chromatography column An organic acid column is a chromatography column which enables (reversed-phase) separation of hydrophilic aliphatic and aromatic organic acids with UV detection. Organic acid columns allow retention of polar and apolar organic acids and are hydrolysis resistant. http://purl.obolibrary.org/obo/OBI_0000467 Bruker US 2 NMR magnet http://purl.obolibrary.org/obo/OBI_0000597 Bruker NMR magnet An actively-shielded superconducting magnet from Bruker that combines Bruker BioSpin's advanced, proprietary UltraShield active shielding and UltraStabilized sub-cooling technologies. This shielded and stabilized (US2) magnet system delivers high sensitivity and spectral dispersion. http://purl.obolibrary.org/obo/OBI_0000468 protein column http://purl.obolibrary.org/obo/OBI_0000038 chromatography column A protein column is a chromatography column used for the separation of complex protein mixtures. Protein columns enable sample desalting, followed by chromatographic separation or fractionation of complex protein samples, e.g. immunodepleted serum or plasma proteins. http://purl.obolibrary.org/obo/OBI_0000469 solvent mixer http://purl.obolibrary.org/obo/OBI_0000485 chromatography instrument A liquid chromatography device that mixes different solvents, e.g. under high pressure and in differrent volumes ranging from 5 ml to 5 L capacity. Powerful magnetic mixers provide vigorous agitation required for high pressure reaction chemistry. http://purl.obolibrary.org/obo/OBI_0000470 mass spectrometry assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that identifies the amount and type of material entities present in a sample by fragmenting the sample and measuring the mass-to-charge ratio of the resulting particles. http://purl.obolibrary.org/obo/OBI_0000471 study design execution http://purl.obolibrary.org/obo/OBI_0000011 planned process a planned process that carries out a study design http://purl.obolibrary.org/obo/OBI_0000473 Bruker NMR Case sample changer http://purl.obolibrary.org/obo/OBI_0000464 Bruker autosampler The NMR Case is an economical NMR sample changer for laboratories with modest automation needs. It expands the maximum number of samples your spectrometer can process during unattended operation to 24. The NMR Case consists of multiple components. The NMR Case exchange module installed atop your cryostat. The two front legs are adjustable, making the NMR Case compatible with many different cryostats. http://purl.obolibrary.org/obo/OBI_0000474 nano pump system http://purl.obolibrary.org/obo/OBI_0000589 chromatography pump system A pump system optimized for nano flow chromatography. http://purl.obolibrary.org/obo/OBI_0000475 Bruker AutoClean system http://purl.obolibrary.org/obo/OBI_0000498 NMR tube washing system NMR tubes are often used once and discarded, creating needless waste. With the Bruker BioSpin Autoclean system you can now recycle 5mm, 3mm, or 5mm/3mm step-down (Wilmad 520-1B) NMR tubes. AutoClean NMR Tube Washing System is a simple way to recoup the substantial investment your organization makes in quality NMR tubes, and cut back on needless waste material. http://purl.obolibrary.org/obo/OBI_0000476 manual injection system http://purl.obolibrary.org/obo/OBI_0000504 sample injection system The traditional hardware system that allows a human to inject a sample into an inlet by hand, using a syringe. http://purl.obolibrary.org/obo/OBI_0000477 Varian GEMINI spectrometer http://purl.obolibrary.org/obo/OBI_0000611 Varian NMR instrument An older Varian Broadband NMR spectrometer. http://purl.obolibrary.org/obo/OBI_0000478 column connector http://purl.obolibrary.org/obo/OBI_0000048 chromatography device A device that connects two or more columns together in a functional way with leak-tight connection, low dead volume, low thermal mass and high inertness. http://purl.obolibrary.org/obo/OBI_0000479 solid NMR probe http://purl.obolibrary.org/obo/OBI_0000516 NMR probe An NMR probe that is designed to hold a solid sample. http://purl.obolibrary.org/obo/OBI_0000481 chromatography detector http://purl.obolibrary.org/obo/OBI_0000485 chromatography instrument A chromatography detector is a device that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a chromatographic process and thus permits the senses to appreciate the nature of the separation. Defining characteristics are Dynamic Range, Response Index or Linearity, Linear Dynamic range, Detector Response, Detector Noise Level, Detector Sensitivity or Minimum Detectable Concentration, Total System Dispersion, Sensor Dimensions, Detector Time Constant, Pressure Sensitivity, Flow Sensitivity, Operating Temperature Range. http://purl.obolibrary.org/obo/OBI_0000482 normal phase column http://purl.obolibrary.org/obo/OBI_0000038 chromatography column A normal phase column is a chromatography column in which the stationary phase is more polar than the mobile phase. Its counterpart is the reversed phase column. http://purl.obolibrary.org/obo/OBI_0000483 APOLLO console http://purl.obolibrary.org/obo/OBI_0000599 tecmag NMR console The APOLLO is a compact, modular, multiple-DSP, Windows XP Professional-based console that can be equipped with up to 8 DDS-based RF transmitter channels configurable from 2 kHz to 3.5 GHz. Each transmitter channel produces a nominal 1V output and has the most agile frequency, phase and amplitude control of any system on the market. An array of additional options are available including multiple RF transmitters, linear high-power RF amplifiers, digital receiver arrays, low noise figure preamplifiers, a gradient control system, shim unit, MAS spin-speed controller, variable temperature unit, digital lock system and probe/coil interface. With its numerous options, the Apollo can be configured for any NMR, NQR or MRI application. http://purl.obolibrary.org/obo/OBI_0000484 NMR sample holder http://purl.obolibrary.org/obo/OBI_0000968 device An NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the nmr sample. http://purl.obolibrary.org/obo/OBI_0000485 chromatography instrument http://purl.obolibrary.org/obo/OBI_0000932 material separation device Any instrument that is used to carry out a chromatography experiment. http://purl.obolibrary.org/obo/OBI_0000486 continuous wave NMR instrument http://purl.obolibrary.org/obo/OBI_0000566 NMR instrument Continuous wave NMR spectrometers are similar to optical spectrometers, but the sample is held in a strong magnetic field, where the frequency of the source is slowly scanned (in some instruments, the source frequency is held constant, and the field is scanned). http://purl.obolibrary.org/obo/OBI_0000487 fourier transformation NMR instrument http://purl.obolibrary.org/obo/OBI_0000566 NMR instrument In fourier transformation NMR, all frequencies in a spectrum are irradiated simultaneously with a radio frequency pulse. Following the pulse, the nuclei return to thermal equilibrium. A time domain emission signal is recorded by the instrument as the nuclei relax. A frequency domain spectrum is obtained by Fourier transformation. http://purl.obolibrary.org/obo/OBI_0000489 nitrogen phosphorous detector http://purl.obolibrary.org/obo/OBI_0000637 gas chromatography detector The nitrogen phosphorus detector (NPD) (sometimes called the thermionic detector) is a very sensitive, specific detector the design of which, is based on the FID. Physically the sensor appears to be very similar to the FID but, in fact, operates on an entirely different principle. The nitrogen phosphorous detector (sometimes called the thermionic detector) is a very sensitive but specific detector that responds almost exclusively to nitrogen and phosphorous compounds. It is based on the flame ionization detector but differs in that it contains a rubidium or cesium silicate (glass) bead situated in a heater coil, a little distance from the hydrogen flame. If the detector is to respond to both nitrogen and phosphorous then the hydrogen flow should be minimal so that the gas does not ignite at the jet. If the detector is to respond to phosphorous only, a large flow of hydrogen is used which is burnt at the jet. The heated bead emits electrons by thermionic emission. These electrons are collected under a potential of a few volts by an appropriately placed anode, and provides a background current. When a solute containing nitrogen or phosphorous is eluted from the column, the partially combusted nitrogen and phosphorous materials are adsorbed on the surface of the bead. The adsorbed material reduces the work function of the surface and, as consequence, the emission of electrons is increased which raises the current collected at the electrode. The sensitivity of the detector to phosphorous is about 10-12 gram per ml and for nitrogen about 10-11 gram per ml at a signal to nose ratio of 2. The alkali bead as a finite life and needs regular replacement. http://purl.obolibrary.org/obo/OBI_0000490 cation exchange column http://purl.obolibrary.org/obo/OBI_0000560 ion exchange column A cation exchange column is a chromatography column that is used in cation exchange chromatography. http://purl.obolibrary.org/obo/OBI_0000491 direct detection NMR probe http://purl.obolibrary.org/obo/OBI_0000516 NMR probe An NMR probe designed to allow the direct detection of acquisition nuclei. http://purl.obolibrary.org/obo/OBI_0000492 Bruker B-ACS system http://purl.obolibrary.org/obo/OBI_0000464 Bruker autosampler The Bruker Automatic Sample Changer (B-ACS 60/120), used in conjunction with Bruker DISNMR, UXNMR or XWIN-NMR software, provides dialog-guided facilities which allow the user to easily and effectively perform automatic (continuous) experiments. Features include a 60 or 120 sample capacity, random accessing of samples, positive sample identification with the optional bar code reader, and temperature control of individual samples with the optional sample heater unit. http://purl.obolibrary.org/obo/OBI_0000493 rapid resolution column http://purl.obolibrary.org/obo/OBI_0000932 material separation device A rapid resolution column is a chromatography column as marketed by Agilent, which is used with a rapid resolution cartridge to ensure a fast chromatography process with good separation resolution. http://purl.obolibrary.org/obo/OBI_0000494 liquid chromatography autosampler http://purl.obolibrary.org/obo/OBI_0000485 chromatography instrument Designed to perform capillary LC with injection of sample volumes ranging from nL to L. http://purl.obolibrary.org/obo/OBI_0000495 vacuum degasser http://purl.obolibrary.org/obo/OBI_0000589 chromatography pump system A degassing system used for degassing solvents in liquid chromatography. Dissolved gasses, usually nitrogen and oxygen from the air, tend to be evolved in the mobile phase as the pressure is reduced when the mobile phase leaves the liquid chromatography column and enters the detector. Gasses in the mobile phase in the detector can produce completely unacceptable noise and, thus, must be removed. The dissolved gasses were originally removed under vacuum but, unfortunately, are soon replaced if the solvent is left in contact with air at atmospheric pressure. For this reason degassing is now usually carried out by bubbling helium through the mobile phase reservoirs. Secondly, vacuum is used in the thermionic detector. This consists of a device, very similar in design to the thermionic valve which is attached to a vacuum and a small quantity of the eluent from a gas chromatography column allowed to bleed through it. Helium is used as the carrier gas. The presence of solute vapor causes the thermionic current to fall. This type of detector tends to become contaminated rather readily. http://purl.obolibrary.org/obo/OBI_0000496 capillary column http://purl.obolibrary.org/obo/OBI_0000038 chromatography column A capillary column is a thin tube with a small inner diameter, usually around 0.5 mm. http://purl.obolibrary.org/obo/OBI_0000497 sample inlet http://purl.obolibrary.org/obo/OBI_0000048 chromatography device The column inlet (or injector) provides the means to introduce a sample into a continuous flow of carrier gas. The inlet is a piece of hardware attached to the column head. http://purl.obolibrary.org/obo/OBI_0000498 NMR tube washing system http://purl.obolibrary.org/obo/OBI_0000968 device An automatic cleaning system for NMR tubes that removes previous probe and sample residues in order to allow for tube recycling. http://purl.obolibrary.org/obo/OBI_0000499 NMR console http://purl.obolibrary.org/obo/OBI_0000968 device A component of an NMR instrument that controls the activities of the other components. http://purl.obolibrary.org/obo/OBI_0000500 dual loop autosampler http://purl.obolibrary.org/obo/OBI_0000494 liquid chromatography autosampler A dual loop autosampler is an autosampler that is designed for handling both analytical (10 mL/min flow rate) to preparative scale sample purification (100 mL/min flow rate). http://purl.obolibrary.org/obo/OBI_0000501 variable wavelength detector http://purl.obolibrary.org/obo/OBI_0000832 measurement device A chromatography detector, that can detect signals within a certain range at user-defined wavelengths. http://purl.obolibrary.org/obo/OBI_0000503 Bruker LC-NMR platform http://purl.obolibrary.org/obo/OBI_0000596 Bruker NMR instrument The LC-NMR/MS setup was first introduced by Bruker BioSpin in 1999. An LC-NMR system including a Bruker Peak Sampling Unit (BPSU-36) was coupled with a Bruker Daltonics esquire series ion trap mass spectrometer via a Bruker NMR-MS interface (BNMI). Since October 2004 the Bruker Daltonics microTOF-LC time-of-flight mass spectrometer can also be integrated in an LC-NMR setup. http://purl.obolibrary.org/obo/OBI_0000504 sample injection system http://purl.obolibrary.org/obo/OBI_0000048 chromatography device An automated chromatography system that injects the sample into the chromatography columns in order to increase speed and minimize human involvement in the purification process for better reproducibility. http://purl.obolibrary.org/obo/OBI_0000505 multiple wavelength detector http://purl.obolibrary.org/obo/OBI_0000832 measurement device A chromatography detector, that can detect many discrete wavelengths in parallel and produces a multiple wavelength chromatographic profile. http://purl.obolibrary.org/obo/OBI_0000507 gas generator http://purl.obolibrary.org/obo/OBI_0000542 gas chromatography equipment An instrument that generates gases for use with the gas chromatograph. Previously gas was obtained from gas tanks or gas cylinders. However, over the past decade the use of gas generators have become more popular as it avoids having gases at high pressure in the laboratory which is perceived by some as potentially dangerous. In addition, the use of a hydrogen generator avoids the use of a cylinder of hydrogen at high pressure which is also perceived by some as a serious fire hazard despite the fact that they have been used in laboratories, quite safely for nearly a century. http://purl.obolibrary.org/obo/OBI_0000508 column jacket http://purl.obolibrary.org/obo/OBI_0000048 chromatography device A column jacket is a piece of column chromatography equipment that covers a column in order to ensure thermoisolation and create a controllable thermostatic microenvironment. http://purl.obolibrary.org/obo/OBI_0000510 reversed phase column http://purl.obolibrary.org/obo/OBI_0000038 chromatography column A reversed phase column is a chromatography column in which the mobile phase is more polar than the stationary phase. Its counterpart is the normal phase column. http://purl.obolibrary.org/obo/OBI_0000511 injector lubricant http://purl.obolibrary.org/obo/OBI_0000601 chromatography consumable A lubricant used in liquid chromatography that eases sample injector penetration. http://purl.obolibrary.org/obo/OBI_0000512 isolation of cell population http://purl.obolibrary.org/obo/OBI_0600014 material component separation a process in which a population of cells with certain characteristics is isolated from a larger population http://purl.obolibrary.org/obo/OBI_0000513 DISCOVERY console http://purl.obolibrary.org/obo/OBI_0000599 tecmag NMR console The Discovery console is a Windows XP Professional-based, integrated console designed especially for Solid-State NMR. The console includes everything needed to interface to any magnet and solids probe - from computer to cables to duplexing network. http://purl.obolibrary.org/obo/OBI_0000514 Bruker AMX series NMR instrument http://purl.obolibrary.org/obo/OBI_0000596 Bruker NMR instrument A series of older Bruker NMR magnets, now out of production. The Bruker AMX500 has proven an extremely reliable workhorse, with excellent lineshape yielding superior water suppression even without gradients. The Oxford 11.7 Tesla 5.2 cm bore magnet rests on a TMC vibration damping table. Homogeneity is controlled by a BSN-18 and BSN-2 with 19 shim controls. In addition to the 5 mm triple resonance probe, the AMX is equipped with a 10mm broadband observe probe. http://purl.obolibrary.org/obo/OBI_0000515 chromatofocusing column http://purl.obolibrary.org/obo/OBI_0000038 chromatography column A chromatofocusing column is a chromatography column in which a resin is equilibrated at one pH and eluted at a second pH. The use of a weak ion-exchange resin causes a pH gradient to be formed at the solvent front owing to the buffering action of the resin. This pH gradient in turn leads to an ordering of proteins by isoelectric point. Molecules of charge sign opposite the resin bind; those of charge sign like the resin do not bind. http://purl.obolibrary.org/obo/OBI_0000516 NMR probe http://purl.obolibrary.org/obo/OBI_0000832 measurement device Part of an NMR instrument that detects the signals emitted from a sample. No single probe can perform the full range of experiments, and probes that are designed to perform more than one type of measurement usually suffer from performance compromises. The probe represents a rather fragile single point of failure that can render an NMR system completely unusable if the probe is dropped or otherwise damaged. Probes are usually characterised by Sample diameter and Frequency.n alt The instrument that transmits and receives radiofrequency to and from the NMR sample. http://purl.obolibrary.org/obo/OBI_0000517 NMR magnet http://purl.obolibrary.org/obo/OBI_0000968 device A magnet which induces a certain frequency (MHz) and which has a certain bore diameter.n alt The NMR signal is a natural physical property of the certain atomic nuclei but it can only be detected with an external magnetic field. A magnet is a fundamental part of an NMR instrument which induces an electromagnetic force field (RF pulse) and by this excites and aligns the spins of the electrons of the NMR acquisition nucleus. It is usually a big (superconducting) electromagnet which is cooled by liquid helium and can be adjusted to a frequency between 200 and 950 MHz. The magnetic field strength is measured in Tesla or Gauss. http://purl.obolibrary.org/obo/OBI_0000518 trap column http://purl.obolibrary.org/obo/OBI_0000038 chromatography column A trap column is a chromatography column which is used prior to a, e.g. mass spectrometry, separation to clean up or concentrate controlled amounts of samples prior to elution to a detector. http://purl.obolibrary.org/obo/OBI_0000519 flow probe http://purl.obolibrary.org/obo/OBI_0000516 NMR probe An NMR probe that allows the automatized flow-through of a sample. The sample is aspirated via a syringe pump into the Flow probe, the NMR spectrum is acquired and when the experiment is complete, the sample is returned to back to an external source (well plate) or flushed to waste. Sometimes pulsed field gradients (PFG) can be established in flow probes. http://purl.obolibrary.org/obo/OBI_0000522 vial http://purl.obolibrary.org/obo/OBI_0000601 chromatography consumable A vial is a cylindrical container often made from glass tubing. http://purl.obolibrary.org/obo/OBI_0000524 Varian VXR spectrometer http://purl.obolibrary.org/obo/OBI_0000611 Varian NMR instrument A Varian NMR spectrometer. http://purl.obolibrary.org/obo/OBI_0000525 splitless GC injector http://purl.obolibrary.org/obo/OBI_0000504 sample injection system Injected sample enters column immediately (while split valve to split vent is closed). Here a sample is introduced into a heated small chamber via a syringe through a septum - the heat facilitates volatilization of the sample and sample matrix. The carrier gas then either sweeps the entirety (splitless mode) or a portion (split mode) of the sample into the column. In split mode, a part of the sample/carrier gas mixture in the injection chamber is exhausted through the split vent. http://purl.obolibrary.org/obo/OBI_0000526 preparative autosampler http://purl.obolibrary.org/obo/OBI_0000494 liquid chromatography autosampler For preparative LC with injection of sample volumes ranging from L to mL ranges. http://purl.obolibrary.org/obo/OBI_0000528 liquid chromatography valve http://purl.obolibrary.org/obo/OBI_0000048 chromatography device A sample valve that must be able to sustain pressures up to 10,000 p.s.i., although it is most likely to operate on a continuous basis, at pressures of 3,000 p.s.i. or less. The higher the operating pressure the tighter the valve seating surfaces must be forced together to eliminate any leak. It follows that any abrasive material, however fine, that passes into the valve can cause the valve seating to become scored each time it is rotated which will ultimately lead to leaks. This will cause the sample size to vary between samples and eventually affect the accuracy of the analysis. It follows that any solid material must be carefully removed from any sample before filling the valve. The sample volume of an internal loop valve is situated in the connecting slot of the valve rotor and can be used only for relatively small sample volumes. Internal sample loop valves provide samples with volumes ranging from 0.1 ml to about 0.5 ml. Valve operation is shown in figure 6. The left-hand side diagram shows the load position. The sample occupies the rotor slot and has been filled by passing the sample from an appropriate syringe through the rotor slot to waste. While loading the sample, the mobile phase supply is passed through the valve directly to the column. To place the sample onto the column, the valve is then rotated and the valve slot containing the sample is now placed between the solvent supply and the column. As a result, the sample is passed into the column by the flow of solvent. http://purl.obolibrary.org/obo/OBI_0000529 JEOL NMR probe http://purl.obolibrary.org/obo/OBI_0000516 NMR probe An NMR probe that is manufactured by JEOL. http://purl.obolibrary.org/obo/OBI_0000530 Bruker UltraShield Plus NMR magnet http://purl.obolibrary.org/obo/OBI_0000597 Bruker NMR magnet An NMR magnet of which Brukers claims it is the latest and most advanced self-shielding NMR magnet technology ever developed. These magnets are the ultimate advancement in high performance, actively-shielded NMR solutions. They offer unprecedented shielding performance whilst ensuring no compromise in system homogeneity, stability or cryogenic specifications. http://purl.obolibrary.org/obo/OBI_0000531 Bruker CryoProbe http://purl.obolibrary.org/obo/OBI_0000561 Bruker NMR probe The Bruker BioSpin CryoProbe is a high-performance cryogenically cooled probe developed for high-resolution applications. It has improved signal/noise (S/N) ratios obtained by reducing the operating temperature of the coil and the pre-amplifier. As a result, the efficiency of the coil is improved and the noise of the coil and the pre-amplifier are reduced.The dramatic increase in the S/N ratio by a factor of 3-4, as compared to conventional probes, leads to a possible reduction in experiment time of up to 16 or a reduction in required sample concentration by a factor of up to 4. The CryoProbes possess key characteristics for NMR analysis:n Significant S/N gains (with moderately salty samples also)n Short pulse widthsn Short ring down timesn Linear behavior in power responsen Gradient capabilityn CryoProbes are available as Triple Resonance, Dual, Selective X Detection, MicroImaging, and Quad Nucleus Probes configurations at 400 MHz and highern All high resolution probes have a lock circuitn All high resolution probes have Z-gradient. http://purl.obolibrary.org/obo/OBI_0000532 column cartridge http://purl.obolibrary.org/obo/OBI_0000048 chromatography device A device that binds the chromatography column and additional connector elements and / or valves or syringes into one physical unity for further processing. http://purl.obolibrary.org/obo/OBI_0000533 affinity column http://purl.obolibrary.org/obo/OBI_0000038 chromatography column An affinity column is a chromatography column that is used in affinity chromatography. Differences in the affinity of molecules to be separated to a stationary phase are used for discriminate retention. http://purl.obolibrary.org/obo/OBI_0000534 tecmag NMR instrument http://purl.obolibrary.org/obo/OBI_0000566 NMR instrument An NMR instrument that is manufactured by tecmag. http://purl.obolibrary.org/obo/OBI_0000535 gel filtration column http://purl.obolibrary.org/obo/OBI_0000618 size exclusion column A Gel filtration column is a chromatography column for size-exclusion chromatography, in which the stationary phase is a gel. The main application of gel filtration chromatography is the fractionation of proteins and other water-soluble polymers. http://purl.obolibrary.org/obo/OBI_0000536 fraction collector http://purl.obolibrary.org/obo/OBI_0000485 chromatography instrument A fraction detector is a device that allows regular or specified samples to be taken from a column eluate and stored in a retrievable form. The storage vessels are usually small sample tubes or vials that are oriented in a rotating disk or in a moving belt, there movement usually being controlled by a microprocessor. On receiving a signal from the microprocessor, the next vial is placed under the column outlet and the eluate collected until receiving another signal from the computer. Once the properties of the chromatogram that describes the separation has been ascertained, then the collection program can be defined. The fractions can be collected on a basis of time either at regular intervals or a specific times to collect specific peaks. Alternatively the fractions can be collected by monitoring the detector output and when a peak starts to elute the fraction collector is activated and the peak collected in a specific vial. When the peak returns to base line the column eluate is then directed to waste until the next peak starts eluting. Fraction collectors are in common use with most liquid chromatographs. They are used to collect samples for further purification, subsequent examination by spectroscopic techniques or for biological or organoleptic testing. http://purl.obolibrary.org/obo/OBI_0000538 in-line filter http://purl.obolibrary.org/obo/OBI_0000592 chromatography detector filter A solvent filter that sits between the pump and the injection valve that prevents dust particles, general debris and, to some extent, bacteria from entering the chromatography system. Contaminants can interfere with the low-pressure gradient former or the pump and particles entering valves may interfere with the proper function. The result could cause an increased baseline noise, non-repeatable gradient forming, unreliable flow rate or other interferences. Solvent in-line filters are low-pressure filters and will allow a high flow rate due to a large surface area and large porosity. http://purl.obolibrary.org/obo/OBI_0000539 imaging NMR probe http://purl.obolibrary.org/obo/OBI_0000516 NMR probe An NMR probe that is designed for generating pictures from sample states via NMR imaging. http://purl.obolibrary.org/obo/OBI_0000540 isolation of adherent cells http://purl.obolibrary.org/obo/OBI_0000512 isolation of cell population a material separation process in which cells that stick to the container in which they are grown as a cell culture are separated from those in the liquid component of the culture. The output of this process are adherent cells. http://purl.obolibrary.org/obo/OBI_0000541 Bruker AC series NMR instrument http://purl.obolibrary.org/obo/OBI_0000596 Bruker NMR instrument A series of older Bruker NMR magnets, now out of production. http://purl.obolibrary.org/obo/OBI_0000542 gas chromatography equipment http://purl.obolibrary.org/obo/OBI_0000048 chromatography device Any device used in a gas chromatography experiment. http://purl.obolibrary.org/obo/OBI_0000543 syringe filter http://purl.obolibrary.org/obo/OBI_0000592 chromatography detector filter A small membrane filter of defined pore size, that filters samples from a syringe. http://purl.obolibrary.org/obo/OBI_0000544 Bruker SampleRail system http://purl.obolibrary.org/obo/OBI_0000968 device This Instrument system automatically prepares an NMR sample, inserts it into an NMR magnet, performs NMR experiments on the sample, and transports it back to the preparation system. The SampleRail fulfills the transporting tasks from the preparation system into the NMR magnet and back. http://purl.obolibrary.org/obo/OBI_0000545 column compartment http://purl.obolibrary.org/obo/OBI_0000048 chromatography device For chromatography analyses, the ability to maintain a stable column environment regardless of ambient temperature fluctuations is critical for maintaining retention time precision. In order to ensure such stable conditions at different chromatography steps a column compartment can be installed that ensures e.g. stable temperature of the column in a given step. http://purl.obolibrary.org/obo/OBI_0000546 capillary pump system http://purl.obolibrary.org/obo/OBI_0000589 chromatography pump system A pump system optimized for capillary chromatography. http://purl.obolibrary.org/obo/OBI_0000547 evaporative light scattering detector http://purl.obolibrary.org/obo/OBI_0000832 measurement device The evaporative light scattering detector, as its name implies, utilizes a spray that continuously atomizes the column eluent into small droplets. These droplets are allowed to evaporate, leaving the solutes as fine particulate matter suspended in the atomizing gas. http://purl.obolibrary.org/obo/OBI_0000548 isolation of PBMCs http://purl.obolibrary.org/obo/OBI_0000512 isolation of cell population a process in which cells with a single nucleus are isolated from a blood sample http://purl.obolibrary.org/obo/OBI_0000549 column cartridger http://purl.obolibrary.org/obo/OBI_0000485 chromatography instrument A chromatography device where the column cartridge is inserted into and stabilised. http://purl.obolibrary.org/obo/OBI_0000550 nitrogen generator http://purl.obolibrary.org/obo/OBI_0000507 gas generator A gas generator that generates nitrogen gas. http://purl.obolibrary.org/obo/OBI_0000551 needle assembly http://purl.obolibrary.org/obo/OBI_0000048 chromatography device The needle assembly attached to the autosampler, comprises the injector needle that feeds a sample or carrier gas into the inlet http://purl.obolibrary.org/obo/OBI_0000553 Bruker Capillary LC-NMR platform http://purl.obolibrary.org/obo/OBI_0000596 Bruker NMR instrument Capillary LC-NMR is a hyphenated technique coupling capillary liquid chromatography and NMR, which increases sensitivity dramatically through the use of miniaturization of the chromatographic techniques and NMR detection volume. LC-NMR hyphenated systems separate a mixture into its pure components and couple the output to NMR for automatic sample analysis. The ever increasing need to measure lower sample amounts and lower level impurities demands the highest NMR sensitivity. Traditional LC-NMR systems with relatively large peak volumes are not optimized for such low levels of detection. Bruker BioSpin, together with Waters and Protasis has developed a Capillary LC-NMR system. The latest capillary LC attributes and highest capillary flow probe sensitivity combine with state of the art NMR systems technology. Greater mass sensitivity and faster spectral analysis with smaller sample volumes is possible. This system is ideal for analysis of metabolites and impurities associated with the drug development process. http://purl.obolibrary.org/obo/OBI_0000554 gas chromatography oven http://purl.obolibrary.org/obo/OBI_0000542 gas chromatography equipment A gas chromatography oven is an oven with a heated connection between the GC and the MS instrument in a GCMS-analysis, that keeps compounds in the gas phase as they leave the GC oven. http://purl.obolibrary.org/obo/OBI_0000555 autosampler http://purl.obolibrary.org/obo/OBI_0000968 device An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument. n alt The autosampler is an automatic sample changer device. http://purl.obolibrary.org/obo/OBI_0000556 isocratic pump system http://purl.obolibrary.org/obo/OBI_0000589 chromatography pump system A pump system optimized for isocratic chromatography. http://purl.obolibrary.org/obo/OBI_0000557 flash pump system http://purl.obolibrary.org/obo/OBI_0000589 chromatography pump system Any pump system used in flash column chromatography to push the solvent through the column. Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography). http://purl.obolibrary.org/obo/OBI_0000558 Varian UNITY INOVA spectrometer http://purl.obolibrary.org/obo/OBI_0000611 Varian NMR instrument The UNITY INOVA is also the easiest spectrometer to use and is also the choice of those interested in using advanced NMR techniques in their own research, but without becoming, or hiring, an NMR expert. A complete set of turnkey operating environments is available for the UNITY INOVA covering the structure and dynamics of biological macromolecules, small molecules, solids, and imaging. These packages put the combined NMR expertise of the entire Varian NMR community at your fingertips. http://purl.obolibrary.org/obo/OBI_0000559 liquid NMR probe http://purl.obolibrary.org/obo/OBI_0000516 NMR probe An NMR probe that is designed to hold a liquid sample. http://purl.obolibrary.org/obo/OBI_0000560 ion exchange column http://purl.obolibrary.org/obo/OBI_0000038 chromatography column An ion exchange column is a chromatography column that is used in ion exchange chromatography and anion or cation exchange resins to enable separation. http://purl.obolibrary.org/obo/OBI_0000561 Bruker NMR probe http://purl.obolibrary.org/obo/OBI_0000516 NMR probe An NMR probe that is manufactured by Bruker. http://purl.obolibrary.org/obo/OBI_0000562 anion trap column http://purl.obolibrary.org/obo/OBI_0000518 trap column An anion trap column is a trap column and ion-exchange column which contains cationic anion-exchange resins. http://purl.obolibrary.org/obo/OBI_0000563 fluorescene detector http://purl.obolibrary.org/obo/OBI_0000832 measurement device A single wavelength detector, where the excitation light wavelength is normally a mercury lamp generated high intensity UV light at 253.7 nm. Many substances that fluoresce will be excited by light of this wavelength and hence be detected. http://purl.obolibrary.org/obo/OBI_0000564 tecmag EAGLE probe http://purl.obolibrary.org/obo/OBI_0000479 solid NMR probe The Eagle is a 4 mm 1H/X solid-state MAS probe with a top spinning speed of 18 kHz. Its simple design is robust, reliable and easy to spin. Configurations are available for 200 to 600 MHz wide bore magnets on Tecmag, Bruker, Chemagnetics, JEOL and Varian spectrometers. http://purl.obolibrary.org/obo/OBI_0000565 electrical conductivity detector http://purl.obolibrary.org/obo/OBI_0000832 measurement device The electrical conductivity detector measures the conductivity of the mobile phase. There is usually background conductivity which must be backed-off by suitable electronic adjustments. If the mobile phase contains buffers, the detector gives a base signal that completely overwhelms that from any solute usually making detection impossible. Thus, the electrical conductivity detector a bulk property detector. and senses all ions whether they are from a solute or from the mobile phase. In order to prevent polarization of the sensing electrodes, AC voltages must be used and so it is the impedance not the resistance of the electrode system that is actually measured. From a physical chemistry stand point the conductivity of a solution is more important than its resistance. However, it is the resistance (impedance) of the electrode system that determines the current across it. The resistance of any conductor varies directly as its length and inversely as its cross sectional area. http://purl.obolibrary.org/obo/OBI_0000567 Bruker UltraShield NMR magnet http://purl.obolibrary.org/obo/OBI_0000597 Bruker NMR magnet An NMR magnet manufactured by Bruker that ensures field homogeneity without amplified effects from vibrations or thermal changes. This magnet technology uses active shielding and optimizes coil design. http://purl.obolibrary.org/obo/OBI_0000568 piston-seal http://purl.obolibrary.org/obo/OBI_0000601 chromatography consumable The seal made by a piston in a diaphragm pump. The unique property of the reciprocating diaphragm pump is that the actuating piston does not come into direct contact with the mobile phase and thus, the demands on the piston-cylinder seal are not so great. The diaphragm has a relatively high surface area and thus, the movement of the diaphragm is relatively small and consequently the pump can be operated at a fairly high frequency. High frequency pumping results in a very significant reduction in pulse amplitude and, in addition, high frequency pulses are more readily damped by the column system. Nevertheless, it must be emphasized that diaphragm pumps are not pulseless. http://purl.obolibrary.org/obo/OBI_0000570 spin column http://purl.obolibrary.org/obo/OBI_0000038 chromatography column A spin column is a chromatography column which is suitable for putting it into a centrifuge. A spin column enforces separation through increased G-forces while spinning the column in a centrifuge. It is often used in DNA gel extraction kits. http://purl.obolibrary.org/obo/OBI_0000571 manufacturer role http://purl.obolibrary.org/obo/BFO_0000023 role Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. http://purl.obolibrary.org/obo/OBI_0000572 transfer line http://purl.obolibrary.org/obo/OBI_0000048 chromatography device A combination of devices that are used in connection with a sampling head for transferring components of an applied sample to the analyzing part of a chromatography system. http://purl.obolibrary.org/obo/OBI_0000573 gradient pump system http://purl.obolibrary.org/obo/OBI_0000589 chromatography pump system A pump system optimized for gradient chromatography. http://purl.obolibrary.org/obo/OBI_0000574 high temperature column http://purl.obolibrary.org/obo/OBI_0000038 chromatography column A high temperature column is a chromatography column which is suitable for and withstands very high temperatures in chromatography ovens. http://purl.obolibrary.org/obo/OBI_0000575 Bruker Ultrastabilized NMR magnet http://purl.obolibrary.org/obo/OBI_0000597 Bruker NMR magnet An NMR magnet manufactured by Bruker for Ultra-High Field NMR, available from 750 MHz to 900 MHz, which provides reliable operation at reduced temperature and ambient pressure via being rigidly mounted and stabilized. http://purl.obolibrary.org/obo/OBI_0000577 obsolete_molecular concentration http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class A concentration is a relational quality that inheres in a material entity towards molecular scattered aggregate that is part of it by virtue of some ratio of masses of the two or the counts of the grains of the two or volume occupied by the larger material entity. http://purl.obolibrary.org/obo/OBI_0000578 NMR sample tube http://purl.obolibrary.org/obo/OBI_0000836 test tube The sample-tube holds the NMR sample and sits in the nmr probe. It is usually a glass tube of 5-20mm diameter. http://purl.obolibrary.org/obo/OBI_0000579 Varian UNITY spectrometer http://purl.obolibrary.org/obo/OBI_0000611 Varian NMR instrument The predecessor series of the Varian UNITY INOVA spectrometer. http://purl.obolibrary.org/obo/OBI_0000580 AVANCE II spectrometer http://purl.obolibrary.org/obo/OBI_0000596 Bruker NMR instrument A spectrometer suitable for metabolomics and in vivo NMR studies but structural analysis of small molecules and low molecular weight proteins can also be performed. To accomplish these studies there are six probe-heads available. A successor, the AVANCE III came out recently. http://purl.obolibrary.org/obo/OBI_0000581 y-column connector http://purl.obolibrary.org/obo/OBI_0000478 column connector A column connector that connects one column on one side with two columns at the other side, hence building a Y shaped structure. http://purl.obolibrary.org/obo/OBI_0000582 Bruker LC-NMR/MS platform http://purl.obolibrary.org/obo/OBI_0000596 Bruker NMR instrument Includes the connection to a high-resolution TOF-LC-MS system. http://purl.obolibrary.org/obo/OBI_0000583 refractive index detector http://purl.obolibrary.org/obo/OBI_0000832 measurement device For analyzing non-UV absorbing substances, such as carbohydrates, lipids and polymers. This is also the detector of choice for gel permeation chromatography. The refractive index detector is one of the least sensitive LC detectors. It is very sensitive to changes in ambient temperature, pressure changes, flow-rate changes and can not be used for gradient elution. Despite these many disadvantages, this detector is extremely useful for detecting those compounds that are nonionic, do not adsorb in the UV, and do not fluoresce. There are many optical systems used in refractive index detectors but one of the most common is the differential refractive index detector. http://purl.obolibrary.org/obo/OBI_0000584 anion exchange column http://purl.obolibrary.org/obo/OBI_0000560 ion exchange column An anion exchange column is a chromatography column that is used in anion exchange chromatography and which enables the separation of anion mixtures. http://purl.obolibrary.org/obo/OBI_0000586 plunger column http://purl.obolibrary.org/obo/OBI_0000038 chromatography column A plunger column is a chromatography column with adjustable heigth control. By means of an adjustable endpiece (plunger) the user can adjust the column length without disturbing the packed bed. Plunger columns can equalize volume changes and thus avoids dead volumes within the column. http://purl.obolibrary.org/obo/OBI_0000589 chromatography pump system http://purl.obolibrary.org/obo/OBI_0000485 chromatography instrument Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography). http://purl.obolibrary.org/obo/OBI_0000590 Bruker 1mm MicroProbe http://purl.obolibrary.org/obo/OBI_0000561 Bruker NMR probe Over the past few years there has been a significantly growing demand for miniaturization in all areas ofmodern research and development. Evoked by many exciting applications, there is a need for analytical methods which require less amounts of sample. Bruker BioSpin meets this challenge with a revolutionary NMR probe design: The 1mm MicroProbe. It operates with disposable 1mm capillary sample tubes and the sample volume of 5 microliters enables the use of lowest amounts of sample to run all high resolution NMR experiments with outstanding sensitivity and up to 16 times faster measurements. Due to the TXI-type probe design, the z-gradient coil and the automatic matching and tuning accessory, the 1mm MicroProbe can be used for a wide variety of NMR experiments. The key advantages of this probe include:n up to 4 times higher mass sensitivity than 5mm conventional probes (with respect to the same sample amount)n excellent solvent suppression propertiesn virtually no salt effectn discrete samples in tubes that can be sealed and storedn automation accessory for sample preparation and handling available. http://purl.obolibrary.org/obo/OBI_0000592 chromatography detector filter http://purl.obolibrary.org/obo/OBI_0000601 chromatography consumable An optical filter that is used to obtain monochromatic light of a defined wavelength from detector lamps. http://purl.obolibrary.org/obo/OBI_0000593 cation trap column http://purl.obolibrary.org/obo/OBI_0000518 trap column A cation trap column is a trap column and ion-exchange column which contains anionic cation-exchange resins. http://purl.obolibrary.org/obo/OBI_0000594 column adapter http://purl.obolibrary.org/obo/OBI_0000048 chromatography device An Adapter that enabled the connection of a column to additional devices. http://purl.obolibrary.org/obo/OBI_0000596 Bruker NMR instrument http://purl.obolibrary.org/obo/OBI_0000566 NMR instrument An NMR instrument that is manufactured by Bruker. http://purl.obolibrary.org/obo/OBI_0000597 Bruker NMR magnet http://purl.obolibrary.org/obo/OBI_0000517 NMR magnet An NMR magnet that is manufactured by Bruker. http://purl.obolibrary.org/obo/OBI_0000598 ozone-induced chemiluminescence detector http://purl.obolibrary.org/obo/OBI_0000637 gas chromatography detector Although there are many direct ozone chemiluminescent reactions with various gaseous molecules, the incorporation of a conversion step to convert various non-chemiluminescent analytes to a species capable of reacting with ozone to produce chemiluminescence broadens the horizon of this technique tremendously. The conversion of nearly all nitrogen- and sulfur-containing compounds to their respective chemiluminescent species for universal nitrogen and sulfur detection has made nitrogen/sulfur chemiluminescence detection the most widely used analytical methods based upon ozone-induced chemiluminescence. In addition to non-chromatographic applications, nitrogen/sulfur chemiluminescence detection has been adapted to various chromatographic techniques from gas chromatography to liquid and supercritical fluid chromatography as specialized element-specific detectors. The characteristics of these detectors are evaluated and compared to other element-selective detection techniques. The unique features of the chemiluminescence detectors have made them powerful tools in many diverse fields of analytical chemistry. http://purl.obolibrary.org/obo/OBI_0000599 tecmag NMR console http://purl.obolibrary.org/obo/OBI_0000499 NMR console An NMR console manufactured by tecmac. http://purl.obolibrary.org/obo/OBI_0000600 JEOL NMR instrument http://purl.obolibrary.org/obo/OBI_0000566 NMR instrument An NMR instrument that is manufactured by JEOL. http://purl.obolibrary.org/obo/OBI_0000601 chromatography consumable http://purl.obolibrary.org/obo/OBI_0000048 chromatography device A chromatography consumable is a consumable that is used in a chromatography experiment. http://purl.obolibrary.org/obo/OBI_0000602 column frit http://purl.obolibrary.org/obo/OBI_0000048 chromatography device A part of the column content that separates column packing compartments. In radial columns the packing is supported between two cylindrical frits and the gap between represents the bed height or column length. The outer frit is the column inlet and consequently the sample initially has a large area of stationary phase with which to interact. Frits are porous metal products to prevent unwanted particles from entering the chromatography system. These particles may come from the sample, the solvent or debris generated by the chromatography system itself. Such particles entering the system may lead to clogging of capillaries, interference with the chromatography by changing chromatographic parameters or disturbance of the detector function. Characteristics of a frit, besides the diameter and the thickness, is the porosity (pore distribution, density). http://purl.obolibrary.org/obo/OBI_0000603 liquid chromatography column http://purl.obolibrary.org/obo/OBI_0000038 chromatography column A liquid chromatography column is a chromatography column that is used in liquid chromatography, i.e. a column that is provided with a liquid sample mix. http://purl.obolibrary.org/obo/OBI_0000604 detector lamp http://purl.obolibrary.org/obo/OBI_0000601 chromatography consumable A lamp used in a chromatography detector that excites sample molecules at certain frequencies / emission wavelengths, e.g. Mercury Vapor Lamp (253.7 nm), Zinc Vapor Lamp (2123.9 nm and 307.6 nm), Cadmium Vapor Lamp (228.8, 326.1,340.3, and 346.6 nm). To obtain monochromatic light an appropriate light filter would be needed. http://purl.obolibrary.org/obo/OBI_0000605 chart recorder http://purl.obolibrary.org/obo/OBI_0000048 chromatography device The chart recorder is a device that transduces signal-intensities into a graphical peak output: As the separated components of the gas sample emerge into the detector, the change in voltage in the detecting bridge circuit causes a representative peak to be drawn on a chart recorder. The position of the peak along the time axis of the chart measures the component's retention time, which identifies the component. This is directly related to carrier gas flow rate, temperature and column packing and dimensions. The area under each peak is proportional to the concentration of the component of the sample. The area of the peaks inscribed on the chart recorder can be determined by multiplying the height of the peak in mm, by the width of the peak in mm at 1/2 the peak height. The calibration curves for use with the chart recorder are therefore peak area plotted against concentration. http://purl.obolibrary.org/obo/OBI_0000606 open tubular column http://purl.obolibrary.org/obo/OBI_0000038 chromatography column An open tubular column is a chromatography column in which the particles of the solid stationary phase or the support coated with a liquid stationary phase are concentrated on or along the inside tube wall leaving an open, unrestricted path for the mobile phase in the middle part of the tube. http://purl.obolibrary.org/obo/OBI_0000608 hydrogen generator http://purl.obolibrary.org/obo/OBI_0000507 gas generator A gas generator that generates hydrogen gas. http://purl.obolibrary.org/obo/OBI_0000609 glass column http://purl.obolibrary.org/obo/OBI_0000038 chromatography column A glass column is a chromatography column made out of glass that is usually used for larger scale and preparative liquid chromatography separations. http://purl.obolibrary.org/obo/OBI_0000610 auto injector http://purl.obolibrary.org/obo/OBI_0000504 sample injection system A gas chromatography device that can auto-inject a small number of samples an inlet. http://purl.obolibrary.org/obo/OBI_0000611 Varian NMR instrument http://purl.obolibrary.org/obo/OBI_0000566 NMR instrument An NMR instrument that is manufactured by Varian. http://purl.obolibrary.org/obo/OBI_0000613 Bruker SPE-NMR platform http://purl.obolibrary.org/obo/OBI_0000596 Bruker NMR instrument A Solid Phase Extraction (SPE) system provides an interface between liquid chromatography (LC) and NMR. For the process of LC-SPE NMR a chromatographic separation is done and the peaks of interest are trapped on an individual SPE cartridge after the column. The peak selection is done either by UV detection or by evaluation of the on-line registered MS or MSn spectra. http://purl.obolibrary.org/obo/OBI_0000614 guard column http://purl.obolibrary.org/obo/OBI_0000048 chromatography device Guard columns are installed between the injection valve and the analytical or preparative column and here will remove contaminants and prolong the lifetime of the columns. http://purl.obolibrary.org/obo/OBI_0000617 fluorine-induced chemiluminescence detector http://purl.obolibrary.org/obo/OBI_0000637 gas chromatography detector A gas chromatographic detection system based on the low pressure, gas phase chemiluminescence of the reaction mixture of molecular fluorine with organo-sulfur, -selenium, and -tellurium compounds separated from (gas phase) headspace samples. This detector was originally developed in the research group of John Birks at the University of Colorado, USA and was manufactured and sold by Sievers Instruments (Boulder Colorado, USA). This system can be divided up into three parts: the chromatograph, transfer line, and reaction cell; PMT and photon counting electronics; and the molecular fluorine generator. http://purl.obolibrary.org/obo/OBI_0000618 size exclusion column http://purl.obolibrary.org/obo/OBI_0000038 chromatography column A size exclusion column is a chromatography column as used in size exclusion chromatography and which enables the separation of mixtures according to differrences in molecular size. http://purl.obolibrary.org/obo/OBI_0000619 chromatography splitter http://purl.obolibrary.org/obo/OBI_0000048 chromatography device An adjustable restriction that is placed in the waste outlet to allow the necessary pressure to develop at the column inlet to force a flow (q ml/min) through the column. If the flow of mobile phase is Q ml/min then the waste flow will be (Q-q) ml/min. by adjusting the waste flow, the proportion of the sample entering the capillary column can be varied over a wide range of values and the necessary minimum permissible volume for the particular column in use can be selected for analysis. Unfortunately, the fraction taken in this way may not be representative of the original sample. This is due to the individual solutes in the mixture having different diffusivities and, thus, they distribute themselves across the sampling tube in an irregular manner. In general, the components with higher diffusivities (e.g., those solutes of lower molecular weight) will diffuse away from the bulk sample more quickly than those having lower diffusivities. http://purl.obolibrary.org/obo/OBI_0000620 Bruker micro imaging probe http://purl.obolibrary.org/obo/OBI_0000561 Bruker NMR probe For medical, biological and material sciences research, avance imaging systems provide optimal object handling and performance with a variety of samples types. Two classes of imaging probes are available: in vivo probes for handling and sustaining live objects such as animals and plants, and conventional imaging probes for materials samples. http://purl.obolibrary.org/obo/OBI_0000621 custom made column http://purl.obolibrary.org/obo/OBI_0000038 chromatography column A custom made column ia a chromatography column which is specifically tailored according to the needs of the separation as requested by a scientist or working group. http://purl.obolibrary.org/obo/OBI_0000622 gel permeation column http://purl.obolibrary.org/obo/OBI_0000038 chromatography column A gel permeation column is a chromatography column which is used in gel permeation chromatography and which employs as the stationary phase a swollen gel made by polymerizing and cross-linking styrene in the presence of a diluent which is a nonsolvent for the styrene polymer. The polymer to be analyzed is introduced at the top of the column and then is elutriated with a solvent. The polymer molecules diffuse through the gel at rates depending on their molecular size. http://purl.obolibrary.org/obo/OBI_0000624 Bruker SampleJet system http://purl.obolibrary.org/obo/OBI_0000464 Bruker autosampler Bruker BioSpin introduces the SampleJet, a robot for NMR tube automation. The SampleJet has been consciously designed to meet the growing customer demand for simplicity, versatility and higher throughput in NMR sample tube automation.n The SampleJet utilizes the modern-day industry standard for sample arrangements-the 96 well plate array. Therefore, the samples may be handled by standard lab automation devices before or after the NMR measurement. http://purl.obolibrary.org/obo/OBI_0000625 JEOL ECX NMR spectrometer http://purl.obolibrary.org/obo/OBI_0000600 JEOL NMR instrument The ECX series of NMR spectrometers is designed for any laboratory needing an easy-to-use, reliable, routine NMR system. The ECX NMR series is available from 300 to 500 MHz. The console is designed around a modular, digital NMR electronics chassis controlled by an intelligent acquisition computer. For unprecedented flexibility, the JEOL NMR system offers a Windows XP, Mac OSX or LINUX. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world. http://purl.obolibrary.org/obo/OBI_0000627 quaternary pump system http://purl.obolibrary.org/obo/OBI_0000589 chromatography pump system A pump system that pump and mix up to four different solvents in parallel. http://purl.obolibrary.org/obo/OBI_0000628 carbon nanotube column http://purl.obolibrary.org/obo/OBI_0000038 chromatography column Carbon nanotubes (CNTs) are known to have high thermal and mechanical stability and have the potential to be high-performance separation media that utilize the nanoscale interactions. CNT can be applied in long capillary tubes for the development of gas chromatography columns. A film of CNTs can be deposited by chemical vapor deposition (CVD) to form the stationary phase in the open tubular format. Altering the CVD conditions can vary the thickness and the morphology of the CNT film, which opens the possibility of selectivity tuning. The ability to fabricate long tubes coated with CNTs can be readily employed in other gas- and liquid-phase separations as well. http://purl.obolibrary.org/obo/OBI_0000631 Varian MERCURY spectrometer http://purl.obolibrary.org/obo/OBI_0000611 Varian NMR instrument MERCURYplus spectrometers provide superior control, stability, and performance for high-productivity environments. Surface-mount electronics enable a small footprint without compromising data quality. Modular design allows flexible configuration. Direct digital synthesis, linear amplifiers, and other innovative RF and digital technologies enable push-button operation. http://purl.obolibrary.org/obo/OBI_0000632 Bruker Metabolic Profiler http://purl.obolibrary.org/obo/OBI_0000596 Bruker NMR instrument An NMR platform for conducting metabonomics studies, traditional metabolism studies, and analysis of complex mixtures, featuring an Avance NMR spectrometer and a microTOF from Bruker Daltonics. By combining the structural resolving power of NMR with mass accuracy of the microTOF Bruker offers a complete system for metabolic research. The Metabolic Profiler provides a simple, easy to use and inexpensive base-system to acquire the spectroscopic data, needed to do basic metabolic profiling including metabonomic statistical analysis. http://purl.obolibrary.org/obo/OBI_0000633 column heater http://purl.obolibrary.org/obo/OBI_0000485 chromatography instrument The glass liner can be fitted with a separate heater and the volatilization temperature can, thus, be controlled. This flash heater system is available in most chromatographs. By using a syringe with a long needle, the tip can be made to penetrate past the liner and discharge its contents directly into the column packing. This procedure is called 'on-column injection' and, as it reduces peak dispersion on injection and thus, provides higher column efficiencies, is often the preferred procedure. http://purl.obolibrary.org/obo/OBI_0000635 JEOL CapNMR probe http://purl.obolibrary.org/obo/OBI_0000529 JEOL NMR probe The JEOL ECA and ECX NMR spectrometers now support the MRM/Protasis CapNMR Probe for well plate-based and microvial-based NMR analysis. The CapNMR probe is available at proton frequencies ranging from 300 MHz to 800 MHz in both indirect configurations (e.g. 1H{13C} and 1H {31P}) and also in triple resonance configurations (e.g. 1H{13C, 15N}, 1H{31P, 15N}). Both employ a high-strength z-directed field gradient. The flowprobes come with the choice of two flowcell volumes: a 5 μl flowcell with an NMR active volume of 2.5 μl, and a 10 μl flowcell with an NMR active volume of 5 μl. The fluidic connections are 75 μm i.d. and 1/32 o.d. FEP Teflon with hastelloy unions for exceptional solvent compatibility. http://purl.obolibrary.org/obo/OBI_0000636 acquisition computer http://purl.obolibrary.org/obo/OBI_0400107 computer A Computer used for NMR, can be divided into central processing unit (CPU), consisting of instruction, interpretation and arithmetic unit plus fast access memory, and peripheral devices such as bulk data storage and input and output devices (including, via the interface, the spectrometer). Under software control, the computer controls the RF pulses and gradients necessary to acquire data, and process the data to produce spectra or images. Note that devices such as the spectrometer may themselves incorporate small computers. http://purl.obolibrary.org/obo/OBI_0000638 gas purifier http://purl.obolibrary.org/obo/OBI_0000542 gas chromatography equipment Gas purifiers are instruments used for the removal of gas impurities like hydrocarbons, oxygen, and moisture from carrier gas and fuel gases for GC or GC-MS systems. http://purl.obolibrary.org/obo/OBI_0000639 material separation objective http://purl.obolibrary.org/obo/OBI_0000456 material transformation objective is an objective to transform a material entity into spatially separated components. http://purl.obolibrary.org/obo/OBI_0000640 indirect detection probe http://purl.obolibrary.org/obo/OBI_0000516 NMR probe An NMR probe designed to allow the indirect detection of acquisition nuclei. http://purl.obolibrary.org/obo/OBI_0000641 JEOL ECA NMR spectrometer http://purl.obolibrary.org/obo/OBI_0000600 JEOL NMR instrument The ECA series of NMR spectrometers is a high performance, research grade NMR system configurable to a wide range off applications. The ECA NMR is available from 300 to 930 MHz field strengths and is 1GHz ready. The system is designed around a modular, digital NMR electronics chassis controlled from a UNIX or Windows workstation and acquisition system. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world. http://purl.obolibrary.org/obo/OBI_0000649 data set of features http://purl.obolibrary.org/obo/IAO_0000100 data set A data set that is produced as the output of a descriptive statistical calculation data transformation and consists of producing a data set that represents one or more features of interest about the input data set. http://purl.obolibrary.org/obo/OBI_0000650 differential expression analysis data transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation A differential expression analysis data transformation is a data transformation that has an objective of differential expression analysis. Frequently this data transformation involves summarizing or otherwise aggregating signals from various samples categorized into groups, and calculating measures of group differences from these aggregated signals. http://purl.obolibrary.org/obo/OBI_0000651 urine specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism a portion of urine collected from an organism http://purl.obolibrary.org/obo/OBI_0000652 material combination http://purl.obolibrary.org/obo/OBI_0000094 material processing is a material processing with the objective to combine two or more material entities as input into a single material entity as output. http://purl.obolibrary.org/obo/OBI_0000653 fuzzy clustering objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A fuzzy clustering objective is a data transformation objective where the aim is to assign input objects (typically vectors of attributes) a probability that a point belongs to a class, where the number of class and their specifications are not known a priori. http://purl.obolibrary.org/obo/OBI_0000654 device setting http://purl.obolibrary.org/obo/BFO_0000019 quality a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device http://purl.obolibrary.org/obo/OBI_0000655 blood specimen http://purl.obolibrary.org/obo/OBI_2000009 bodily fluid specimen a material entity derived from a portion of blood collected from an organism http://purl.obolibrary.org/obo/OBI_0000656 data set of predicted values according to fitted curve http://purl.obolibrary.org/obo/IAO_0000100 data set A data set which is the output of a curve fitting data transformation in which the aim is to find a curve which matches a series of data points and possibly other constraints. http://purl.obolibrary.org/obo/OBI_0000660 background corrected data set http://purl.obolibrary.org/obo/IAO_0000100 data set A data set that is produced as the output of a background correction data transformation. http://purl.obolibrary.org/obo/OBI_0000662 error corrected data set http://purl.obolibrary.org/obo/IAO_0000100 data set A data set that is produced as the output of an error correction data transformation and consists of producing a data set which has had erroneous contributions from the input to the data transformation removed (corrected for). http://purl.obolibrary.org/obo/OBI_0000664 BrdU incorporation assay http://purl.obolibrary.org/obo/OBI_0000891 cell proliferation assay A cell proliferation assay in which cells are cultured in the presence of BrdU which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle), substituting for thymidine during DNA replication, which can be quantified by BrdU specific antibodies. http://purl.obolibrary.org/obo/OBI_0000666 background correction data transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation A background correction data transformation (sometimes called supervised classification) is a data transformation that has the objective background correction. http://purl.obolibrary.org/obo/OBI_0000668 error correction data transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation An error correction data transformation is a data transformation that has the objective of error correction, where the aim is to remove (correct for) erroneous contributions from the input to the data transformation. http://purl.obolibrary.org/obo/OBI_0000669 tritiated thymidine incorporation assay http://purl.obolibrary.org/obo/OBI_0000891 cell proliferation assay A cell proliferation assay in which cells are cultured in the presence of tritiated thymidine which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle). The radioactivity of tritiated thymidine in a cell is a proxy for cells that were actively replicating. http://purl.obolibrary.org/obo/OBI_0000671 sample from organism http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism a material obtained from an organism in order to be a representative of the whole http://purl.obolibrary.org/obo/OBI_0000673 statistical hypothesis test http://purl.obolibrary.org/obo/OBI_0200000 data transformation A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test. http://purl.obolibrary.org/obo/OBI_0000676 reduced dimension data set http://purl.obolibrary.org/obo/IAO_0000100 data set A data set that is produced as the output of a data vector reduction data transformation and consists of producing a data set which has fewer vectors than the input data set. http://purl.obolibrary.org/obo/OBI_0000678 portioning objective http://purl.obolibrary.org/obo/OBI_0000639 material separation objective A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material. http://purl.obolibrary.org/obo/OBI_0000680 whole organism preparation http://purl.obolibrary.org/obo/OBI_0100051 specimen A material entity which is the output of a process in which one or more whole organisms are prepared in a way to make it easier to study them, and in which the great majority of organismal parts are maintained http://purl.obolibrary.org/obo/OBI_0000681 separation into different composition objective http://purl.obolibrary.org/obo/OBI_0000639 material separation objective A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities). http://purl.obolibrary.org/obo/OBI_0000682 obsolete_study result http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class Study result is an information content entity that is a specified data output of a study. http://purl.obolibrary.org/obo/OBI_0000684 specimen collection objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification A objective specification to obtain a material entity for potential use as an input during an investigation. http://purl.obolibrary.org/obo/OBI_0000685 creating a mixture of molecules in solution http://purl.obolibrary.org/obo/OBI_0000652 material combination is a process with the objective to prepare a liquid solution of one or more chemicals at desired concentrations. http://purl.obolibrary.org/obo/OBI_0000686 material combination objective http://purl.obolibrary.org/obo/OBI_0000456 material transformation objective is an objective to obtain an output material that contains several input materials. http://purl.obolibrary.org/obo/OBI_0000687 nucleotide overhang cloning http://purl.obolibrary.org/obo/OBI_0600064 recombinant vector cloning Nucleotide overhang cloning is the process of inserting nucleic acid into a vector using nucleotide overhangs used to prevent self ligation http://purl.obolibrary.org/obo/OBI_0000688 rodent care protocol http://purl.obolibrary.org/obo/OBI_0000715 animal care protocol A rodent care protocol is an animal protocol in which the animals being taken care of are rodents. http://purl.obolibrary.org/obo/OBI_0000690 immunoprecipitation http://purl.obolibrary.org/obo/OBI_0600014 material component separation is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity http://purl.obolibrary.org/obo/OBI_0000691 ABI 377 automated sequencer http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer is a DNA sequencer which is manufactured by Applied Biosystems corporation (formerly Perkin-Elmer). It allows automated chain termination DNA sequencing. It has part polyacrylamide gel electrophoresis system and a laser -based detection system to detect fluorescence intensity emitted by the dyes attached to the dideoxyterminator nucleotides or to the primers. http://purl.obolibrary.org/obo/OBI_0000692 recombination enzyme based cloning http://purl.obolibrary.org/obo/OBI_0600064 recombinant vector cloning a recombination enzyme based cloning is a recombinant vector cloning process that uses complementary nucleotide sequences in both the insert genetic material and the cloning vector with a recombination enzyme to directly create a recombinant vector http://purl.obolibrary.org/obo/OBI_0000694 animal feeding http://purl.obolibrary.org/obo/OBI_0000011 planned process animal feeding is a process in which animals are provided with food http://purl.obolibrary.org/obo/OBI_0000696 AB SOLiD System http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation http://purl.obolibrary.org/obo/OBI_0000699 survival assessment assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that measures the occurrence of death events in one or more organisms over time http://purl.obolibrary.org/obo/OBI_0000703 Illumina Genome Analyzer II http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer is a DNA sequence which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology http://purl.obolibrary.org/obo/OBI_0000704 decision tree induction objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. http://purl.obolibrary.org/obo/OBI_0000705 Edman degradation http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay A sequencing assay in which the amino acid sequence of input peptides or proteins is determined by iteratively cleaving of the amino-terminal (N-terminal) residue without disrupting the peptide bonds and identifying it by e.g. chromatography or electropheresis. http://purl.obolibrary.org/obo/OBI_0000706 SOLiD sequencing assay http://purl.obolibrary.org/obo/OBI_0000723 DNA sequencing by ligation assay A DNA sequencing by ligation assay that identifies sequence information using primers to hybridize to the P1 adapter sequence within the library template, fluorescently labeled di-base probes to compete for ligation to the sequencing primer, multiple cycles of ligation, detection and cleavage to determine the eventual read length, following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n-1 position for a second round of ligation cycles. http://purl.obolibrary.org/obo/OBI_0000707 decision tree building data transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation A decision tree building data transformation is a data transformation that has objective decision tree induction. http://purl.obolibrary.org/obo/OBI_0000708 laboratory animal care http://purl.obolibrary.org/obo/OBI_0000011 planned process a process that realizes an animal care protocol that specifies how animals are kept and maintained http://purl.obolibrary.org/obo/OBI_0000710 Li-Cor 4300 DNA Analysis System http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing http://purl.obolibrary.org/obo/OBI_0000712 pathogen challenge http://purl.obolibrary.org/obo/OBI_0600007 administering substance in vivo A pathogen challenge is the administration of a live pathogenic organism to a host http://purl.obolibrary.org/obo/OBI_0000713 GenePattern software http://purl.obolibrary.org/obo/IAO_0000010 software a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. http://purl.obolibrary.org/obo/OBI_0000714 graph of vertices http://purl.obolibrary.org/obo/IAO_0000038 graph A construct that consists of many nodes connected with edges. The edges represent a relationship between the objects represented by the nodes. A graph can be equivalently represented as a matrix. http://purl.obolibrary.org/obo/OBI_0000715 animal care protocol http://purl.obolibrary.org/obo/OBI_0000272 protocol An animal care protocol is a protocol which specifies the environment in which animals are being kept in captivity for research purposes http://purl.obolibrary.org/obo/OBI_0000717 HeliScope Single Molecule Sequencer http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry http://purl.obolibrary.org/obo/OBI_0000718 pathogen role http://purl.obolibrary.org/obo/BFO_0000023 role pathogen role is a role which inheres in an organism and realized in the process of disease course in the organism bearing host role caused by the organism bearing pathogen role http://purl.obolibrary.org/obo/OBI_0000719 vaccine preparation http://purl.obolibrary.org/obo/OBI_0000094 material processing vaccine preparation is a planned process with specified output a vaccine http://purl.obolibrary.org/obo/OBI_0000720 immunologic adjuvant role http://purl.obolibrary.org/obo/OBI_1110092 adjuvant role The role a material entity plays when it is co-administered with an immunogen in order to enhance the immune response to the immunogen. http://purl.obolibrary.org/obo/OBI_0000721 glucose tolerance test http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that measures glucose clearance from blood over time by repeated glucose measurement in blood serum or plasma after the administration of a glucose bolus in-vivo. This assay can be used to evaluate the severity of insulin resistance or the efficiency of glucose clearance. http://purl.obolibrary.org/obo/OBI_0000723 DNA sequencing by ligation assay http://purl.obolibrary.org/obo/OBI_0000626 DNA sequencing assay A DNA sequencing assay that performs chain extension during the sequencing reaction step using DNA ligase http://purl.obolibrary.org/obo/OBI_0000725 host role http://purl.obolibrary.org/obo/BFO_0000023 role host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role http://purl.obolibrary.org/obo/OBI_0000726 peak matching http://purl.obolibrary.org/obo/OBI_0200000 data transformation Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold http://purl.obolibrary.org/obo/OBI_0000728 rodent care http://purl.obolibrary.org/obo/OBI_0000708 laboratory animal care rodent care is the process by which rodents are being provided with a controlled living environment while kept in captivity for the purpose of research. http://purl.obolibrary.org/obo/OBI_0000729 cloning plasmid http://purl.obolibrary.org/obo/OBI_0000737 cloning vector A cloning plasmid is a plasmid that was engineered to contain a bacterial origin of replication, encodes for a selectable gene product and contains a cloning site. http://purl.obolibrary.org/obo/OBI_0000730 pyrosequencing assay http://purl.obolibrary.org/obo/OBI_0000734 DNA sequencing by synthesis assay A DNA sequencing by synthesis assay which sequences a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. The template DNA is immobilized, and solutions of A, C, G, and T nucleotides are added and removed after the reaction, sequentially. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions which produce chemiluminescent signals allows the determination of the sequence of the template. ssDNA template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase, ATP sulfurylase, luciferase and apyrase, and with the substrates adenosine 5-prime phosphosulfate (APS) and luciferin. http://purl.obolibrary.org/obo/OBI_0000731 recombinant vector http://purl.obolibrary.org/obo/OBI_0000047 processed material A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector. http://purl.obolibrary.org/obo/OBI_0000732 restriction enzyme http://purl.obolibrary.org/obo/PR_000000001 protein an enzyme that has a specific target cleavage sites within nucleic acids http://purl.obolibrary.org/obo/OBI_0000734 DNA sequencing by synthesis assay http://purl.obolibrary.org/obo/OBI_0000626 DNA sequencing assay A DNA sequencing assay that relies on DNA polymerase activity to perform chain extension during the sequencing reaction step. http://purl.obolibrary.org/obo/OBI_0000735 NTP-2000 http://purl.obolibrary.org/obo/OBI_0000047 processed material a material consisting of 14.5% protein, 8.5% fat and 9.5% fiber produced to feed rodents http://purl.obolibrary.org/obo/OBI_0000737 cloning vector http://purl.obolibrary.org/obo/OBI_1110108 material to be added A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site. http://purl.obolibrary.org/obo/OBI_0000738 restriction enzyme based cloning http://purl.obolibrary.org/obo/OBI_0600064 recombinant vector cloning restriction enzyme based cloning is a recombinant vector cloning process that has as an input genetic material that was cleaved with restriction enzymes, and a cloning vector that was cleaved with complementary restriction enzymes. It uses ligase to chemically join the input genetic material and the cloning vector to create a recombinant vector. http://purl.obolibrary.org/obo/OBI_0000739 Student's t-test http://purl.obolibrary.org/obo/OBI_0000673 statistical hypothesis test Studen't t-test is a data transformation with the objective of a statistical hypothesis test in which the test statistic has a Student's t distribution if the null hypothesis is true. It is applied when the population is assumed to be normally distributed but the sample sizes are small enough that the statistic on which inference is based is not normally distributed because it relies on an uncertain estimate of standard deviation rather than on a precisely known value. http://purl.obolibrary.org/obo/OBI_0000740 material sample role http://purl.obolibrary.org/obo/OBI_0000112 specimen role A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. http://purl.obolibrary.org/obo/OBI_0000741 topologically preserved clustered data set http://purl.obolibrary.org/obo/OBI_0000648 clustered data set A clustered data set in which the topology, i.e. the spatial properties between data points, is preserved from the original input data from which it was derived. http://purl.obolibrary.org/obo/OBI_0000742 nucleic acid restriction enzyme digest http://purl.obolibrary.org/obo/CHEBI_33696 nucleic acid A nucleic acid digest is a material that is the output of a process in which nucleic acids are combined with a restriction enzyme resulting in digested fragments with defined ends based on the enzymes cleavage site http://purl.obolibrary.org/obo/OBI_0000743 immune response assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that determines information about an immune response http://purl.obolibrary.org/obo/OBI_0000748 bisulfite sequencing assay http://purl.obolibrary.org/obo/OBI_0000634 DNA methylation profiling assay A DNA methylation profiling assay which determines the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location. http://purl.obolibrary.org/obo/OBI_0000784 anticoagulant-containing test tube http://purl.obolibrary.org/obo/OBI_0000836 test tube A 'blue top' test tube that contains anticoagulant for storing blood specimens' http://purl.obolibrary.org/obo/OBI_0000788 fluorescently labeled MHC multimer http://purl.obolibrary.org/obo/OBI_0001936 molecular-labeled material A complex of two or more linked MHC molecules including a fluorescent label that can be loaded with a ligand, and is used in flow cytometry assay to bind to T cell receptors of T cells specific for the ligand http://purl.obolibrary.org/obo/OBI_0000789 survival rate http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement data that represents the percentage of people or animals in a study or treatment group who are alive for a given period of time after diagnosis or initiation of monitoring. http://purl.obolibrary.org/obo/OBI_0000790 recombinant BAC cloning http://purl.obolibrary.org/obo/OBI_0600064 recombinant vector cloning Recombinant BAC cloning is a process with the objective to insert genetic material into an F plasmid based bacterial artificial chromosome for future replication of the inserted material http://purl.obolibrary.org/obo/OBI_0000792 statistical model validation http://purl.obolibrary.org/obo/OBI_0200171 partitioning data transformation A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. http://purl.obolibrary.org/obo/OBI_0000793 double blind study execution http://purl.obolibrary.org/obo/OBI_0000822 single blind study execution A double blind study execution is defined as any study execution in which neither the subjects nor the investigators are informed of which study arm the subjects are part of during the portion of the trial when the subjects are being treated http://purl.obolibrary.org/obo/OBI_0000797 obsolete_primary structure of protein http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class The primary structure of a protein that is completely defined by the set of its amino acid residue parts and the linear order induced by the peptide bonds that hold them together http://purl.obolibrary.org/obo/OBI_0000798 capsule shell http://purl.obolibrary.org/obo/BFO_0000040 material entity a small rounded gelatinous container http://purl.obolibrary.org/obo/OBI_0000799 recombinant phage cloning http://purl.obolibrary.org/obo/OBI_0600064 recombinant vector cloning Recombinant phage cloning is the process of using a phage plus some insert nucleic acid for the purposes of amplification of the insert material achieved by phage assembly in vitro. http://purl.obolibrary.org/obo/OBI_0000800 cross linking http://purl.obolibrary.org/obo/OBI_0000094 material processing A process in which bonds are created that link one polymer to another http://purl.obolibrary.org/obo/OBI_0000802 prothrombin time assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that measures the prothrombin ratio, which is the prothrombin time for a patient, divided by the result for control plasma. Most commonly the test is preformed using blood plasma. Blood is drawn into a test tube containing liquid citrate, which acts as an anticoagulant. An excess of calcium is added to enable the blood to clot again.Tissue factor (also known as factor III or thromboplastin) is added, and the time the sample takes to clot is measured optically as the prothrombin time, which is compared to a control sample. http://purl.obolibrary.org/obo/OBI_0000803 denaturing http://purl.obolibrary.org/obo/OBI_0000094 material processing Is a process in which the tertiary or secondary structure of a polymer is disrupted http://purl.obolibrary.org/obo/OBI_0000804 informing investigator of subject study arm http://purl.obolibrary.org/obo/OBI_0000011 planned process A process in which an investigator is made aware of which study arm that a patient is participating in, for example whether they are receiving a placebo or a treatment with an investigational compound. http://purl.obolibrary.org/obo/OBI_0000806 material maintenance objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification An objective specification maintains some or all of the qualities of a material over time. http://purl.obolibrary.org/obo/OBI_0000808 spectrolyse heparin antifactor-Xa assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that quantitatively measures heparin in human plasma using Factor Xa and Antithrombin III in excess, where the rate of Factor Xa inhibition is directly proportional to the heparin concentration. The residual Factor Xa activity, measured with a Factor Xa-specific chromogenic substrate, is inversely proportional to the heparin concentration. http://purl.obolibrary.org/obo/OBI_0000809 amplified DNA http://purl.obolibrary.org/obo/CHEBI_16991 deoxyribonucleic acid DNA that has been produced in an enzymatic amplification process http://purl.obolibrary.org/obo/OBI_0000810 informed consent process http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate. http://purl.obolibrary.org/obo/OBI_0000811 primary structure of DNA macromolecule http://purl.obolibrary.org/obo/SO_0000001 region a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues. http://purl.obolibrary.org/obo/OBI_0000812 measuring neural activity in the caudate nucleus assay http://purl.obolibrary.org/obo/OBI_0000454 extracellular electrophysiology recording assay An assay that measures neural activity in the caudate nucleus http://purl.obolibrary.org/obo/OBI_0000813 to be treated with active ingredient role http://purl.obolibrary.org/obo/OBI_0000097 participant under investigation role A study subject role which begins to exist when a subject is assigned to be one of those who will receive active ingredient, and is realized in a study execution in which they receive the active ingredient http://purl.obolibrary.org/obo/OBI_0000814 guar gum http://purl.obolibrary.org/obo/BFO_0000040 material entity Guar gum, also called guaran, is a galactomannan. It is primarily the ground endosperm of guar beans. The guar seeds are dehusked, milled and screened to obtain the guar gum.[1] It is typically produced as a free flowing, pale, off-white colored, coarse to fine ground powder. http://purl.obolibrary.org/obo/OBI_0000815 Berichrom(r) Antithrombin III (A) Kit http://purl.obolibrary.org/obo/OBI_0000047 processed material For the chromogenic determination of antithrombin III. Autoanalyzer method for undiluted samples. For the quantitative chromogenic determination of the functional activity of antithrombin III in plasma on autoanalyzers for the diagnosis of diminished AT III synthesis, increased consumption, and for monitoring substitution therapy. Berichrom(r) Antithrombin III (A) is used for the rapid determination of the physiologically active antithrombin III and permits the diagnosis of congenital and acquired antithrombin III deficiency, a condition frequently associated with an increased risk of thrombosis. Acquired antithrombin III deficiencies frequently occur due to consumption following major operations or due to disseminated intravascular coagulation (DIC) in cases of septicaemia, nephroses, liver parenchymal damage (hepatitis, drug intoxication, alcoholism) and estrogen-containing contraceptives. The test permits early detection of patients at increased risk for thrombosis. Kit contains: 6 x for 5.0 mL Thrombin (bovine), 3 x for 3.0 mL Substrate Reagent, 1 x 30.0 mL Buffer Solution http://purl.obolibrary.org/obo/OBI_0000817 fucoidan http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity Fucoidan is a sulfated polysaccharide (MW: average 20,000) found mainly in various species of brown seaweed such as kombu, limu moui,bladderwrack, wakame, mozuku, and hijiki (variant forms of fucoidan have also been found in animal species, including the sea cucumber). http://purl.obolibrary.org/obo/OBI_0000818 calibration http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process with the objective to establish the relationship between data produced by a measurement device and physical qualities. This is done by using the measurement device under defined conditions, and either tuning it to adjust the measured output, or record the output and use it as a reference in future measurements. http://purl.obolibrary.org/obo/OBI_0000819 anticoagulant tube storage of blood specimen http://purl.obolibrary.org/obo/OBI_0302893 storage Storage of a blood specimen in a tube with anticoagulant http://purl.obolibrary.org/obo/OBI_0000821 filled capsule http://purl.obolibrary.org/obo/OBI_0000827 pill A pill in the form of a small rounded gelatinous container with medicine inside. http://purl.obolibrary.org/obo/OBI_0000822 single blind study execution http://purl.obolibrary.org/obo/OBI_0000826 treatment portion of study execution A single blind study execution is defined as any study execution in which the subjects are not informed of which study arm they are part of during the portion of the trial when the subjects are being treated http://purl.obolibrary.org/obo/OBI_0000823 thrombin time assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that measures the time between the addition of the thrombin and the clot formation in plasma. http://purl.obolibrary.org/obo/OBI_0000824 recombinant YAC cloning http://purl.obolibrary.org/obo/OBI_0600064 recombinant vector cloning Recombinant YAC cloning is a process with the objective to insert genetic material into a yeast artificial chromosome vector for future replication of the inserted material http://purl.obolibrary.org/obo/OBI_0000825 to be treated with placebo role http://purl.obolibrary.org/obo/OBI_0000097 participant under investigation role A study subject role which begins to exist when a subject is assigned to be one of those who will receive a placebo, and realized in a study execution in which they receive the placebo http://purl.obolibrary.org/obo/OBI_0000826 treatment portion of study execution http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process, part of a study design execution, during which the treatment of subjects is ongoing http://purl.obolibrary.org/obo/OBI_0000827 pill http://purl.obolibrary.org/obo/OBI_0000047 processed material A dose of medicine or placebo in the form of a small pellet. http://purl.obolibrary.org/obo/OBI_0000828 research organization http://purl.obolibrary.org/obo/OBI_0000245 organization An organization formed with a goal to have its members conduct investigations http://purl.obolibrary.org/obo/OBI_0000830 obsolete_primary structure of sequence macromolecule http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class A quality inhering in a molecule that is completely defined by the linear sequence of a set of residues which are connected by directional, linear bonds http://purl.obolibrary.org/obo/OBI_0000831 DNA residue methylation http://purl.obolibrary.org/obo/PATO_0001241 physical object quality a quality of a DNA residue that has a methyl group attached to it http://purl.obolibrary.org/obo/OBI_0000832 measurement device http://purl.obolibrary.org/obo/OBI_0000968 device A device in which a measure function inheres. http://purl.obolibrary.org/obo/OBI_0000834 high molecular weight DNA extract http://purl.obolibrary.org/obo/OBI_0001051 DNA extract The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas. http://purl.obolibrary.org/obo/OBI_0000835 manufacturer http://purl.obolibrary.org/obo/BFO_0000040 material entity A person or organization that has a manufacturer role http://purl.obolibrary.org/obo/OBI_0000837 oral ingestion of pill http://purl.obolibrary.org/obo/OBI_0000952 oral administration An adding a material entity to target with the entity is a pill and the target is the mouth http://purl.obolibrary.org/obo/OBI_0000838 material maintenance http://purl.obolibrary.org/obo/OBI_0000011 planned process a process with that achieves the objective to maintain some or all of the characteristics of an input material over time http://purl.obolibrary.org/obo/OBI_0000839 labeled oligonucleotide http://purl.obolibrary.org/obo/OBI_0001936 molecular-labeled material a labeled oligonucleotide is a short nucleic acid which underwent a labeling process resulting in a radioactive isotope such as P32 or P33 added to its backbone for instance by end labeling with polynucleotide kinase which added radiolabeled ATP to the 5' end of oligonucleotide http://purl.obolibrary.org/obo/OBI_0000840 unblinding process http://purl.obolibrary.org/obo/OBI_0000011 planned process The part of the study execution in which the subjects are told what study arm they are in and in which the investigators are told which subjects are in which trials http://purl.obolibrary.org/obo/OBI_0000841 subject agrees they understand informed consent document http://purl.obolibrary.org/obo/OBI_0000011 planned process A process in which a subject receives an informed consent document and agrees that they have understood it http://purl.obolibrary.org/obo/OBI_0000842 informing subject of study arm http://purl.obolibrary.org/obo/OBI_0000011 planned process A process in which the subject is made aware of which study arm they are participating in, for example whether they are receiving a placebo or a treatment with an investigational compound. http://purl.obolibrary.org/obo/OBI_0000843 Sysmex CA-6000 Coagulation Analyzer http://purl.obolibrary.org/obo/OBI_0000832 measurement device The Sysmex CA-6000 automated coagulation analyzer is a random access instrument that is capable of performing 20 clot-based and chromogenic assays http://purl.obolibrary.org/obo/OBI_0000844 hospital http://purl.obolibrary.org/obo/OBI_0000245 organization A medical organization at which sick or injured people are given clinical care http://purl.obolibrary.org/obo/OBI_0000845 primary structure of RNA molecule http://purl.obolibrary.org/obo/SO_0000001 region The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together http://purl.obolibrary.org/obo/OBI_0000847 test substance role http://purl.obolibrary.org/obo/BFO_0000023 role A role born by a material entity and realized in a process where the substance is used as specified as the independent variable for an investigation http://purl.obolibrary.org/obo/OBI_0000848 polyA RNA extraction http://purl.obolibrary.org/obo/OBI_0666666 RNA extraction A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA. http://purl.obolibrary.org/obo/OBI_0000849 organellar RNA extraction http://purl.obolibrary.org/obo/OBI_0666666 RNA extraction A RNA extraction process in which the desired output material is RNA in the organelle(s). http://purl.obolibrary.org/obo/OBI_0000852 record of missing knowledge http://purl.obolibrary.org/obo/IAO_0000030 information content entity a information content entity created to indicate that information about something is not available to the person recording it. http://purl.obolibrary.org/obo/OBI_0000854 western blot analysis http://purl.obolibrary.org/obo/OBI_0001978 immunoblot assay An analyte assay that detects specific peptides in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules. http://purl.obolibrary.org/obo/OBI_0000855 total RNA extraction http://purl.obolibrary.org/obo/OBI_0666666 RNA extraction A RNA extraction process in which total cellular and organelle RNA are extracted. http://purl.obolibrary.org/obo/OBI_0000856 obsolete intracellular material detection by flow cytometry assay http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class An assay in which the presence of a material inside a cell is measured by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer. http://purl.obolibrary.org/obo/OBI_0000857 complementary nucleotide probe role http://purl.obolibrary.org/obo/BFO_0000023 role A role played by a nucleic acid molecule that is used in a planned process for its ability to bind a nucleic acid molecules with complementary nucleotide sequence http://purl.obolibrary.org/obo/OBI_0000858 record of unknown sex http://purl.obolibrary.org/obo/OBI_0000852 record of missing knowledge a record indicating that the biological sex of an organism is not known. http://purl.obolibrary.org/obo/OBI_0000859 cytoplasmic RNA extraction http://purl.obolibrary.org/obo/OBI_0666666 RNA extraction A RNA extraction process in which the desired output material is RNA in the cytoplasm. http://purl.obolibrary.org/obo/OBI_0000861 Likelihood-ratio test http://purl.obolibrary.org/obo/OBI_0200000 data transformation Likelihood-ratio is a data transformation which tests whether there is evidence of the need to move from a simple model to a more complicated one (where the simple model is nested within the complicated one); tests of the goodness-of-fit between two models. http://purl.obolibrary.org/obo/OBI_0000862 nuclear RNA extract http://purl.obolibrary.org/obo/OBI_0000880 RNA extract A RNA extract that is the output of an extraction process in which RNA molecules found in the nucleus, including mRNA precursors (pre-mRNA), are extracted. http://purl.obolibrary.org/obo/OBI_0000867 establishing cancer cell line http://purl.obolibrary.org/obo/OBI_0001867 establishing cell line is a planned process in which the objective is to generate a cell line from a natural population of cancer cells which are already immortal http://purl.obolibrary.org/obo/OBI_0000868 pattern matching objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A pattern matching objective aims to detect the presence of the constituents of a given pattern. In contrast to pattern recognition, the pattern is rigidly specified. Patterns are typicall sequences or trees. http://purl.obolibrary.org/obo/OBI_0000869 polyA RNA extract http://purl.obolibrary.org/obo/OBI_0000880 RNA extract A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3' end are purified. http://purl.obolibrary.org/obo/OBI_0000870 single-nucleotide-resolution nucleic acid structure mapping assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that provides information about the secondary structure of nucleic acids using chemical or enzymatic probing to establish the extent of base-pairing or solvent accessiblity. http://purl.obolibrary.org/obo/OBI_0000873 pre-mortem specimen http://purl.obolibrary.org/obo/OBI_0001506 specimen with pre- or post-mortem status a specimen that was taken from a live organism http://purl.obolibrary.org/obo/OBI_0000874 detection of specific nucleic acid polymers with complementary probes http://purl.obolibrary.org/obo/OBI_0000443 analyte assay An analyte assay in which a specified input material (the evaluant) is examined for the presence or quantity of specified nucleic acid polymers, which are identified based on the use of complementary nucleic acid probes. http://purl.obolibrary.org/obo/OBI_0000876 cytoplasmic RNA extract http://purl.obolibrary.org/obo/OBI_0000880 RNA extract A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted. http://purl.obolibrary.org/obo/OBI_0000879 random primed DNA labeling http://purl.obolibrary.org/obo/OBI_0600038 addition of molecular label a labeling in which random primers are used to uniformly label input DNA http://purl.obolibrary.org/obo/OBI_0000880 RNA extract http://purl.obolibrary.org/obo/OBI_0001010 nucleic acid extract an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen. http://purl.obolibrary.org/obo/OBI_0000882 cell-cell killing assay http://purl.obolibrary.org/obo/OBI_0001977 cytometry assay A cytometry assay that monitors a cell population to track how many are killed by other cells. http://purl.obolibrary.org/obo/OBI_0000883 in vivo cell killing assay http://purl.obolibrary.org/obo/OBI_0000882 cell-cell killing assay A cell killing assay that measures if and how many target cells are killed within an organism. http://purl.obolibrary.org/obo/OBI_0000885 secondary structure of sequence macromolecule http://purl.obolibrary.org/obo/PATO_0001241 physical object quality A quality inhering in a molecule that refers to general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids (DNA/RNA). It does not, however, describe specific atomic positions in three-dimensional space, which are considered to be tertiary structure. Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 Lane medical lectures at Stanford. http://purl.obolibrary.org/obo/OBI_0000888 nuclear RNA extraction http://purl.obolibrary.org/obo/OBI_0666666 RNA extraction A RNA extraction process in which the desired output material is RNA in the nucleus. http://purl.obolibrary.org/obo/OBI_0000889 survival curve http://purl.obolibrary.org/obo/IAO_0000573 line graph A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time. http://purl.obolibrary.org/obo/OBI_0000891 cell proliferation assay http://purl.obolibrary.org/obo/OBI_0001977 cytometry assay A cytometry assay which measures the degreee to which input cells are replicating. http://purl.obolibrary.org/obo/OBI_0000894 protein extract http://purl.obolibrary.org/obo/OBI_0000423 extract a protein extract is the output of an extraction process from tissues or cell cultures resulting in a solution of cellular and/or organellar proteins in buffer solution used to prevent degradation, http://purl.obolibrary.org/obo/OBI_0000895 total RNA extract http://purl.obolibrary.org/obo/OBI_0000880 RNA extract A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen. http://purl.obolibrary.org/obo/OBI_0000896 secondary structure of RNA molecule http://purl.obolibrary.org/obo/OBI_0000885 secondary structure of sequence macromolecule http://purl.obolibrary.org/obo/OBI_0000897 DEPC structure mapping assay http://purl.obolibrary.org/obo/OBI_0001017 single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing A single-nucleotide-resolution nucleic acid structure mapping assay which determines nucleic acid secondary structure at a nucleotide resolution scale using DEPC as reagent and chemical probe http://purl.obolibrary.org/obo/OBI_0000899 organellar RNA extract http://purl.obolibrary.org/obo/OBI_0000880 RNA extract A RNA extract that is the output of an extraction process in which RNA molecules found in an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus, are extracted. http://purl.obolibrary.org/obo/OBI_0000902 post mortem specimen http://purl.obolibrary.org/obo/OBI_0001506 specimen with pre- or post-mortem status a specimen that was taken from a dead organism http://purl.obolibrary.org/obo/OBI_0000903 in vitro cell killing assay http://purl.obolibrary.org/obo/OBI_0000882 cell-cell killing assay A cell killing assay that measures if and how many target cells are actively killed by other cells in a cell culture. http://purl.obolibrary.org/obo/OBI_0000904 reporter cell line analyte detection bioassay http://purl.obolibrary.org/obo/OBI_0000443 analyte assay An analyte assay in which a cell line whose growth is known to be affected by the presence of a specific type of material (the anlyte) is cultured in the presence of an input material (the evaluant) in order to detect presence of the analyte in the evaluant. http://purl.obolibrary.org/obo/OBI_0000905 sequence feature annotation http://purl.obolibrary.org/obo/IAO_0000030 information content entity Information about a sequence region http://purl.obolibrary.org/obo/OBI_0000907 supplying http://purl.obolibrary.org/obo/OBI_0000011 planned process The planned process of providing material entities to be used in an investigation. http://purl.obolibrary.org/obo/OBI_0000908 labeled DNA extract http://purl.obolibrary.org/obo/OBI_0001143 labeled nucleic acid extract a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments. http://purl.obolibrary.org/obo/OBI_0000909 cloacal specimen http://purl.obolibrary.org/obo/OBI_0100051 specimen A specimen obtained by inserting a swab deeply into the vent of the cloaca of an organism and vigorously swabbing the wall. The swab should be deeply stained with fecal material and is then placed in transport medium. http://purl.obolibrary.org/obo/OBI_0000910 radio immuno assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay in which a radioactive labeled antigen or antibody is used to determine the interaction between an antigen and its receptor. This can be used to detect the presence of an antigen of interest in an input sample or determine the specificity of an input antibody. http://purl.obolibrary.org/obo/OBI_0000912 X-ray crystallography assay http://purl.obolibrary.org/obo/OBI_0600045 3D structure determination assay A 3D structure determination assay in which the diffraction of pattern of X-ray beams in a crystal of purified material entities is used to resolve the 3-dimensional structure of the material entity of interest. http://purl.obolibrary.org/obo/OBI_0000913 promoter activity detection by reporter gene assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay in which the activity of a promoter in a cell is monitored by using a reporter gene that was inserted in a genomic location under control of the promoter and whose expression can be easily detected based on qualities or functions of the gene. http://purl.obolibrary.org/obo/OBI_0000914 nasopharyngeal aspirate specimen http://purl.obolibrary.org/obo/OBI_0100051 specimen A speciemn which derives from nasopharyngeal mucosa after aspiration. http://purl.obolibrary.org/obo/OBI_0000915 freezing storage http://purl.obolibrary.org/obo/OBI_0302893 storage A storage process in temperature that maintenance the frozen status of the stored entities. http://purl.obolibrary.org/obo/OBI_0000916 flow cytometry assay http://purl.obolibrary.org/obo/OBI_0001977 cytometry assay A cytometry assay in which an input cell population is put in solution, is passed by a laser, and optical sensors are used to detect scattering of the laser light and/or fluorescence of specific markers to count and characterize the particles in solution. http://purl.obolibrary.org/obo/OBI_0000917 nasal swab specimen http://purl.obolibrary.org/obo/OBI_0002599 swab specimen A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of exudate and epithelial debris for microbiological or cellular examination. http://purl.obolibrary.org/obo/OBI_0000921 labeled RNA extract http://purl.obolibrary.org/obo/OBI_0001143 labeled nucleic acid extract a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments. http://purl.obolibrary.org/obo/OBI_0000922 frozen specimen http://purl.obolibrary.org/obo/OBI_0001472 specimen with known storage state A specimen that has been frozen in order to store it. http://purl.obolibrary.org/obo/OBI_0000923 surface plasmon resonance binding assay http://purl.obolibrary.org/obo/OBI_0001146 binding assay A binding assay that uses the detection of electromagnetic waves in a surface to detect material entities adsorbed to the surface, which change the local optical index of refraction. http://purl.obolibrary.org/obo/OBI_0000924 labeled specimen http://purl.obolibrary.org/obo/OBI_0001936 molecular-labeled material A specimen that has been modified in order to be able to detect it in future experiments http://purl.obolibrary.org/obo/OBI_0000925 infectious agent http://purl.obolibrary.org/obo/OBI_0100026 organism is a material entity bearing the disposition to infect an organism http://purl.obolibrary.org/obo/OBI_0000927 lyophilization storage http://purl.obolibrary.org/obo/OBI_0302893 storage a storage process with input material entity and output freeze dried material for long time storage http://purl.obolibrary.org/obo/OBI_0000928 material combination function http://purl.obolibrary.org/obo/BFO_0000034 function A material separation function is a function that decreases the resolution between two or more material entities. http://purl.obolibrary.org/obo/OBI_0000929 obsolete_training service provider role http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class a service provider role which is realized by a servicer provider organization performing some training http://purl.obolibrary.org/obo/OBI_0000931 study intervention http://purl.obolibrary.org/obo/OBI_0000011 planned process the part of the execution of an intervention design study which is varied between two or more subjects in the study http://purl.obolibrary.org/obo/OBI_0000932 material separation device http://purl.obolibrary.org/obo/OBI_0000968 device A device with a separation function realized in a planed process http://purl.obolibrary.org/obo/OBI_0000934 intramuscular injection http://purl.obolibrary.org/obo/OBI_0600007 administering substance in vivo is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe http://purl.obolibrary.org/obo/OBI_0000935 micromanipulator http://purl.obolibrary.org/obo/OBI_0000968 device A device that is used to physically interact with a sample under a microscope, where a level of precision of movement is necessary that cannot be achieved by the unaided human hand. http://purl.obolibrary.org/obo/OBI_0000936 obsolete_material access provider role http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class a service provider role which is realized by a servicer provider organization performing access to some material http://purl.obolibrary.org/obo/OBI_0000939 training process http://purl.obolibrary.org/obo/OBI_0000011 planned process a process that achieves a training objective http://purl.obolibrary.org/obo/OBI_0000940 optical microscope http://purl.obolibrary.org/obo/OBI_0400169 microscope A microscope that produces an image of an object by targeting it with an electro-magnetic beam in the visible frequency range http://purl.obolibrary.org/obo/OBI_0000941 service consumer role http://purl.obolibrary.org/obo/BFO_0000023 role a role which inheres in a person who uses a service http://purl.obolibrary.org/obo/OBI_0000942 intradermal injection http://purl.obolibrary.org/obo/OBI_0600007 administering substance in vivo is the injection of a material entity (bearing the administered substance role) into the dermis (bearing the target role) of an organism using a syringe http://purl.obolibrary.org/obo/OBI_0000943 chemical cleavage http://purl.obolibrary.org/obo/OBI_0000094 material processing chemical cleavage is a protocol application relying on a chemical compound to cause the fragmentation of an input material that is susceptible to that chemical agent http://purl.obolibrary.org/obo/OBI_0000945 vibration isolation table http://purl.obolibrary.org/obo/OBI_0001034 environmental control device A device that supports another device such as a precision instrument by isolating it from vibration that is transmitted from the floor. http://purl.obolibrary.org/obo/OBI_0000946 sterilization function http://purl.obolibrary.org/obo/BFO_0000034 function a function to remove viable organisms from an input material http://purl.obolibrary.org/obo/OBI_0000947 service provider role http://purl.obolibrary.org/obo/BFO_0000023 role is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person http://purl.obolibrary.org/obo/OBI_0000948 oscilloscope http://purl.obolibrary.org/obo/OBI_0000832 measurement device A device that measures and displayes signal voltages, usually as a two-dimensional graph of one or more electrical potential differences (vertical axis) plotted as a function of time or of some other voltage (horizontal axis). http://purl.obolibrary.org/obo/OBI_0000949 accessed material role http://purl.obolibrary.org/obo/BFO_0000023 role is realized in a planned process where the bearer participates http://purl.obolibrary.org/obo/OBI_0000950 paraffin specimen http://purl.obolibrary.org/obo/OBI_0001472 specimen with known storage state a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin http://purl.obolibrary.org/obo/OBI_0000951 compound treatment design http://purl.obolibrary.org/obo/OBI_0000115 intervention design an intervention design in which the treatment is the administration of a compound http://purl.obolibrary.org/obo/OBI_0000952 oral administration http://purl.obolibrary.org/obo/OBI_0600007 administering substance in vivo An administering substance in vivo into the mouth of an organism http://purl.obolibrary.org/obo/OBI_0000953 processed specimen http://purl.obolibrary.org/obo/OBI_0100051 specimen A specimen that has been intentionally physically modified. http://purl.obolibrary.org/obo/OBI_0000954 subcutaneous injection http://purl.obolibrary.org/obo/OBI_0600007 administering substance in vivo is the injection of a material entity (bearing the administered substance role) into the hypodermis (bearing the target role) of an organism using a syringe http://purl.obolibrary.org/obo/OBI_0000955 electrode puller http://purl.obolibrary.org/obo/OBI_0000968 device A device used in the first step in making electrodes, that applies constant tension on a glass capillary tube and eventually breaks it while heating it; this produces a very fine point on the capillary tube. http://purl.obolibrary.org/obo/OBI_0000957 self reported handedness assessment http://purl.obolibrary.org/obo/OBI_0000944 handedness assay An assay where a person makes a statement that indicates what handedness he has from a choice of different categories. http://purl.obolibrary.org/obo/OBI_0000959 vibrotome http://purl.obolibrary.org/obo/OBI_0000932 material separation device A preparation device that uses a vibrating razor blade to cut through tissue. http://purl.obolibrary.org/obo/OBI_0000960 reagent application function http://purl.obolibrary.org/obo/BFO_0000034 function A function that is realized when a reagent is automatically added to some research material. http://purl.obolibrary.org/obo/OBI_0000961 addition of molecular tracer function http://purl.obolibrary.org/obo/OBI_0000960 reagent application function A reagent application function that is realized when a molecular tracer, such as an antibody or probe is automatically transferred to a biological specimen. http://purl.obolibrary.org/obo/OBI_0000962 training objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification An objective specification which is fulfilled by the provision of some training. http://purl.obolibrary.org/obo/OBI_0000963 categorical label http://purl.obolibrary.org/obo/IAO_0000009 datum label A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. http://purl.obolibrary.org/obo/OBI_0000964 in live cell assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay in which a measurement is made by observing entities located in a live cell. http://purl.obolibrary.org/obo/OBI_0000965 lyophilized specimen http://purl.obolibrary.org/obo/OBI_0001472 specimen with known storage state a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage. http://purl.obolibrary.org/obo/OBI_0000967 container http://purl.obolibrary.org/obo/OBI_0000968 device A device that can be used to restrict the location of material entities over time http://purl.obolibrary.org/obo/OBI_0000971 fresh specimen http://purl.obolibrary.org/obo/OBI_0001472 specimen with known storage state a specimen that is output of a specimen creation process used for an investigation without storage. http://purl.obolibrary.org/obo/OBI_0000972 obsolete_electrically powered device http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class a processed material created to have a function and which requires electrical power to execute http://purl.obolibrary.org/obo/OBI_0000973 sequence data http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. http://purl.obolibrary.org/obo/OBI_0000975 cell-cell binding detection by flow cytometry assay http://purl.obolibrary.org/obo/OBI_0001977 cytometry assay A binding assay which uses a flow cytometer to detect pairs of cells that are bound to each other by staining them with different fluorescent labels. http://purl.obolibrary.org/obo/OBI_0000976 handedness categorical measurement datum http://purl.obolibrary.org/obo/OBI_0000938 categorical measurement datum A datum used to record the answer to a self assessment of whether a person uses their left hand, right hand primarily or each hand equally http://purl.obolibrary.org/obo/OBI_0000977 paraffin storage http://purl.obolibrary.org/obo/OBI_0302893 storage a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage http://purl.obolibrary.org/obo/OBI_0000978 in container assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay in which a measurement is made by observing entities located in a container. http://purl.obolibrary.org/obo/OBI_0000980 obsolete_protocol service provider role http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class a service provider role which is realized by a servicer provider organization performing a protocol execution http://purl.obolibrary.org/obo/OBI_0000981 agar stab specimen http://purl.obolibrary.org/obo/OBI_0001472 specimen with known storage state a specimen that is output of a process that cell culture inoculated into agar for long term storage. http://purl.obolibrary.org/obo/OBI_0000983 intranasal mucosal administration http://purl.obolibrary.org/obo/OBI_0600007 administering substance in vivo The administration of a substance into the intranasal mucosis of an organism http://purl.obolibrary.org/obo/OBI_0000984 dose http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses. http://purl.obolibrary.org/obo/OBI_0000985 growth condition intervention design http://purl.obolibrary.org/obo/OBI_0000115 intervention design A study design in which the independent variable is the environmental condition in which the specimen is growing http://purl.obolibrary.org/obo/OBI_0000986 obsolete_DNA sequencing training service http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class A training process with the objective to provide a trainee with the skill to run DNA sequencing experiments http://purl.obolibrary.org/obo/OBI_0000988 performing a diagnosis http://purl.obolibrary.org/obo/OBI_0200000 data transformation The interpretation of the information available about bodily features (clinical picture) of a patient resulting in a diagnosis http://purl.obolibrary.org/obo/OBI_0000989 PCR instrument http://purl.obolibrary.org/obo/OBI_0400116 thermal cycler A device that is used to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence. http://purl.obolibrary.org/obo/OBI_0000990 electron microscope http://purl.obolibrary.org/obo/OBI_0400169 microscope A microscope that produces an image of an object by targeting it with an electron beam http://purl.obolibrary.org/obo/OBI_0000991 Edinburgh score http://purl.obolibrary.org/obo/OBI_0000970 scalar score from composite inputs A score that measures the dominance of a person's right or left hand in everyday activities. http://purl.obolibrary.org/obo/OBI_0000992 DNA sequencing service http://purl.obolibrary.org/obo/OBI_0001904 sequencing service A DNA sequencing process provided as a service - which is the realization of some DNA sequencing in which the service provider role is realized. http://purl.obolibrary.org/obo/OBI_0000993 service provision objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification An objective which is fulfilled by the provision of some service e.g. a training service http://purl.obolibrary.org/obo/OBI_0000994 intravenous injection http://purl.obolibrary.org/obo/OBI_0600007 administering substance in vivo is the injection of a material entity (bearing the administered substance role) into the vein (bearing the target role) of an organism using a syringe http://purl.obolibrary.org/obo/OBI_0000995 administration of material to specimen http://purl.obolibrary.org/obo/OBI_0000274 adding a material entity into a target The directed combination of a material entity with a specimen. http://purl.obolibrary.org/obo/OBI_0000996 device creation objective http://purl.obolibrary.org/obo/OBI_0000456 material transformation objective an objective which aims to create a device with a specified function http://purl.obolibrary.org/obo/OBI_0000997 growth environment http://purl.obolibrary.org/obo/BFO_0000040 material entity The collection of material entities and their qualities that are located near a live organism, tissue or cell and can influence its growth. http://purl.obolibrary.org/obo/OBI_0001000 questionnaire http://purl.obolibrary.org/obo/IAO_0000310 document A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study. http://purl.obolibrary.org/obo/OBI_0001001 Edinburgh handedness assay http://purl.obolibrary.org/obo/OBI_0000944 handedness assay An assay that uses a set of questions (the Edinburgh Handedness inventory) to generate a score that can be used to assess the dominance of a person's right or left hand in everyday activities. The inventory can be used by an observer assessing the person, or by a person self-reporting hand use. The latter method tends to be less reliable due to a person over-attributing tasks to the dominant hand. http://purl.obolibrary.org/obo/OBI_0001003 agar stab storage http://purl.obolibrary.org/obo/OBI_0302893 storage a storage process with input cell culture and agar and output agar stab for long time storage http://purl.obolibrary.org/obo/OBI_0001009 obsolete_qualitative binding detection assay http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class A binding assay where the specified output determines if two or more material entities do or do not have the disposition to form a complex above a threshold level of significance. The threshold can be defined through detection limits of the instrument, the use of experimental controls that establish what is considered significant binding, or a predefined cutoff based on what binding is considered significant in a certain context. http://purl.obolibrary.org/obo/OBI_0001010 nucleic acid extract http://purl.obolibrary.org/obo/OBI_0000953 processed specimen An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. http://purl.obolibrary.org/obo/OBI_0001013 kethoxal structure mapping assay http://purl.obolibrary.org/obo/OBI_0001017 single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using kethoxal as reagent and chemical probe http://purl.obolibrary.org/obo/OBI_0001014 single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing http://purl.obolibrary.org/obo/OBI_0000870 single-nucleotide-resolution nucleic acid structure mapping assay A single-nucleotide-resolution nucleic acid structure mapping assay that determines structural information about the RNA species under study using proteins acting as enzymatic probes. http://purl.obolibrary.org/obo/OBI_0001017 single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing http://purl.obolibrary.org/obo/OBI_0000870 single-nucleotide-resolution nucleic acid structure mapping assay A single-nucleotide-resolution nucleic acid structure mapping assay that determines structural information about the RNA species under study using small chemical compounds acting as chemical probes. http://purl.obolibrary.org/obo/OBI_0001022 gene dosage assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that measures changes in phenotype due to increased or decreased dosage of a single allele of a gene. http://purl.obolibrary.org/obo/OBI_0001025 binding constant determination assay http://purl.obolibrary.org/obo/OBI_0001146 binding assay A binding assay where the specified output is a binding constant http://purl.obolibrary.org/obo/OBI_0001028 feature extraction http://purl.obolibrary.org/obo/OBI_0200000 data transformation A planed process with objective of obtaining quantified values from an image. http://purl.obolibrary.org/obo/OBI_0001032 light emission device http://purl.obolibrary.org/obo/OBI_0000968 device A device which has a function to emit light. http://purl.obolibrary.org/obo/OBI_0001033 perturbation device http://purl.obolibrary.org/obo/OBI_0000968 device A perturbation device is a device which is designed to perform a perturb function http://purl.obolibrary.org/obo/OBI_0001034 environmental control device http://purl.obolibrary.org/obo/OBI_0000968 device An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity. http://purl.obolibrary.org/obo/OBI_0001036 specimen fixation function http://purl.obolibrary.org/obo/BFO_0000034 function a function that allows specific identification of individual speciment from one another. http://purl.obolibrary.org/obo/OBI_0001037 obsolete_specimen fixation function http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class A specimen fixation function is a function that holds or fastens an entity in a fixed position. http://purl.obolibrary.org/obo/OBI_0001038 Ruthenium structure mapping assay http://purl.obolibrary.org/obo/OBI_0001017 single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Rhutenium as reagent and chemical probe http://purl.obolibrary.org/obo/OBI_0001039 inline probing RNA structure mapping assay http://purl.obolibrary.org/obo/OBI_0001017 single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using intromolecular reactivity http://purl.obolibrary.org/obo/OBI_0001040 current amplification function http://purl.obolibrary.org/obo/BFO_0000034 function A current amplification function is an amplification function that increases the amplitude of a current. http://purl.obolibrary.org/obo/OBI_0001042 pump function http://purl.obolibrary.org/obo/OBI_0000383 transfer function a transfer unction where the transfer requires work to move the entity, often against a gradient. http://purl.obolibrary.org/obo/OBI_0001043 cell transfer function http://purl.obolibrary.org/obo/OBI_0000383 transfer function is a transfer function that displaces cells from one place to another http://purl.obolibrary.org/obo/OBI_0001044 angiograph http://purl.obolibrary.org/obo/OBI_0000832 measurement device A device that records the patterns of pulse waves inside blood vessels. http://purl.obolibrary.org/obo/OBI_0001045 capillary blotter http://purl.obolibrary.org/obo/OBI_0000968 device A device that is used to transfer nucleic acids from agarose gels onto a membrane, based on the movement of buffer from a reservoir through the gel and the blotting membrane to a stack of dry blotting paper by capillary force. The molecules are carried to the blotting membrane on which they are adsorbed. http://purl.obolibrary.org/obo/OBI_0001046 bioreactor http://purl.obolibrary.org/obo/OBI_0001034 environmental control device A device or system that supports a biologically active environment. ALAN SAYS NOT AN INSTRUMENT http://purl.obolibrary.org/obo/OBI_0001047 pH meter http://purl.obolibrary.org/obo/OBI_0000832 measurement device A device that is used to measure the pH (acidity or alkalinity) of a liquid. http://purl.obolibrary.org/obo/OBI_0001048 digital camera http://purl.obolibrary.org/obo/OBI_0000398 image creation device An image acquisition device that takes video or still photographs, or both, digitally by recording images via an electronic image sensor. http://purl.obolibrary.org/obo/OBI_0001049 chip spotting device http://purl.obolibrary.org/obo/OBI_0000968 device A device for dropping and immobilizing a solution of biomolecules, for example, nucleic acids such as probe DNA, mRNA, and peptide nucleic acid (PNA), and proteins on a DNA microarray surface to manufacture a DNA microarray. http://purl.obolibrary.org/obo/OBI_0001050 RNA extraction/purification instrument http://purl.obolibrary.org/obo/OBI_0001114 nucleic acid extraction/purification instrument A device that is used to isolate and collect RNA for subsequent molecular analysis. http://purl.obolibrary.org/obo/OBI_0001051 DNA extract http://purl.obolibrary.org/obo/OBI_0001010 nucleic acid extract The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas. http://purl.obolibrary.org/obo/OBI_0001052 two-photon laser/detector http://purl.obolibrary.org/obo/OBI_0400065 light source A light source used in fluorescence imaging that allows the imaging of living tissue up to a depth of 1 mm, based on the concept that two photons of low energy can excite a fluorophore in a quantum event, resulting in the emission of a fluorescence photon, typically at a higher energy than either of the two excitatory photons. http://purl.obolibrary.org/obo/OBI_0001053 electrophoresis system http://purl.obolibrary.org/obo/OBI_0000932 material separation device A device that moves charged particles through a medium by using an electric field induced by electrodes. http://purl.obolibrary.org/obo/OBI_0001054 PET synthesizer http://purl.obolibrary.org/obo/OBI_0000968 device A device that is used to produce targeted molecular pharmaceuticals for use in positron emission tomography. http://purl.obolibrary.org/obo/OBI_0001055 spinning-disk confocal microscope http://purl.obolibrary.org/obo/OBI_0001079 confocal microscope A confocal microscope that uses a Nipkow disk, a mechanical, geometrically operating image scanning device. http://purl.obolibrary.org/obo/OBI_0001056 DNA synthesizer http://purl.obolibrary.org/obo/OBI_0400113 oligonucleotide synthesizer An oligonucleotide synthesizer that is used to custom-build DNA molecules to contain a particular sequence of nucleotides. http://purl.obolibrary.org/obo/OBI_0001057 high performance liquid chromatography instrument http://purl.obolibrary.org/obo/OBI_0001139 liquid chromatography instrument A liquid chromatography instrument that consists of a reservoir of mobile phase, a pump, an injector, a separation column, and a detector. The pump (rather than gravity) provides the higher pressure required to propel the mobile phase and analyte through the densely packed column. http://purl.obolibrary.org/obo/OBI_0001058 microplate reader http://purl.obolibrary.org/obo/OBI_0000832 measurement device A measurement device that detects biological, chemical or physical events of samples in microtiter plates. http://purl.obolibrary.org/obo/OBI_0001059 ELISA microplate reader http://purl.obolibrary.org/obo/OBI_0001058 microplate reader A microplate reader that is used for enzyme-linked immunosorbent assays (ELISA). http://purl.obolibrary.org/obo/OBI_0001060 spot cutter http://purl.obolibrary.org/obo/OBI_0000968 device A robotic device that is used to excise spots from gels. http://purl.obolibrary.org/obo/OBI_0001061 microwave synthesis system http://purl.obolibrary.org/obo/OBI_0000968 device A device that is used to apply microwave irradiation to chemical reactions. http://purl.obolibrary.org/obo/OBI_0001062 densitometer http://purl.obolibrary.org/obo/OBI_0000832 measurement device A device that measures the degree of darkness (the optical density) of a photographic or semitransparent material or of a reflecting surface. http://purl.obolibrary.org/obo/OBI_0001063 automatic staining machine http://purl.obolibrary.org/obo/OBI_0000968 device A device that is used to automatically stain tissue sections on slides or tissue specimens. http://purl.obolibrary.org/obo/OBI_0001064 automatic tissue processor http://purl.obolibrary.org/obo/OBI_0000968 device A device for processing histological tissue having a tissue carrier basket suspended from a turntable overlying a plurality of beakers suspended from a carrier plate. The turntable is raised, indexed, and lowered by a suitable driving mechanism to move the tissue basket sequentially through the beakers. Timers can each be programmed to control the movement of the turntable to provide various different cycles for processing the tissue. Some of the beakers are received in individual thermal baths to heat and control the temperature of the substances received in the beakers for treating the tissue. http://purl.obolibrary.org/obo/OBI_0001065 stereo microscope http://purl.obolibrary.org/obo/OBI_0000940 optical microscope An optical microscope that uses two separate optical paths with two objectives and two eyepieces to provide slightly different viewing angles to the left and right eyes. http://purl.obolibrary.org/obo/OBI_0001066 top loading balance http://purl.obolibrary.org/obo/OBI_0001135 balance A balance that consists of a metal plate on which to place an object and a digital readout of the measurement of its mass. http://purl.obolibrary.org/obo/OBI_0001067 perfusion station http://purl.obolibrary.org/obo/OBI_0000968 device A device or system in which perfusion units are integrated. http://purl.obolibrary.org/obo/OBI_0001068 SPECT scanner http://purl.obolibrary.org/obo/OBI_0000398 image creation device A nuclear medicine tomographic imaging device that uses gamma rays to provide 3D information, typically presented as cross-sectional slices through the specimen but with the ability to be freely reformatted or manipulated as required. http://purl.obolibrary.org/obo/OBI_0001069 array manufacturer role http://purl.obolibrary.org/obo/OBI_0000571 manufacturer role a manufacturer role which is played by the person or organization that manufactured the array http://purl.obolibrary.org/obo/OBI_0001070 scintillation counter http://purl.obolibrary.org/obo/OBI_0000832 measurement device A device that is used to measure ionizing radiation. http://purl.obolibrary.org/obo/OBI_0001071 programmable array microscope http://purl.obolibrary.org/obo/OBI_0001079 confocal microscope A confocal microscope that uses a programmable spatial light modulator for generating an arbitrary pattern of conjugate illumination and detection apertures. http://purl.obolibrary.org/obo/OBI_0001072 cryostat http://purl.obolibrary.org/obo/OBI_0001034 environmental control device A device consisting of a vessel, similar in construction to a vacuum flask, that is used to maintain cold cryogenic temperatures. FIX THIS DEFINITION http://purl.obolibrary.org/obo/OBI_0001073 microtome knife maker http://purl.obolibrary.org/obo/OBI_0000968 device A glass cutting and breaking device that is used to produce glass knives used in ultramicrotomy. http://purl.obolibrary.org/obo/OBI_0001074 cryofixation device http://purl.obolibrary.org/obo/OBI_0000968 device A device that is used for the fixation or stabilization of biological materials as the first step in specimen preparation for electron microscopy. http://purl.obolibrary.org/obo/OBI_0001075 hybridization oven http://purl.obolibrary.org/obo/OBI_0002089 physical store A device that creates an appropriate environment for nucleic acid hybridization. http://purl.obolibrary.org/obo/OBI_0001076 incubator shaker http://purl.obolibrary.org/obo/OBI_0002089 physical store An incubating device that provides shaking motion for biomedical applications (e.g., cell cultures). http://purl.obolibrary.org/obo/OBI_0001077 small-animal image acquisition device http://purl.obolibrary.org/obo/OBI_0000398 image creation device A device that is used to image small laboratory animals (e.g., rats and mice) in vivo. http://purl.obolibrary.org/obo/OBI_0001078 infrared image acquisition device http://purl.obolibrary.org/obo/OBI_0000398 image creation device An image acquisition device that is responsive to an infrared emissive target within a given field of view. http://purl.obolibrary.org/obo/OBI_0001079 confocal microscope http://purl.obolibrary.org/obo/OBI_0400169 microscope A microscope that is used to increase micrograph contrast and/or reconstruct three-dimensional images by using a spatial pinhole to eliminate out-of-focus light in specimens that are thicker than the focal plane. http://purl.obolibrary.org/obo/OBI_0001080 patch clamp device http://purl.obolibrary.org/obo/OBI_0000832 measurement device A device used in electrophysiology that allows the study of single or multiple ion channels in cells. http://purl.obolibrary.org/obo/OBI_0001081 gel imaging system http://purl.obolibrary.org/obo/OBI_0000398 image creation device A device that is used to acquire images of laboratory gels. http://purl.obolibrary.org/obo/OBI_0001082 protein separation apparatus http://purl.obolibrary.org/obo/OBI_0000932 material separation device A device that is used for the separation of proteins. http://purl.obolibrary.org/obo/OBI_0001083 multichannel electronic pipette http://purl.obolibrary.org/obo/OBI_0001118 multichannel pipette A multichannel pipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense the aspirated volume or a series of aliquots in successive dispensing operations. http://purl.obolibrary.org/obo/OBI_0001084 vitrification apparatus http://purl.obolibrary.org/obo/OBI_0000968 device A device that is used to effect the transition of a substance into a glass. http://purl.obolibrary.org/obo/OBI_0001085 radiography instrument http://purl.obolibrary.org/obo/OBI_0000398 image creation device An image acquisition device that uses ionizing electromagnetic radiation such as X-rays to view objects. http://purl.obolibrary.org/obo/OBI_0001086 radiation measurement device http://purl.obolibrary.org/obo/OBI_0000832 measurement device A device that consists of a radiosensitive detector and a means of recording the effects of radiation on the detector. http://purl.obolibrary.org/obo/OBI_0001087 lyophilizer http://purl.obolibrary.org/obo/OBI_0000968 device A device that is used to freeze dry material. http://purl.obolibrary.org/obo/OBI_0001088 tandem mass spectrometer http://purl.obolibrary.org/obo/OBI_0000049 mass spectrometer A mass spectrometer in which ions are subjected to two or more sequential stages of analysis (which may be separated spatially or temporally) according to the quotient mass/charge. http://purl.obolibrary.org/obo/OBI_0001089 microhardness tester http://purl.obolibrary.org/obo/OBI_0000832 measurement device A hardness testing device that is used in light-optical microscopes. http://purl.obolibrary.org/obo/OBI_0001090 multimode microplate reader http://purl.obolibrary.org/obo/OBI_0001058 microplate reader A microplate reader that can detect multiple types of absorbance, luminescence or fluorescence. http://purl.obolibrary.org/obo/OBI_0001091 mechanical balance http://purl.obolibrary.org/obo/OBI_0001135 balance A balance that is used to compare the weights of two bodies, to determine the difference in mass (or weight). http://purl.obolibrary.org/obo/OBI_0001092 computer cluster http://purl.obolibrary.org/obo/OBI_0400107 computer A group of linked computers, working together closely so that in many respects they form a single computer. http://purl.obolibrary.org/obo/OBI_0001093 microtome knife sharpener http://purl.obolibrary.org/obo/OBI_0000968 device A device that is used to sharpen knives used in microtomy. http://purl.obolibrary.org/obo/OBI_0001094 plate shaker http://purl.obolibrary.org/obo/OBI_0000968 device A device that provides shaking motion for microplates. http://purl.obolibrary.org/obo/OBI_0001095 coagulation analyzer http://purl.obolibrary.org/obo/OBI_0000832 measurement device A device for automatically analyzing blood coagulation in a clinical laboratory. http://purl.obolibrary.org/obo/OBI_0001096 laser capture microdissection microscope http://purl.obolibrary.org/obo/OBI_0400169 microscope A microscope that uses low-energy laser beams and special transfer film to lift single cells from a tissue. http://purl.obolibrary.org/obo/OBI_0001097 liquid extraction robot http://purl.obolibrary.org/obo/OBI_0400112 liquid handler A liquid handling device that provides automatic liquid extraction. http://purl.obolibrary.org/obo/OBI_0001098 ultrasound machine http://purl.obolibrary.org/obo/OBI_0000398 image creation device A device that is used to visualize subcutaneous body structures including tendons, muscles, joints, vessels and internal organs. http://purl.obolibrary.org/obo/OBI_0001099 immunoblot scanner http://purl.obolibrary.org/obo/OBI_0000398 image creation device A device that is used for the imaging of immunoblots. http://purl.obolibrary.org/obo/OBI_0001100 microcentrifuge http://purl.obolibrary.org/obo/OBI_0400106 centrifuge A type of centrifuge that is designed for small tubes (0.2 ml to 2.0 ml), has a compact design, and has a small footprint. http://purl.obolibrary.org/obo/OBI_0001101 electronic repeater pipette http://purl.obolibrary.org/obo/OBI_0001128 micropipette A micropipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense a series of aliquots in successive dispensing operations. http://purl.obolibrary.org/obo/OBI_0001102 electron paramagnetic resonance spectrometer http://purl.obolibrary.org/obo/OBI_0400115 spectrophotometer An spectrophotometer that is used to investigate chemical species that have one or more unpaired electrons, such as organic and inorganic free radicals or inorganic complexes possessing a transition metal ion. http://purl.obolibrary.org/obo/OBI_0001103 rocker http://purl.obolibrary.org/obo/OBI_0000968 device A device that provides three-dimensional motion for biomedical applications (e.g., gel trays). http://purl.obolibrary.org/obo/OBI_0001104 analytical balance http://purl.obolibrary.org/obo/OBI_0001135 balance A balance with weighing pan(s) inside a transparent enclosure that is used to measure mass to a very high degree of precision and accuracy. http://purl.obolibrary.org/obo/OBI_0001105 scanning force microscope http://purl.obolibrary.org/obo/OBI_0400169 microscope A microscope that forms images of surfaces using a physical probe that scans the specimen. http://purl.obolibrary.org/obo/OBI_0001106 pulsed-field gel electrophoresis system http://purl.obolibrary.org/obo/OBI_0001121 gel electrophoresis system A gel electrophoresis system that is used to separate very large molecules of DNA. http://purl.obolibrary.org/obo/OBI_0001107 tissue embedding station http://purl.obolibrary.org/obo/OBI_0000968 device A device that is used to perform paraffin embedding of tissue specimens. http://purl.obolibrary.org/obo/OBI_0001108 nucleic acid sequencer http://purl.obolibrary.org/obo/OBI_0000832 measurement device An device that is used to determine the order of nucleotides in nucleic acid sequences. http://purl.obolibrary.org/obo/OBI_0001109 bead array reader http://purl.obolibrary.org/obo/OBI_0000398 image creation device A device that is used to acquire and image bead array data. http://purl.obolibrary.org/obo/OBI_0001110 real-time PCR machine http://purl.obolibrary.org/obo/OBI_0000989 PCR instrument An PCR instrument that enables both detection and quantification of one or more specific sequences in a DNA sample. http://purl.obolibrary.org/obo/OBI_0001111 paraffin oven http://purl.obolibrary.org/obo/OBI_0001034 environmental control device A device that is used for the warming of paraffin embedding medium. http://purl.obolibrary.org/obo/OBI_0001112 autoclave http://purl.obolibrary.org/obo/OBI_0001034 environmental control device A device that is used to sterilize equipment and supplies by subjecting them to high pressure steam at 121 C or more, typically for 15 to 20 minutes depending on the size of the load and the contents. http://purl.obolibrary.org/obo/OBI_0001113 microplate washer http://purl.obolibrary.org/obo/OBI_0000968 device A device that is used to wash immunoassays in microwell strips and plates with professional accuracy. WHAT IS PROFESSIONAL ACCURACY?? http://purl.obolibrary.org/obo/OBI_0001114 nucleic acid extraction/purification instrument http://purl.obolibrary.org/obo/OBI_0000932 material separation device A device that is used to isolate and collect nucleic acids (DNA or RNA) for subsequent molecular analysis. http://purl.obolibrary.org/obo/OBI_0001115 ELISA microplate washer http://purl.obolibrary.org/obo/OBI_0001113 microplate washer A microplate washer that is used for enzyme-linked immunosorbent assays (ELISA). http://purl.obolibrary.org/obo/OBI_0001116 vacuum manifold http://purl.obolibrary.org/obo/OBI_0000968 device A device that is used for the vacuum-driven processing of multiwell strips or plates, or spin columns. IS THIS AN INSTRUMENT? IS THE DEFINTION CORRECT - TO DISTRIBUTE PRESSURE EVENLY. http://purl.obolibrary.org/obo/OBI_0001117 DNA extraction/purification instrument http://purl.obolibrary.org/obo/OBI_0001114 nucleic acid extraction/purification instrument A device that is used to isolate and collect DNA for subsequent molecular analysis. http://purl.obolibrary.org/obo/OBI_0001118 multichannel pipette http://purl.obolibrary.org/obo/OBI_0000832 measurement device A pipetting system that has a plurality of tip fittings and is used for multi-well plate applications. http://purl.obolibrary.org/obo/OBI_0001119 cell harvester http://purl.obolibrary.org/obo/OBI_0000968 device A device that is used to harvest cells from microplates and deposit samples on a filter mat. NOT AN INSTRUMENT? http://purl.obolibrary.org/obo/OBI_0001120 portable fluorometer http://purl.obolibrary.org/obo/OBI_0400143 fluorometer A compact fluorometer that can be carried or moved with ease. http://purl.obolibrary.org/obo/OBI_0001122 diffractometer http://purl.obolibrary.org/obo/OBI_0000832 measurement device A measurement device for analyzing the structure of a material from the scattering pattern produced when a beam of radiation or particles (e.g. X rays or neutrons) interacts with it. http://purl.obolibrary.org/obo/OBI_0001123 microdissection instrument http://purl.obolibrary.org/obo/OBI_0000968 device A device that is used for the dissection of tissues under magnification. http://purl.obolibrary.org/obo/OBI_0001124 micropipette puller http://purl.obolibrary.org/obo/OBI_0000968 device A device that is used to fabricate glass micropipettes. http://purl.obolibrary.org/obo/OBI_0001125 laser scanning confocal microscope http://purl.obolibrary.org/obo/OBI_0001079 confocal microscope A confocal microscope that obtains high-resolution optical images with depth selectivity, in which a laser beam passes through a light source aperture and then is focused by an objective lens into a small (ideally diffraction limited) focal volume within or on the surface of a specimen. http://purl.obolibrary.org/obo/OBI_0001126 digital microscope http://purl.obolibrary.org/obo/OBI_0400169 microscope A microscope that uses optics and a charge-coupled device (CCD) camera to output a digital image to a monitor. http://purl.obolibrary.org/obo/OBI_0001127 freeze substitution system http://purl.obolibrary.org/obo/OBI_0000968 device A device or system for dehydrating and then chemically fixing electron microscopy samples at low temperatures in preparation for various treatments including embedding in resins. http://purl.obolibrary.org/obo/OBI_0001128 micropipette http://purl.obolibrary.org/obo/OBI_0000832 measurement device A microinjection device that is used to measure very small volumes of liquids. http://purl.obolibrary.org/obo/OBI_0001129 voltage clamp device http://purl.obolibrary.org/obo/OBI_0000832 measurement device A device that is used to measure the ion currents across the membrane of excitable cells, such as neurons, while holding the membrane voltage at a set level. http://purl.obolibrary.org/obo/OBI_0001130 vacuum oven http://purl.obolibrary.org/obo/OBI_0001034 environmental control device A device that heats materials in a vacuum. http://purl.obolibrary.org/obo/OBI_0001131 slide warmer http://purl.obolibrary.org/obo/OBI_0001034 environmental control device A device that is used to heat microscope slides. http://purl.obolibrary.org/obo/OBI_0001132 capillary electrophoresis instrument http://purl.obolibrary.org/obo/OBI_0001053 electrophoresis system An electrophoresis system that is used to separate ionic species by their charge and frictional forces and mass. http://purl.obolibrary.org/obo/OBI_0001133 denaturing high-performance liquid chromatography instrument http://purl.obolibrary.org/obo/OBI_0000932 material separation device A high performance liquid chromatography instrument that employs temperature-dependent separation of DNA containing mismatched base pairs from PCR-amplified DNA fragments for chromatographic mutation analysis. http://purl.obolibrary.org/obo/OBI_0001134 agarose gel electrophoresis system http://purl.obolibrary.org/obo/OBI_0001053 electrophoresis system A gel electrophoresis system that is used to separate DNA or RNA molecules by size, achieved by moving negatively charged nucleic acid molecules through an agarose matrix with an electric field. http://purl.obolibrary.org/obo/OBI_0001135 balance http://purl.obolibrary.org/obo/OBI_0000832 measurement device A measuring instrument that is used to determine the weight or mass of an object. http://purl.obolibrary.org/obo/OBI_0001136 surface plasmon resonance instrument http://purl.obolibrary.org/obo/OBI_0000832 measurement device A tool for measuring adsorption of material onto planar metal (typically gold and silver) surfaces or onto the surface of metal nanoparticles. http://purl.obolibrary.org/obo/OBI_0001137 protein sequencer http://purl.obolibrary.org/obo/OBI_0000832 measurement device An device that is used to determine the order of amino acids in protein sequences. http://purl.obolibrary.org/obo/OBI_0001139 liquid chromatography instrument http://purl.obolibrary.org/obo/OBI_0000048 chromatography device A chromatography device that dissolves a mixture in liquid mobile phase to separate the analyte to be measured from other molecules in the mixture and allows it to be isolated http://purl.obolibrary.org/obo/OBI_0001140 spike-in quality control role http://purl.obolibrary.org/obo/OBI_0000025 reference substance role a reference substance role that is borne by a material entity with a known amount which is mixed into the evaluant of assays for quality control or data normalization purposes http://purl.obolibrary.org/obo/OBI_0001141 individual organism identifier http://purl.obolibrary.org/obo/IAO_0000577 centrally registered identifier symbol a CRID symbol used to distinguish one individual organism from another. http://purl.obolibrary.org/obo/OBI_0001142 dye swap quality control role http://purl.obolibrary.org/obo/OBI_0000025 reference substance role a reference substance role that is borne by a material entity used in a dye swap design experiment for quality control or data normalization purposes http://purl.obolibrary.org/obo/OBI_0001144 binding constant http://purl.obolibrary.org/obo/OBI_0001181 binding datum A binding datum about the disposition of two or more material entities to form complexes which comes in the form of a scalar and unit that are utilized in equations that model the binding process http://purl.obolibrary.org/obo/OBI_0001145 3D structure determination of bound complex assay http://purl.obolibrary.org/obo/OBI_0600045 3D structure determination assay A 3D structure determination assay in which a complex of 2 or more material enties is characterized which provides information on their binding configuration. http://purl.obolibrary.org/obo/OBI_0001146 binding assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay with the objective to characterize the disposition of two or more material entities to form a complex. http://purl.obolibrary.org/obo/OBI_0001147 cell culture expansion http://purl.obolibrary.org/obo/OBI_0000094 material processing a process that results in the increase of cell numbers http://purl.obolibrary.org/obo/OBI_0001148 gene knock out http://purl.obolibrary.org/obo/OBI_0600043 genetic transformation a genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods. http://purl.obolibrary.org/obo/OBI_0001149 gene knock in http://purl.obolibrary.org/obo/OBI_0600043 genetic transformation a genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion. http://purl.obolibrary.org/obo/OBI_0001150 chromosomal substitution http://purl.obolibrary.org/obo/OBI_0600043 genetic transformation A genetic transformation in which all, or part, of a chromosome from a donor replaces that of the recipient. It does not include chromosome recombination. For single gene insertion, use the term 'gene knock in'. http://purl.obolibrary.org/obo/OBI_0001151 genetically modified material http://purl.obolibrary.org/obo/OBI_0000047 processed material a material entity, organism or cell, that is the output of a genetic transformation process. http://purl.obolibrary.org/obo/OBI_0001152 transfection http://purl.obolibrary.org/obo/OBI_0600043 genetic transformation a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA or RNA into a cell http://purl.obolibrary.org/obo/OBI_0001153 genetic transformation objective http://purl.obolibrary.org/obo/OBI_0000456 material transformation objective a material transformation objective aims to create genetically modified organism or cell http://purl.obolibrary.org/obo/OBI_0001154 induced mutation http://purl.obolibrary.org/obo/OBI_0600043 genetic transformation a genetic transformation that the modification of the genetic material (either coding or non-coding) of an organism is caused by mutagenic compounds or irradiation. http://purl.obolibrary.org/obo/OBI_0001155 3D structural organization datum http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement datum that describes the structural orientation of a material entity in 3D space. http://purl.obolibrary.org/obo/OBI_0001156 age since planting measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since planting, the process of placing a plant in media (e.g. soil) to allow it to grow, which excludes sowing. http://purl.obolibrary.org/obo/OBI_0001157 age since hatching measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since hatching, the process of emergence from an egg. http://purl.obolibrary.org/obo/OBI_0001159 age since egg laying measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since egg laying, the process of the production of egg(s) by an organism. http://purl.obolibrary.org/obo/OBI_0001160 assay validation objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification an objective specification to check the accuracy or the quality of the results of an assay by comparison with independent results http://purl.obolibrary.org/obo/OBI_0001161 age since germination measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since germination, the process consisting of physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth. http://purl.obolibrary.org/obo/OBI_0001162 validation by reverse transcription PCR design http://purl.obolibrary.org/obo/OBI_0500000 study design a study design in which checks the accuracy or the quality of the result of an assay by comparing with reverse transcription PCR results http://purl.obolibrary.org/obo/OBI_0001163 age since eclosion measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since eclosion, the process of emergence of an adult insect from its pupa or cocoon. http://purl.obolibrary.org/obo/OBI_0001164 age since sowing measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since sowing, the process of placing a seed or spore in some media with the intention to invoke germination. http://purl.obolibrary.org/obo/OBI_0001165 age since coitus measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since coitus, the process of copulation that occurs during the process of sexual reproduction. http://purl.obolibrary.org/obo/OBI_0001166 validation by real time PCR design http://purl.obolibrary.org/obo/OBI_0500000 study design a study design in which the accuracy or the quality of the result of an assay is checked by comparing with real time PCR results http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum that is the result of measurement of age of an organism http://purl.obolibrary.org/obo/OBI_0001168 age since fertilization measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. http://purl.obolibrary.org/obo/OBI_0001169 age since birth measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother. http://purl.obolibrary.org/obo/OBI_0001170 reverse transcription polymerase chain reaction assay http://purl.obolibrary.org/obo/OBI_0002692 polymerase chain reaction assay An assay that determines the concentration of RNA in a sample in which an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional or real-time PCR. http://purl.obolibrary.org/obo/OBI_0001172 dose response curve http://purl.obolibrary.org/obo/IAO_0000573 line graph A data item of paired values, one indicating the dose of a material, the other quantitating a measured effect at that dose. The dosing intervals are chosen so that effect values be interpolated by a plotting a curve. http://purl.obolibrary.org/obo/OBI_0001173 service http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer. http://purl.obolibrary.org/obo/OBI_0001175 selective organism creation objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification an objective specification to generate a population or type of organism within species that have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms. http://purl.obolibrary.org/obo/OBI_0001176 Individual epitope immunization in vivo http://purl.obolibrary.org/obo/OBI_1110015 Immunization in vivo An immunization in which an individual epitope is administered into a host organism. http://purl.obolibrary.org/obo/OBI_0001177 RNA sequencing assay http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay An assay that determines the sequence of an RNA molecule. http://purl.obolibrary.org/obo/OBI_0001180 half maximal effective concentration (EC50) http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum half maximal effective concentration (EC50) is a scalar measurement datum corresponding to the concentration of a compound which induces a response halfway between the baseline and maximum after some specified exposure time. http://purl.obolibrary.org/obo/OBI_0001181 binding datum http://purl.obolibrary.org/obo/IAO_0000027 data item A data item that states if two or more material entities have the disposition to form a complex, and if so, how strong that disposition is. http://purl.obolibrary.org/obo/OBI_0001182 negative binding datum http://purl.obolibrary.org/obo/OBI_0001181 binding datum A binding datum that states that there is no significant disposition of two or more entities to form a complex http://purl.obolibrary.org/obo/OBI_0001187 infectious agent detection assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that measures the presence or amount of an infectious agent in an evaluant http://purl.obolibrary.org/obo/OBI_0001191 half maximal inhibitory concentration (IC50) http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum Half maximal inhibitory concentration (IC50) is a scalar measurement datum that measures the effectiveness of a compound to competitively inhibit a given process, and corresponds to the concentration of the compound at which it reaches half of its maximum inhibitory effect. http://purl.obolibrary.org/obo/OBI_0001192 epitope specific immune intervention http://purl.obolibrary.org/obo/OBI_0001174 passive immunization An administration in vivo to either actively or passively immunize an organism in order to induce a response against a specific immune epitope http://purl.obolibrary.org/obo/OBI_0001193 epitope specific cytokine production by T cells http://purl.obolibrary.org/obo/GO_0001816 cytokine production A process of cytokine production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001194 ELISPOT assay measuring epitope specific transforming growth factor-beta production by T cells http://purl.obolibrary.org/obo/OBI_0001264 biological activity assay measuring epitope specific transforming growth factor-beta production by T cells An assay of epitope specific transforming growth factor-beta production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001195 operator variation design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that assesses the operator performance and relation to data consistency and quality. http://purl.obolibrary.org/obo/OBI_0001196 cytometric bead array assay measuring epitope specific IP-10 production by T cells http://purl.obolibrary.org/obo/OBI_0001308 biological activity assay measuring epitope specific IP-10 production by T cells An assay of epitope specific IP-10 production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001197 comparative genome hybridization by array design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that detects genomic copy number variations using microarray technology. http://purl.obolibrary.org/obo/OBI_0001198 biological activity assay measuring epitope specific interleukin-27 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects interleukin-27 production by T cells. http://purl.obolibrary.org/obo/OBI_0001199 in vivo design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model. http://purl.obolibrary.org/obo/OBI_0001200 genotyping by high throughput sequencing design http://purl.obolibrary.org/obo/OBI_0001444 genotyping design A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using high througput sequencing techniques. http://purl.obolibrary.org/obo/OBI_0001201 epitope specific tolerance induction by T cells http://purl.obolibrary.org/obo/GO_0002507 tolerance induction A process of tolerance induction by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001202 innate behavior design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which the innate behavior of the organism is examined, e.g. path finding in bees. http://purl.obolibrary.org/obo/OBI_0001203 detection of specific nucleic acids with complementary probes assay measuring epitope specific transforming growth factor-beta production by T cells http://purl.obolibrary.org/obo/OBI_0001264 biological activity assay measuring epitope specific transforming growth factor-beta production by T cells An assay of epitope specific transforming growth factor-beta production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001204 SNP microarray http://purl.obolibrary.org/obo/OBI_0400148 DNA microarray A DNA microarray used to detect polymorphisms in DNA samples http://purl.obolibrary.org/obo/OBI_0001205 cell component comparison design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that compares samples from different cell components. http://purl.obolibrary.org/obo/OBI_0001206 ELISPOT assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells http://purl.obolibrary.org/obo/OBI_0001233 biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001207 epitope specific macrophage inflammatory protein-1 alpha production by T cells http://purl.obolibrary.org/obo/GO_0071608 macrophage inflammatory protein-1 alpha production A process of macrophage inflammatory protein-1 alpha production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001208 epitope specific T cell activation http://purl.obolibrary.org/obo/GO_0042110 T cell activation A process of T cell activation resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001209 biological activity assay measuring epitope specific interleukin-10 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects interleukin-10 production by T cells. http://purl.obolibrary.org/obo/OBI_0001210 cytometric bead array assay measuring epitope specific transforming growth factor-beta production by T cells http://purl.obolibrary.org/obo/OBI_0001264 biological activity assay measuring epitope specific transforming growth factor-beta production by T cells An assay of epitope specific transforming growth factor-beta production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001211 ex vivo design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design where all or part of an organism is removed and studied in vitro, e.g. part of a mouse is removed and cultured in vitro. A cell culture with an established cell line is an in vitro experiment. http://purl.obolibrary.org/obo/OBI_0001212 epitope specific type IV hypersensitivity by T cells http://purl.obolibrary.org/obo/GO_0001806 type IV hypersensitivity A process of type IV hypersensitivity by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001214 normalization testing design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that tests different normalization procedures. http://purl.obolibrary.org/obo/OBI_0001215 intracellular material detection assay measuring epitope specific perforin release http://purl.obolibrary.org/obo/OBI_0001497 biological activity assay measuring epitope specific perforin release by T cells A T cell epitope specific perforin release assay that uses an intracellular material detection by flow cytometry assay. http://purl.obolibrary.org/obo/OBI_0001216 cell culture analyte detection bioassay measuring epitope specific interleukin-2 production by T cells http://purl.obolibrary.org/obo/OBI_0001445 biological activity assay measuring epitope specific interleukin-2 production by T cells An assay of epitope specific interleukin-2 production by T cells that uses a cell culture analyte detection bioassay. http://purl.obolibrary.org/obo/OBI_0001217 biological activity assay measuring epitope specific interleukin-22 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects interleukin-22 production by T cells. http://purl.obolibrary.org/obo/OBI_0001218 biological activity assay measuring epitope specific interleukin-8 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects interleukin-8 production by T cells. http://purl.obolibrary.org/obo/OBI_0001219 epitope specific chemokine (C-C motif) ligand 1 production by T cells http://purl.obolibrary.org/obo/GO_0071610 chemokine (C-C motif) ligand 1 production A process of chemokine (C-C motif) ligand 1 production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001220 cell culture analyte detection bioassay measuring epitope specific interleukin-10 production by T cells http://purl.obolibrary.org/obo/OBI_0001209 biological activity assay measuring epitope specific interleukin-10 production by T cells An assay of epitope specific interleukin-10 production by T cells that uses a cell culture analyte detection bioassay. http://purl.obolibrary.org/obo/OBI_0001221 ChIP-chip by SNP array assay http://purl.obolibrary.org/obo/OBI_0001248 ChIP-chip assay A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a SNP array to detect polymorphism specific DNA elements in the isolated chromatin http://purl.obolibrary.org/obo/OBI_0001222 ELISA measuring epitope specific RANTES production by T cells http://purl.obolibrary.org/obo/OBI_0001232 biological activity assay measuring epitope specific RANTES production by T cells An assay of epitope specific RANTES production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001223 cytometric bead array assay measuring epitope specific interleukin-1 beta production by T cells http://purl.obolibrary.org/obo/OBI_0001449 biological activity assay measuring epitope specific interleukin-1 beta production by T cells An assay of epitope specific interleukin-1 beta production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001225 genetic population background information http://purl.obolibrary.org/obo/OBI_0001404 genetic characteristics information a genetic characteristics information which is a part of genotype information that identifies the population of organisms http://purl.obolibrary.org/obo/OBI_0001226 environmental history design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc. http://purl.obolibrary.org/obo/OBI_0001227 ELISPOT assay measuring epitope specific interleukin-6 production by T cells http://purl.obolibrary.org/obo/OBI_0001451 biological activity assay measuring epitope specific interleukin-6 production by T cells An assay of epitope specific interleukin-6 production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001228 biological activity assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response http://purl.obolibrary.org/obo/OBI_0001495 biological activity assay measuring epitope specific T cell helper activity A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance an antibody response. http://purl.obolibrary.org/obo/OBI_0001229 plasmon resonance assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex http://purl.obolibrary.org/obo/OBI_0002097 assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex A T cell epitope equilibrium dissociation constant (KD) determination assay that uses a surface plasmon resonance assay. http://purl.obolibrary.org/obo/OBI_0001230 biological activity assay measuring epitope specific interleukin-5 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects interleukin-5 production by T cells. http://purl.obolibrary.org/obo/OBI_0001231 ELISA measuring epitope specific transforming growth factor-beta production by T cells http://purl.obolibrary.org/obo/OBI_0001264 biological activity assay measuring epitope specific transforming growth factor-beta production by T cells An assay of epitope specific transforming growth factor-beta production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001232 biological activity assay measuring epitope specific RANTES production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects RANTES production by T cells. http://purl.obolibrary.org/obo/OBI_0001233 biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects granulocyte macrophage colony stimulating factor production by T cells. http://purl.obolibrary.org/obo/OBI_0001234 epigenetic modification identification objective http://purl.obolibrary.org/obo/OBI_0000131 molecular feature identification objective A molecular feature identification objective that aims to detect epigenetic modifications, such as DNA methylation, histone modifications. http://purl.obolibrary.org/obo/OBI_0001235 transcription profiling by tiling array assay http://purl.obolibrary.org/obo/OBI_0001463 transcription profiling by array assay A transcription profiling by array assay that uses a tiling path array. http://purl.obolibrary.org/obo/OBI_0001236 ELISA measuring epitope specific interleukin-22 production by T cells http://purl.obolibrary.org/obo/OBI_0001217 biological activity assay measuring epitope specific interleukin-22 production by T cells An assay of epitope specific interleukin-22 production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001237 biological activity assay measuring epitope specific interleukin-21 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects interleukin-21 production by T cells. http://purl.obolibrary.org/obo/OBI_0001238 ELISA measuring epitope specific interleukin-9 production by T cells http://purl.obolibrary.org/obo/OBI_0001253 biological activity assay measuring interleukin-9 production by T cells An assay of epitope specific interleukin-9 production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001239 transcription profiling by high throughput sequencing design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and/or to quantitate transcript abundance http://purl.obolibrary.org/obo/OBI_0001240 intracellular cytokine staining assay measuring epitope specific interleukin-6 production by T cells http://purl.obolibrary.org/obo/OBI_0001451 biological activity assay measuring epitope specific interleukin-6 production by T cells An assay of epitope specific interleukin-6 production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001241 cell culture analyte detection bioassay measuring epitope specific interleukin-4 production by T cells http://purl.obolibrary.org/obo/OBI_0001450 biological activity assay measuring epitope specific interleukin-4 production by T cells An assay of epitope specific interleukin-4 production by T cells that uses a cell culture analyte detection bioassay. http://purl.obolibrary.org/obo/OBI_0001242 detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor production by T cells http://purl.obolibrary.org/obo/OBI_0001788 detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells A T cell epitope specific tumor necrosis factor production assay that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001243 cytometric bead array assay measuring epitope specific monocyte chemotactic protein-1 production by T cells http://purl.obolibrary.org/obo/OBI_0001465 biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001244 ELISA measuring epitope specific interleukin-23 production by T cells http://purl.obolibrary.org/obo/OBI_0001363 biological activity assay measuring epitope specific interleukin-23 production by T cells An assay of epitope specific interleukin-23 production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001245 detection of specific nucleic acids with complementary probes assay measuring epitope specific perforin release http://purl.obolibrary.org/obo/OBI_0001497 biological activity assay measuring epitope specific perforin release by T cells A T cell epitope specific perforin release assay that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001246 ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells http://purl.obolibrary.org/obo/OBI_0001400 biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001247 genotyping by high throughput sequencing assay http://purl.obolibrary.org/obo/OBI_0000435 genotyping assay A genotyping assay that uses a high througput sequencer http://purl.obolibrary.org/obo/OBI_0001249 epitope specific T cell tolerance induction http://purl.obolibrary.org/obo/GO_0002517 T cell tolerance induction A process of T cell tolerance induction resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001250 obsolete intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulation http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class An intracellular material detection by flow cytometry assay that measures epitope specific cytotoxic T cell degranulation http://purl.obolibrary.org/obo/OBI_0001251 biological activity assay measuring epitope specific interleukin-13 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects interleukin-13 production by T cells. http://purl.obolibrary.org/obo/OBI_0001252 array platform variation design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which the array platform is compared, e.g. Agilent versus Affymetrix. http://purl.obolibrary.org/obo/OBI_0001253 biological activity assay measuring interleukin-9 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects interleukin-9 production by T cells. http://purl.obolibrary.org/obo/OBI_0001254 epitope specific interleukin-3 production by T cells http://purl.obolibrary.org/obo/GO_0032632 interleukin-3 production A process of interleukin-3 production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001255 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-5 production by T cells http://purl.obolibrary.org/obo/OBI_0001230 biological activity assay measuring epitope specific interleukin-5 production by T cells An assay of epitope specific interleukin-5 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001256 epitope specific lymphotoxin A production by T cells http://purl.obolibrary.org/obo/GO_0032641 lymphotoxin A production A process of lymphotoxin A production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001257 epitope specific interleukin-1 alpha production by T cells http://purl.obolibrary.org/obo/GO_0032610 interleukin-1 alpha production A process of interleukin-1 alpha production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001258 ChIP-seq design http://purl.obolibrary.org/obo/OBI_0001425 protein binding site identification design A study design which aims to identify protein and DNA interactions using a combination of chromatin immunoprecipitation and high throughput sequencing. Massively parallel sequence analyses are used in conjunction with whole-genome sequence databases to analyze the interaction pattern of any protein with DNA, or the pattern of any epigenetic chromatin modifications. http://purl.obolibrary.org/obo/OBI_0001259 translational bias design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that characterizes the association of transcripts and translation machinery. http://purl.obolibrary.org/obo/OBI_0001260 ELISA measuring epitope specific interleukin-3 production by T cells http://purl.obolibrary.org/obo/OBI_0001406 biological activity assay measuring epitope specific interleukin-3 production by T cells An assay of epitope specific interleukin-3 production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001261 ELISA measuring epitope specific interleukin-1 alpha production by T cells http://purl.obolibrary.org/obo/OBI_0001388 biological activity assay measuring epitope specific interleukin-1 alpha production by T cells An assay of epitope specific interleukin-1 alpha production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001262 epitope specific interleukin-27 production by T cells http://purl.obolibrary.org/obo/GO_0032631 interleukin-27 production A process of interleukin-27 production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001263 biological activity assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response http://purl.obolibrary.org/obo/OBI_0001495 biological activity assay measuring epitope specific T cell helper activity A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell response. http://purl.obolibrary.org/obo/OBI_0001264 biological activity assay measuring epitope specific transforming growth factor-beta production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects transforming growth factor-beta production by T cells. http://purl.obolibrary.org/obo/OBI_0001265 FWER adjusted p-value http://purl.obolibrary.org/obo/OBI_0000071 quantitative confidence value A quantitative confidence value resulting from a multiple testing error correction method which adjusts the p-value used as input to control for Type I error in the context of multiple pairwise tests http://purl.obolibrary.org/obo/OBI_0001266 DNA methylation profiling by high throughput sequencing assay http://purl.obolibrary.org/obo/OBI_0000634 DNA methylation profiling assay A DNA methylation profiling assay in which the methylation state of DNA is determined and can be compared between samples using sequencing based technology http://purl.obolibrary.org/obo/OBI_0001267 epitope specific transforming growth factor-beta production by T cells http://purl.obolibrary.org/obo/GO_0071604 transforming growth factor beta production A process of transforming growth factor-beta production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001268 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-12 production by T cells http://purl.obolibrary.org/obo/OBI_0001391 biological activity assay measuring epitope specific interleukin-12 production by T cells An assay of epitope specific interleukin-12 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001269 biological activity assay measuring epitope specific cytotoxic T cell degranulation http://purl.obolibrary.org/obo/OBI_0002055 assay measuring T cell epitope specific biological activity A T cell epitope dependent biological activity assay that detects cytotoxic T cell degranulation. http://purl.obolibrary.org/obo/OBI_0001270 cell culture analyte detection bioassay measuring epitope specific transforming growth factor-beta production by T cells http://purl.obolibrary.org/obo/OBI_0001264 biological activity assay measuring epitope specific transforming growth factor-beta production by T cells An assay of epitope specific transforming growth factor-beta production by T cells that uses a cell culture analyte detection bioassay. http://purl.obolibrary.org/obo/OBI_0001272 ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells http://purl.obolibrary.org/obo/OBI_0001400 biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001273 cell culture analyte detection bioassay measuring epitope specific interleukin-5 production by T cells http://purl.obolibrary.org/obo/OBI_0001230 biological activity assay measuring epitope specific interleukin-5 production by T cells An assay of epitope specific interleukin-5 production by T cells that uses a cell culture analyte detection bioassay. http://purl.obolibrary.org/obo/OBI_0001274 genotyping by array assay http://purl.obolibrary.org/obo/OBI_0001985 microarray assay A genotyping assay that uses an array http://purl.obolibrary.org/obo/OBI_0001275 epitope specific interleukin-16 production by T cells http://purl.obolibrary.org/obo/GO_0032619 interleukin-16 production A process of interleukin-16 production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001276 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 1 by T cells. http://purl.obolibrary.org/obo/OBI_0001277 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-2 production by T cells http://purl.obolibrary.org/obo/OBI_0001445 biological activity assay measuring epitope specific interleukin-2 production by T cells An assay of epitope specific interleukin-2 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001278 DNA methylation profiling by array design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which the methylation state of DNA is determined and is compared between samples using array technology. http://purl.obolibrary.org/obo/OBI_0001279 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-22 production by T cells http://purl.obolibrary.org/obo/OBI_0001217 biological activity assay measuring epitope specific interleukin-22 production by T cells An assay of epitope specific interleukin-22 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001280 biological activity assay measuring epitope specific interleukin-16 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects interleukin-16 production by T cells. http://purl.obolibrary.org/obo/OBI_0001281 ELISA measuring epitope specific IP-10 production by T cells http://purl.obolibrary.org/obo/OBI_0001308 biological activity assay measuring epitope specific IP-10 production by T cells An assay of epitope specific IP-10 production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001282 translation profiling assay http://purl.obolibrary.org/obo/OBI_0000443 analyte assay An assay in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, which mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation. http://purl.obolibrary.org/obo/OBI_0001283 ELISA measuring epitope specific interleukin-15 production by T cells http://purl.obolibrary.org/obo/OBI_0001292 biological activity assay measuring epitope specific interleukin-15 production by T cells An assay of epitope specific interleukin-15 production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001284 cytometric bead array assay measuring epitope specific interleukin-12 production by T cells http://purl.obolibrary.org/obo/OBI_0001391 biological activity assay measuring epitope specific interleukin-12 production by T cells An assay of epitope specific interleukin-12 production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001285 in vitro design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that is done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture. http://purl.obolibrary.org/obo/OBI_0001286 RNAi profiling by array design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which experiment double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression. http://purl.obolibrary.org/obo/OBI_0001288 ELISA measuring epitope specific lymphotoxin A production by T cells http://purl.obolibrary.org/obo/OBI_0001327 biological activity assay measuring epitope specific lymphotoxin A production by T cells An assay of epitope specific lymphotoxin A production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001289 cytometric bead array assay measuring epitope specific interleukin-5 production by T cells http://purl.obolibrary.org/obo/OBI_0001230 biological activity assay measuring epitope specific interleukin-5 production by T cells An assay of epitope specific interleukin-5 production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001290 transcription profiling by array design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that identifies forms and abundance of transcripts in the genome using microarray technology. http://purl.obolibrary.org/obo/OBI_0001291 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17 production by T cells http://purl.obolibrary.org/obo/OBI_0001295 biological activity assay measuring epitope specific interleukin-17 production by T cells An assay of epitope specific interleukin-17 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001292 biological activity assay measuring epitope specific interleukin-15 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects interleukin-15 production by T cells. http://purl.obolibrary.org/obo/OBI_0001293 disease state design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress. http://purl.obolibrary.org/obo/OBI_0001294 wild type organism genotype information http://purl.obolibrary.org/obo/OBI_0001305 genotype information a genotype information about an organism and includes information that there are no known modifications to the genetic background. Generally it is the genotype information of a representative individual from a class of organisms. http://purl.obolibrary.org/obo/OBI_0001295 biological activity assay measuring epitope specific interleukin-17 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects interleukin-17 production by T cells. http://purl.obolibrary.org/obo/OBI_0001296 cytometric bead array assay measuring epitope specific interleukin-17 production by T cells http://purl.obolibrary.org/obo/OBI_0001295 biological activity assay measuring epitope specific interleukin-17 production by T cells An assay of epitope specific interleukin-17 production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001297 cytometric bead array assay measuring epitope specific interleukin-10 production by T cells http://purl.obolibrary.org/obo/OBI_0001209 biological activity assay measuring epitope specific interleukin-10 production by T cells An assay of epitope specific interleukin-10 production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001298 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-21 production by T cells http://purl.obolibrary.org/obo/OBI_0001237 biological activity assay measuring epitope specific interleukin-21 production by T cells An assay of epitope specific interleukin-21 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001299 intracellular cytokine staining assay measuring epitope specific interleukin-5 production by T cells http://purl.obolibrary.org/obo/OBI_0001230 biological activity assay measuring epitope specific interleukin-5 production by T cells An assay of epitope specific interleukin-5 production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001300 cytometric bead array assay measuring epitope specific interleukin-2 production by T cells http://purl.obolibrary.org/obo/OBI_0001445 biological activity assay measuring epitope specific interleukin-2 production by T cells An assay of epitope specific interleukin-2 production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001301 cell culture analyte detection bioassay measuring epitope specific interleukin-16 production by T cells http://purl.obolibrary.org/obo/OBI_0001280 biological activity assay measuring epitope specific interleukin-16 production by T cells An assay of epitope specific interleukin-16 production by T cells that uses a cell culture analyte detection bioassay. http://purl.obolibrary.org/obo/OBI_0001302 ELISA measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells http://purl.obolibrary.org/obo/OBI_0001333 biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001303 intracellular cytokine staining assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells http://purl.obolibrary.org/obo/OBI_0001233 biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001304 RNAi profiling by array assay http://purl.obolibrary.org/obo/OBI_0001985 microarray assay An assay in which double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression. http://purl.obolibrary.org/obo/OBI_0001305 genotype information http://purl.obolibrary.org/obo/OBI_0001404 genetic characteristics information a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc. http://purl.obolibrary.org/obo/OBI_0001306 RNA stability design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that examines the stability and/or decay of RNA transcripts. http://purl.obolibrary.org/obo/OBI_0001308 biological activity assay measuring epitope specific IP-10 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects IP-10 production by T cells. http://purl.obolibrary.org/obo/OBI_0001309 intracellular cytokine staining assay measuring epitope specific interleukin-13 production by T cells http://purl.obolibrary.org/obo/OBI_0001251 biological activity assay measuring epitope specific interleukin-13 production by T cells An assay of epitope specific interleukin-13 production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001310 species comparison design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that assays differences between distinct species. http://purl.obolibrary.org/obo/OBI_0001311 X-ray crystallography assay determining the 3D structure of a T cell epitope:MHC:TCR complex http://purl.obolibrary.org/obo/OBI_0001999 3D structure determining assay of a T cell epitope:MHC:TCR complex A T cell epitope 3D structure determination assay that uses an X-ray crystallography assay. http://purl.obolibrary.org/obo/OBI_0001313 transcription profiling by RT-PCR design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design which aims to examine the transcriptome of a biological sample by reverse transcription PCR (RT-PCR). http://purl.obolibrary.org/obo/OBI_0001314 epitope specific T cell enhancement of B cell mediated immune response http://purl.obolibrary.org/obo/GO_0035399 helper T cell enhancement of B cell mediated immune response A process of T cell enhancement of B cell mediated immune response resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001315 ELISA measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells http://purl.obolibrary.org/obo/OBI_0001276 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001316 epitope specific interleukin-21 production by T cells http://purl.obolibrary.org/obo/GO_0032625 interleukin-21 production A process of interleukin-21 production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001317 flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex http://purl.obolibrary.org/obo/OBI_1110124 assay measuring qualitiative binding of a T cell epitope:MHC:TCR complex A T cell epitope qualitative binding assay that uses a cell-cell binding detection by flow cytometry assay. http://purl.obolibrary.org/obo/OBI_0001318 proteomic profiling by array assay http://purl.obolibrary.org/obo/OBI_0001985 microarray assay An assay that detects proteins in a sample (quantified or otherwise analyzed), e.g. antibody profiling using an array based technology. http://purl.obolibrary.org/obo/OBI_0001319 cell culture analyte detection bioassay measuring epitope specific interferon-gamma production by T cells http://purl.obolibrary.org/obo/OBI_0001414 biological activity assay measuring epitope specific interferon-gamma production by T cells An assay of epitope specific interferon-gamma production by T cells that uses a cell culture analyte detection bioassay. http://purl.obolibrary.org/obo/OBI_0001322 ELISPOT assay measuring epitope specific granzyme B release by T cells http://purl.obolibrary.org/obo/OBI_0001436 biological activity assay measuring epitope specific granzyme B release by T cells A T cell epitope specific granzyme B release assay that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001323 microRNA profiling by array design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which a microRNA array is used to analyse the microRNA component of the transcriptome. http://purl.obolibrary.org/obo/OBI_0001324 in vivo assay measuring T cell epitope specific tolerance induction http://purl.obolibrary.org/obo/OBI_0001484 biological activity assay measuring T cell epitope specific in vivo activity An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment. http://purl.obolibrary.org/obo/OBI_0001325 detection of specific nucleic acids with complementary probes assay measuring epitope specific RANTES production by T cells http://purl.obolibrary.org/obo/OBI_0001232 biological activity assay measuring epitope specific RANTES production by T cells An assay of epitope specific RANTES production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001326 cytometric bead array assay measuring epitope specific interleukin-4 production by T cells http://purl.obolibrary.org/obo/OBI_0001450 biological activity assay measuring epitope specific interleukin-4 production by T cells An assay of epitope specific interleukin-4 production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001327 biological activity assay measuring epitope specific lymphotoxin A production by T cells http://purl.obolibrary.org/obo/OBI_0001400 biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells A T cell epitope specific cytokine production assay that detects lymphotoxin A production by T cells. http://purl.obolibrary.org/obo/OBI_0001328 organism development design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that assays events associated with development. Development applies to organism(s) acquiring a mature state. http://purl.obolibrary.org/obo/OBI_0001329 family history design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which the family history such as traits, characteristics, susceptibility to disease is studied. http://purl.obolibrary.org/obo/OBI_0001330 ELISA measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells http://purl.obolibrary.org/obo/OBI_0001459 biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001331 transcription profiling identification objective http://purl.obolibrary.org/obo/OBI_0000131 molecular feature identification objective A molecular feature identification objective that aims to characterize the abundance of transcripts http://purl.obolibrary.org/obo/OBI_0001332 DNA methylation profiling by array assay http://purl.obolibrary.org/obo/OBI_0000634 DNA methylation profiling assay A DNA methylation profiling assay in which the methylation state of DNA is determined and can be compared between samples using array technology http://purl.obolibrary.org/obo/OBI_0001333 biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 alpha production by T cells. http://purl.obolibrary.org/obo/OBI_0001334 epitope specific granulocyte colony stimulating factor production by T cells http://purl.obolibrary.org/obo/GO_0071611 granulocyte colony-stimulating factor production A process of granulocyte colony stimulating factor production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001335 microRNA profiling by array assay http://purl.obolibrary.org/obo/OBI_0001926 microRNA profiling assay An assay that analyses the microRNA component of the transcriptome using a microRNA array. http://purl.obolibrary.org/obo/OBI_0001336 quality control testing design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which some aspects of the experiment is quality controlled for the purposes of quality assurance. http://purl.obolibrary.org/obo/OBI_0001337 clinical history design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that the organism's clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied. http://purl.obolibrary.org/obo/OBI_0001339 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-4 production by T cells http://purl.obolibrary.org/obo/OBI_0001450 biological activity assay measuring epitope specific interleukin-4 production by T cells An assay of epitope specific interleukin-4 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001341 cell culture analyte detection bioassay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells http://purl.obolibrary.org/obo/OBI_0001233 biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses a cell culture analyte detection bioassay. http://purl.obolibrary.org/obo/OBI_0001342 intracellular cytokine staining assay measuring epitope specific interleukin-21 production by T cells http://purl.obolibrary.org/obo/OBI_0001237 biological activity assay measuring epitope specific interleukin-21 production by T cells An assay of epitope specific interleukin-21 production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001343 detection of specific nucleic acids with complementary probes assay measuring epitope specific monocyte chemotactic protein-1 production by T cells http://purl.obolibrary.org/obo/OBI_0001465 biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001344 ELISA measuring epitope specific monocyte chemotactic protein-1 production by T cells http://purl.obolibrary.org/obo/OBI_0001465 biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001345 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 4 production by T cells. http://purl.obolibrary.org/obo/OBI_0001346 ELISA measuring epitope specific interleukin-21 production by T cells http://purl.obolibrary.org/obo/OBI_0001237 biological activity assay measuring epitope specific interleukin-21 production by T cells An assay of epitope specific interleukin-21 production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001348 in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity http://purl.obolibrary.org/obo/OBI_0001484 biological activity assay measuring T cell epitope specific in vivo activity An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity. http://purl.obolibrary.org/obo/OBI_0001349 cytometric bead array assay measuring epitope specific interleukin-13 production by T cells http://purl.obolibrary.org/obo/OBI_0001251 biological activity assay measuring epitope specific interleukin-13 production by T cells An assay of epitope specific interleukin-13 production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001350 detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-gamma production by T cells http://purl.obolibrary.org/obo/OBI_0001414 biological activity assay measuring epitope specific interferon-gamma production by T cells An assay of epitope specific interferon-gamma production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001351 epitope specific tumor necrosis factor superfamily cytokine production by T cells http://purl.obolibrary.org/obo/GO_0071706 tumor necrosis factor superfamily cytokine production A process of tumor necrosis factor superfamily cytokine production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001352 allele information http://purl.obolibrary.org/obo/OBI_0001364 genetic alteration information a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition. http://purl.obolibrary.org/obo/OBI_0001353 cytometric bead array assay measuring epitope specific tumor necrosis factor production by T cells http://purl.obolibrary.org/obo/OBI_0001416 biological activity assay measuring epitope specific tumor necrosis factor production by T cells A T cell epitope specific tumor necrosis factor production assay that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001354 ELISPOT assay measuring epitope specific interleukin-17 production by T cells http://purl.obolibrary.org/obo/OBI_0001295 biological activity assay measuring epitope specific interleukin-17 production by T cells An assay of epitope specific interleukin-17 production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001356 detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-beta production by T cells http://purl.obolibrary.org/obo/OBI_0001390 biological activity assay measuring epitope specific interferon-beta production by T cells An assay of epitope specific interferon-beta production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001357 detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells http://purl.obolibrary.org/obo/OBI_0001233 biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001358 post-transcriptional modification design http://purl.obolibrary.org/obo/OBI_0000115 intervention design A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting. http://purl.obolibrary.org/obo/OBI_0001359 ELISA measuring epitope specific interleukin-8 production by T cells http://purl.obolibrary.org/obo/OBI_0001218 biological activity assay measuring epitope specific interleukin-8 production by T cells An assay of epitope specific interleukin-8 production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001360 cytometric bead array assay measuring epitope specific interleukin-6 production by T cells http://purl.obolibrary.org/obo/OBI_0001451 biological activity assay measuring epitope specific interleukin-6 production by T cells An assay of epitope specific interleukin-6 production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001361 transcription profiling by RT-PCR assay http://purl.obolibrary.org/obo/OBI_0002692 polymerase chain reaction assay A transcription profiling assay that uses reverse transcription PCR (RT-PCR). http://purl.obolibrary.org/obo/OBI_0001362 epitope specific chemokine (C-C motif) ligand 4 production by T cells http://purl.obolibrary.org/obo/GO_0071606 chemokine (C-C motif) ligand 4 production A process of chemokine (C-C motif) ligand 4 production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001363 biological activity assay measuring epitope specific interleukin-23 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects interleukin-23 production by T cells. http://purl.obolibrary.org/obo/OBI_0001364 genetic alteration information http://purl.obolibrary.org/obo/OBI_0001404 genetic characteristics information a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc. http://purl.obolibrary.org/obo/OBI_0001365 cellular process design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that aims to study the processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. http://purl.obolibrary.org/obo/OBI_0001366 epitope specific RANTES production by T cells http://purl.obolibrary.org/obo/GO_0071609 chemokine (C-C motif) ligand 5 production A process of RANTES production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001367 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-10 production by T cells http://purl.obolibrary.org/obo/OBI_0001209 biological activity assay measuring epitope specific interleukin-10 production by T cells An assay of epitope specific interleukin-10 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001368 cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells http://purl.obolibrary.org/obo/OBI_0001400 biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001369 wild type allele information http://purl.obolibrary.org/obo/OBI_0001352 allele information an allele information that is about the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism. http://purl.obolibrary.org/obo/OBI_0001370 intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells http://purl.obolibrary.org/obo/OBI_0001345 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001371 epitope specific granzyme B production by T cells http://purl.obolibrary.org/obo/GO_0071613 granzyme B production A process of granzyme B production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001373 epitope specific interleukin-8 production by T cells http://purl.obolibrary.org/obo/GO_0032637 interleukin-8 production A process of interleukin-8 production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001374 injury design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which the response of an organism(s) to injury or damage is studied. http://purl.obolibrary.org/obo/OBI_0001376 intracellular cytokine staining assay measuring epitope specific interleukin-3 production by T cells http://purl.obolibrary.org/obo/OBI_0001406 biological activity assay measuring epitope specific interleukin-3 production by T cells An assay of epitope specific interleukin-3 production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001377 organism status comparison design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that compares samples from live and dead organisms. http://purl.obolibrary.org/obo/OBI_0001378 ELISA measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells http://purl.obolibrary.org/obo/OBI_0001345 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001379 cytometric bead array assay measuring epitope specific interferon-gamma production by T cells http://purl.obolibrary.org/obo/OBI_0001414 biological activity assay measuring epitope specific interferon-gamma production by T cells An assay of epitope specific interferon-gamma production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001380 biological activity assay measuring epitope specific interleukin-18 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects interleukin-18 production by T cells. http://purl.obolibrary.org/obo/OBI_0001381 epitope specific interleukin-23 production by T cells http://purl.obolibrary.org/obo/GO_0032627 interleukin-23 production A process of interleukin-23 production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001382 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-27 production by T cells http://purl.obolibrary.org/obo/OBI_0001198 biological activity assay measuring epitope specific interleukin-27 production by T cells An assay of epitope specific interleukin-27 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001383 detection of specific nucleic acids with complementary probes assay measuring epitope specific IP-10 production by T cells http://purl.obolibrary.org/obo/OBI_0001308 biological activity assay measuring epitope specific IP-10 production by T cells An assay of epitope specific IP-10 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001384 cell culture analyte detection bioassay measuring epitope specific interleukin-3 production by T cells http://purl.obolibrary.org/obo/OBI_0001406 biological activity assay measuring epitope specific interleukin-3 production by T cells An assay of epitope specific interleukin-3 production by T cells that uses a cell culture analyte detection bioassay. http://purl.obolibrary.org/obo/OBI_0001385 intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells http://purl.obolibrary.org/obo/OBI_0001400 biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001386 epitope specific monocyte chemotactic protein-1 production by T cells http://purl.obolibrary.org/obo/GO_0071605 monocyte chemotactic protein-1 production A process of monocyte chemotactic protein-1 production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001387 genotyping by array design http://purl.obolibrary.org/obo/OBI_0001444 genotyping design A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using microarray technology. http://purl.obolibrary.org/obo/OBI_0001388 biological activity assay measuring epitope specific interleukin-1 alpha production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects interleukin-1 alpha production by T cells. http://purl.obolibrary.org/obo/OBI_0001389 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-6 production by T cells http://purl.obolibrary.org/obo/OBI_0001451 biological activity assay measuring epitope specific interleukin-6 production by T cells An assay of epitope specific interleukin-6 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001390 biological activity assay measuring epitope specific interferon-beta production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects interferon-beta production by T cells. http://purl.obolibrary.org/obo/OBI_0001391 biological activity assay measuring epitope specific interleukin-12 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects interleukin-12 production by T cells. http://purl.obolibrary.org/obo/OBI_0001392 in vivo assay measuring epitope specific T cell killing http://purl.obolibrary.org/obo/OBI_1110130 biological activity assay measuring epitope specific T cell killing A T cell epitope specific killing assay that uses an in vivo cell mediated cell killing assay. http://purl.obolibrary.org/obo/OBI_0001394 epitope specific cytotoxic T cell degranulation http://purl.obolibrary.org/obo/GO_0043316 cytotoxic T cell degranulation A process of cytotoxic T cell degranulation resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001395 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-23 production by T cells http://purl.obolibrary.org/obo/OBI_0001363 biological activity assay measuring epitope specific interleukin-23 production by T cells An assay of epitope specific interleukin-23 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001396 stimulus or stress design http://purl.obolibrary.org/obo/OBI_0000115 intervention design A study design in which the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc. http://purl.obolibrary.org/obo/OBI_0001397 cytometric bead array assay measuring epitope specific granulocyte colony stimulating factor production by T cells http://purl.obolibrary.org/obo/OBI_0001600 biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001398 protein and DNA interaction identification objective http://purl.obolibrary.org/obo/OBI_0000113 sequence feature identification objective A sequence feature identification objective that aims to characterize the interactions between protein and DNA which includes identification of transcription factor binding sites. http://purl.obolibrary.org/obo/OBI_0001399 epitope specific interleukin-22 production by T cells http://purl.obolibrary.org/obo/GO_0032626 interleukin-22 production A process of interleukin-22 production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001400 biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects tumor necrosis factor superfamily cytokine production by T cells. http://purl.obolibrary.org/obo/OBI_0001401 protocol optimization design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design where different protocols or protocol parameters are compared aims to find an optimized protocol http://purl.obolibrary.org/obo/OBI_0001402 promoter activity detection by reporter gene assay measuring epitope specific interleukin-2 production by T cells http://purl.obolibrary.org/obo/OBI_0001445 biological activity assay measuring epitope specific interleukin-2 production by T cells An assay of epitope specific interleukin-2 production by T cells that uses a promoter activity detection by reporter gene assay. http://purl.obolibrary.org/obo/OBI_0001404 genetic characteristics information http://purl.obolibrary.org/obo/IAO_0000027 data item a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes. http://purl.obolibrary.org/obo/OBI_0001405 cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells http://purl.obolibrary.org/obo/OBI_0001333 biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001406 biological activity assay measuring epitope specific interleukin-3 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects interleukin-3 production by T cells. http://purl.obolibrary.org/obo/OBI_0001407 biological activity assay measuring epitope specific T cell activation http://purl.obolibrary.org/obo/OBI_0002055 assay measuring T cell epitope specific biological activity A T cell epitope dependent biological activity assay that detects T cell activation. http://purl.obolibrary.org/obo/OBI_0001408 imprinting design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design where differences in genetic imprinting of maternally- and paternally-inherited chromosomes (e.g., due to in vivo differences in chemical modification and/or chromatin structure) are compared. http://purl.obolibrary.org/obo/OBI_0001409 cell cycle design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that assays events that occur in relation to the cell cycle, which is the period between the formation of a cell, by division of its mother cell and the time when the cell itself divides to form two daughter cells. http://purl.obolibrary.org/obo/OBI_0001410 translation profiling design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, where mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation. http://purl.obolibrary.org/obo/OBI_0001411 cell type comparison design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that compares cells of different type, for example different cell lines. http://purl.obolibrary.org/obo/OBI_0001412 cytometric bead array assay measuring epitope specific RANTES production by T cells http://purl.obolibrary.org/obo/OBI_0001232 biological activity assay measuring epitope specific RANTES production by T cells An assay of epitope specific RANTES production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001413 cell culture analyte detection bioassay measuring epitope specific interleukin-6 production by T cells http://purl.obolibrary.org/obo/OBI_0001451 biological activity assay measuring epitope specific interleukin-6 production by T cells An assay of epitope specific interleukin-6 production by T cells that uses a cell culture analyte detection bioassay. http://purl.obolibrary.org/obo/OBI_0001414 biological activity assay measuring epitope specific interferon-gamma production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects interferon-gamma production by T cells. http://purl.obolibrary.org/obo/OBI_0001415 epitope specific interleukin-9 production by T cells http://purl.obolibrary.org/obo/GO_0032638 interleukin-9 production A process of interleukin-9 production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001416 biological activity assay measuring epitope specific tumor necrosis factor production by T cells http://purl.obolibrary.org/obo/OBI_0001400 biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that detects tumor necrosis factor production. http://purl.obolibrary.org/obo/OBI_0001417 ChIP-chip by tiling array design http://purl.obolibrary.org/obo/OBI_0001403 ChIP-chip design A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and tiling microarray (chip) assays. http://purl.obolibrary.org/obo/OBI_0001418 dose response design http://purl.obolibrary.org/obo/OBI_0000951 compound treatment design A study design that examines the relationship between the size of the administered dose and the extent of the response. http://purl.obolibrary.org/obo/OBI_0001419 ChIP-chip by tiling array assay http://purl.obolibrary.org/obo/OBI_0001248 ChIP-chip assay A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a tiling array that covers stretches of DNA to to detect which elements in those stretches are present in the isolated chromatin http://purl.obolibrary.org/obo/OBI_0001420 epitope specific helper T cell enhancement of T cell mediated immune response http://purl.obolibrary.org/obo/GO_0035398 helper T cell enhancement of T cell mediated immune response A process of helper T cell enhancement of T cell mediated immune response resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001421 epitope specific interferon-beta production by T cells http://purl.obolibrary.org/obo/GO_0032608 interferon-beta production A process of interferon-beta production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001422 organism part comparison design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that compares tissues, regions, organs within or between organisms http://purl.obolibrary.org/obo/OBI_0001423 intracellular material detection measuring epitope specific granzyme B release by T cells http://purl.obolibrary.org/obo/OBI_0001436 biological activity assay measuring epitope specific granzyme B release by T cells A T cell epitope specific granzyme B release assay that uses an intracellular material detection by flow cytometry assay. http://purl.obolibrary.org/obo/OBI_0001425 protein binding site identification design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that investigates protein binding sites on nucleic acids. http://purl.obolibrary.org/obo/OBI_0001426 sex comparison design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that assays differences associated with an organism's sex, gender or mating type. http://purl.obolibrary.org/obo/OBI_0001427 transcription profiling by tiling array design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which gene expression on a genome-wide basis is evaluated, without bias toward coding or noncoding regions, using tiling arrays containing oligonucleotides that are either overlapping or spaced at regular intervals. http://purl.obolibrary.org/obo/OBI_0001429 cell differentiation design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that assays events associated with cell development or differentiation. http://purl.obolibrary.org/obo/OBI_0001430 transcription profiling design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that identifies forms and abundance of transcripts in the genome. http://purl.obolibrary.org/obo/OBI_0001432 operon identification design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that identifies locations and members of operons in a genome. http://purl.obolibrary.org/obo/OBI_0001433 radio immuno assay measuring epitope specific interferon-gamma production by T cells http://purl.obolibrary.org/obo/OBI_0001414 biological activity assay measuring epitope specific interferon-gamma production by T cells An assay of epitope specific interferon-gamma production by T cells that uses a radio immuno assay. http://purl.obolibrary.org/obo/OBI_0001435 DNA methylation profiling by high throughput sequencing design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which the methylation state of DNA is determined and is compared between samples using high throughput sequencing technology. http://purl.obolibrary.org/obo/OBI_0001436 biological activity assay measuring epitope specific granzyme B release by T cells http://purl.obolibrary.org/obo/OBI_0001269 biological activity assay measuring epitope specific cytotoxic T cell degranulation A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme B release by T cells. http://purl.obolibrary.org/obo/OBI_0001437 intracellular cytokine staining assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells http://purl.obolibrary.org/obo/OBI_0001459 biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001438 ELISA measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells http://purl.obolibrary.org/obo/OBI_0001456 biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001439 epitope specific chemokine (C-X-C motif) ligand 9 production by T cells http://purl.obolibrary.org/obo/GO_0035393 chemokine (C-X-C motif) ligand 9 production A process of chemokine (C-X-C motif) ligand 9 production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001440 all pairs design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which all specimens are compared to every other specimen. http://purl.obolibrary.org/obo/OBI_0001441 proteomic profiling by array design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which proteins in a sample are detected, quantified or otherwise analysed, through an array-based technology. http://purl.obolibrary.org/obo/OBI_0001444 genotyping design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs. http://purl.obolibrary.org/obo/OBI_0001445 biological activity assay measuring epitope specific interleukin-2 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects interleukin-2 production by T cells. http://purl.obolibrary.org/obo/OBI_0001446 epitope specific interleukin-15 production by T cells http://purl.obolibrary.org/obo/GO_0032618 interleukin-15 production A process of interleukin-15 production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001447 epitope specific macrophage inflammatory protein-1 gamma production by T cells http://purl.obolibrary.org/obo/GO_0071607 macrophage inflammatory protein-1 gamma production A process of macrophage inflammatory protein-1 gamma production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001448 individual genetic characteristics comparison design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design where genotype, haplotype, or other individual genetic characteristics are compared. http://purl.obolibrary.org/obo/OBI_0001449 biological activity assay measuring epitope specific interleukin-1 beta production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects interleukin-1 beta production by T cells. http://purl.obolibrary.org/obo/OBI_0001450 biological activity assay measuring epitope specific interleukin-4 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects interleukin-4 production by T cells. http://purl.obolibrary.org/obo/OBI_0001451 biological activity assay measuring epitope specific interleukin-6 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects interleukin-6 production by T cells. http://purl.obolibrary.org/obo/OBI_0001452 cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor production by T cells http://purl.obolibrary.org/obo/OBI_0001416 biological activity assay measuring epitope specific tumor necrosis factor production by T cells A T cell epitope specific tumor necrosis factor production assay that uses a cell culture analyte detection bioassay. http://purl.obolibrary.org/obo/OBI_0001453 intracellular cytokine staining assay measuring epitope specific lymphotoxin A production by T cells http://purl.obolibrary.org/obo/OBI_0001385 intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells An assay of epitope specific lymphotoxin A production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001454 pathogenicity design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed. http://purl.obolibrary.org/obo/OBI_0001455 ELISPOT assay measuring epitope specific interleukin-5 production by T cells http://purl.obolibrary.org/obo/OBI_0001230 biological activity assay measuring epitope specific interleukin-5 production by T cells An assay of epitope specific interleukin-5 production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001456 biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 gamma production by T cells. http://purl.obolibrary.org/obo/OBI_0001457 cytometric bead array assay measuring epitope specific interleukin-8 production by T cells http://purl.obolibrary.org/obo/OBI_0001218 biological activity assay measuring epitope specific interleukin-8 production by T cells An assay of epitope specific interleukin-8 production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001459 biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. http://purl.obolibrary.org/obo/OBI_0001460 genetic modification design http://purl.obolibrary.org/obo/OBI_0000115 intervention design A study design in which an organism(s) is studied that has had genetic material removed, rearranged, mutagenized or added, such as in a knock out. http://purl.obolibrary.org/obo/OBI_0001461 ELISA measuring epitope specific granzyme B release by T cells http://purl.obolibrary.org/obo/OBI_0001436 biological activity assay measuring epitope specific granzyme B release by T cells A T cell epitope specific granzyme B release assay that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001462 epitope specific IP-10 production by T cells http://purl.obolibrary.org/obo/GO_0071612 IP-10 production A process of IP-10 production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001464 strain comparison design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species. http://purl.obolibrary.org/obo/OBI_0001465 biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects monocyte chemotactic protein-1 production by T cells. http://purl.obolibrary.org/obo/OBI_0001466 intracellular cytokine staining assay measuring epitope specific interleukin-12 production by T cells http://purl.obolibrary.org/obo/OBI_0001391 biological activity assay measuring epitope specific interleukin-12 production by T cells An assay of epitope specific interleukin-12 production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001467 in vivo assay measuring T cell epitope specific disease exacerbation http://purl.obolibrary.org/obo/OBI_0001484 biological activity assay measuring T cell epitope specific in vivo activity An efficacy of T cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment. http://purl.obolibrary.org/obo/OBI_0001468 cell specimen http://purl.obolibrary.org/obo/OBI_0100051 specimen A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture. http://purl.obolibrary.org/obo/OBI_0001469 monospecific T cell recognition assay measuring MHC ligand processing and presentation http://purl.obolibrary.org/obo/OBI_1110125 assay measuring MHC ligand processing and presentation A MHC ligand processing and presentation assay in which the presence of a specific ligand in an eluate is detected using the response of T cells that are known to be monospecific for that ligand as a readout. http://purl.obolibrary.org/obo/OBI_0001470 epitope specific interleukin-17F production by T cells http://purl.obolibrary.org/obo/GO_0097088 interleukin-17F production A process of interleukin-17F production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001471 T cell epitope specific immune intervention http://purl.obolibrary.org/obo/OBI_0001192 epitope specific immune intervention An epitope specific immune intervention in which the induced response targets a T cell epitope http://purl.obolibrary.org/obo/OBI_0001472 specimen with known storage state http://purl.obolibrary.org/obo/OBI_0100051 specimen A specimen for which it is known whether it has been subjected to storage of a specified type. http://purl.obolibrary.org/obo/OBI_0001473 in vivo assay measuring T cell epitope specific protection from tumor challenge http://purl.obolibrary.org/obo/OBI_0002073 in vivo assay measuring T cell epitope specific protection from challenge A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on tumor burden. http://purl.obolibrary.org/obo/OBI_0001474 lowess group transformation http://purl.obolibrary.org/obo/OBI_0001477 lowess transformation A lowess transformation where a potentially different normalization curve is generated and used for two or more groups (delineated by some criteria); criteria could include blocks (e.g. print-tip groups) on an array, or the day on which mass spectrometry was performed. http://purl.obolibrary.org/obo/OBI_0001475 in vivo assay measuring T cell epitope specific protection from infectious challenge based on pathogen burden http://purl.obolibrary.org/obo/OBI_0002073 in vivo assay measuring T cell epitope specific protection from challenge A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on pathogen burden. http://purl.obolibrary.org/obo/OBI_0001476 phage display binding assay http://purl.obolibrary.org/obo/OBI_0001146 binding assay A binding assay in which a collection of phages expressing a library of different peptides or protein fragnments is used to infect cells, followed by screening for cells that bind a protein of interest, and identifiying the sequence of infecting phages to determine a suitable binding partner. http://purl.obolibrary.org/obo/OBI_0001477 lowess transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A data transformation of normalizing ratio data by using a locally weighted polynomial regression (typically after a log transformation). The regression can be performed on log ratios resulting from the relation of two data sets versus the average log intensity data from the same two data sets or it can be performed on raw or log transformed values from one data set versus values from another. The goal could be to remove intensity-dependent dye-specific effects from the set of pair wise ratios. This method can be applied globally, or limited by one or more specified criteria. http://purl.obolibrary.org/obo/OBI_0001478 mass spectrometry assay measuring MHC ligand processing and presentation http://purl.obolibrary.org/obo/OBI_1110125 assay measuring MHC ligand processing and presentation A MHC ligand processing and presentation assay that uses a mass spectrometry assay to identify eluted ligands http://purl.obolibrary.org/obo/OBI_0001480 phage display library panning http://purl.obolibrary.org/obo/OBI_0000094 material processing Phage display library panning is a process in which a diverse collection of phages encoding peptides or proteins are screened and the ones encoding active peptides/proteins are selected in an iterative process similar to natural selection. http://purl.obolibrary.org/obo/OBI_0001481 lowess global transformation http://purl.obolibrary.org/obo/OBI_0001477 lowess transformation A lowess transformation where the same normalization curve is used for all members of the data set; e.g. Features on an array, picked spots on a gel, or measured metabolites in a sample. http://purl.obolibrary.org/obo/OBI_0001482 intracellular cytokine staining assay measuring epitope specific transforming growth factor-beta production by T cells http://purl.obolibrary.org/obo/OBI_0001264 biological activity assay measuring epitope specific transforming growth factor-beta production by T cells An assay of epitope specifictransforming growth factor-beta production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001483 cell collecting http://purl.obolibrary.org/obo/OBI_0600014 material component separation A planned process that collects cells from culture. http://purl.obolibrary.org/obo/OBI_0001484 biological activity assay measuring T cell epitope specific in vivo activity http://purl.obolibrary.org/obo/OBI_0002055 assay measuring T cell epitope specific biological activity A T cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment. http://purl.obolibrary.org/obo/OBI_0001485 purified MHC molecule preparation http://purl.obolibrary.org/obo/OBI_0001633 purified material A mixture containing MHC molecules that was purified to remove non-MHC molecular entities. http://purl.obolibrary.org/obo/OBI_0001487 B cell epitope specific immune intervention http://purl.obolibrary.org/obo/OBI_0001192 epitope specific immune intervention An epitope specific immune intervention in which the induced response targets a B cell epitope http://purl.obolibrary.org/obo/OBI_0001489 mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from cellular MHC http://purl.obolibrary.org/obo/OBI_0001478 mass spectrometry assay measuring MHC ligand processing and presentation A mass spectrometry of MHC ligands assay that identifies eluted ligands from cell bound MHC. http://purl.obolibrary.org/obo/OBI_0001490 cytometric bead array measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells http://purl.obolibrary.org/obo/OBI_0001233 biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001491 radioactivity detection binding assay http://purl.obolibrary.org/obo/OBI_0001146 binding assay A binding assay that uses radioactivity detection as an indicator of binding. http://purl.obolibrary.org/obo/OBI_0001492 in vivo assay measuring T cell epitope specific protection based on survival http://purl.obolibrary.org/obo/OBI_0002073 in vivo assay measuring T cell epitope specific protection from challenge A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on survival. http://purl.obolibrary.org/obo/OBI_0001493 cell bound MHC competitive binding assay of a MHC:ligand complex using T cell epitope recognition http://purl.obolibrary.org/obo/OBI_0001550 cell bound MHC binding assay measuring binding of a MHC:ligand complex A cell bound MHC binding assay that uses a T cell epitope recognition assay. http://purl.obolibrary.org/obo/OBI_0001494 linear amplification http://purl.obolibrary.org/obo/OBI_0600058 enzymatic amplification An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template. http://purl.obolibrary.org/obo/OBI_0001495 biological activity assay measuring epitope specific T cell helper activity http://purl.obolibrary.org/obo/OBI_0002055 assay measuring T cell epitope specific biological activity A T cell epitope dependent biological activity assay that detects the ability of epitope specific helper T cells to enhance either B cell or T cell adaptive immune response function. http://purl.obolibrary.org/obo/OBI_0001496 intracellular cytokine staining assay measuring epitope specific interleukin-22 production by T cells http://purl.obolibrary.org/obo/OBI_0001217 biological activity assay measuring epitope specific interleukin-22 production by T cells An assay of epitope specific interleukin-22 production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001497 biological activity assay measuring epitope specific perforin release by T cells http://purl.obolibrary.org/obo/OBI_0001269 biological activity assay measuring epitope specific cytotoxic T cell degranulation A T cell epitope specific cytotoxic T cell degranulation assay that detects perforin release by T cells. http://purl.obolibrary.org/obo/OBI_0001498 atmosphere http://purl.obolibrary.org/obo/OBI_0000997 growth environment A growth environment pertaining to the atmospheric conditions that is used to culture or grow an organism. http://purl.obolibrary.org/obo/OBI_0001499 fluorescence detection binding assay http://purl.obolibrary.org/obo/OBI_0001146 binding assay A binding assay that uses fluorescence detection as an indicator of binding http://purl.obolibrary.org/obo/OBI_0001500 coelution assay measuring MHC ligand processing and presentation using T cell recognition of HPLC fractionated eluate compared to synthetic ligand http://purl.obolibrary.org/obo/OBI_1110125 assay measuring MHC ligand processing and presentation A MHC ligand processing and presentation assay in which an HPL chromatography is run to separate an input mixture of ligands eluted from MHC into fractions. These fractions are tested for recognition by T cells and compared to the recognition of a synthetic ligand that is presumed to be the recognized epitope. Identical HPLC fractionation and T cell recognition patterns confirm that the specific ligand was presented by MHC molecules. http://purl.obolibrary.org/obo/OBI_0001501 fluorescence detection assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay in which a material's fluorescence is determined. http://purl.obolibrary.org/obo/OBI_0001502 epitope specific perforin production by T cells http://purl.obolibrary.org/obo/GO_0035944 perforin production The production of perforin, an immune mediator molecule involved in T cell degranulation, resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001503 MHC protein complex binding to ligand http://purl.obolibrary.org/obo/OBI_0001588 binding The process in which a ligand binds to an MHC molecule to form a stable complex http://purl.obolibrary.org/obo/OBI_0001504 dissection http://purl.obolibrary.org/obo/OBI_0000094 material processing A planned process that separates and isolates tissues for surgical purposes, or for the analysis or study of their structures. http://purl.obolibrary.org/obo/OBI_0001505 purification http://purl.obolibrary.org/obo/OBI_0600014 material component separation A planned process to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest http://purl.obolibrary.org/obo/OBI_0001506 specimen with pre- or post-mortem status http://purl.obolibrary.org/obo/OBI_0100051 specimen A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism. http://purl.obolibrary.org/obo/OBI_0001507 in vivo assay measuring T cell epitope specific treatment of disease http://purl.obolibrary.org/obo/OBI_0001484 biological activity assay measuring T cell epitope specific in vivo activity An efficacy of T cell epitope intervention experiment that detects a decrease in disease. http://purl.obolibrary.org/obo/OBI_0001510 mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from secreted MHC http://purl.obolibrary.org/obo/OBI_0001478 mass spectrometry assay measuring MHC ligand processing and presentation A mass spectrometry of MHC ligands that identifies eluted ligands from secreted MHC. http://purl.obolibrary.org/obo/OBI_0001511 disposition to be a product of antigen processing and presentation http://purl.obolibrary.org/obo/BFO_0000016 disposition A disposition of a material entity to be presented by MHC molecules on the cell surface as a result of antigen processing by an antigen presenting cell. http://purl.obolibrary.org/obo/OBI_0001512 cytometric bead array assay measuring epitope specific interleukin-17A production by T cells http://purl.obolibrary.org/obo/OBI_0001773 biological activity assay measuring epitope specific interleukin-17A production by T cells A T cell epitope specific interleukin-17A production assay that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001513 purified MHC competitive binding assay of a MHC:ligand complex using radioactivity detection http://purl.obolibrary.org/obo/OBI_0001555 purified MHC binding assay measuring binding of a MHC:ligand complex A purified MHC binding assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. http://purl.obolibrary.org/obo/OBI_0001514 minimal inhibitory concentration http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum A scalar measurement datum that indicates the lowest concentration at which a specific compound significantly inhibits a process from occurring compared to in the absence of the compound. http://purl.obolibrary.org/obo/OBI_0001515 material maintenance service http://purl.obolibrary.org/obo/OBI_0001528 material service A material processing service in which a service provider makes physical modifications to a specified input material, such that at least one of the specified outputs of this process is a modified version of a specified input material. http://purl.obolibrary.org/obo/OBI_0001516 cell lysate MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using radioactivity detection http://purl.obolibrary.org/obo/OBI_0001991 assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex A cell lysate MHC ligand binding half maximal effective concentration (EC50) determination assay that uses radioactivity detection to measure direct ligand binding. http://purl.obolibrary.org/obo/OBI_0001517 cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection http://purl.obolibrary.org/obo/OBI_0001992 assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex A cell bound MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. http://purl.obolibrary.org/obo/OBI_0001518 epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells http://purl.obolibrary.org/obo/GO_0072535 tumor necrosis factor (ligand) superfamily member 11 production A process of tumor necrosis factor (ligand) superfamily member 11 production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001519 cell lysate MHC direct binding assay of a MHC:ligand complex using fluorescence detection http://purl.obolibrary.org/obo/OBI_0001579 cell lysate MHC binding assay measuring binding of a MHC:ligand complex A cell lysate MHC binding assay that uses fluorescence detection to detect direct binding. http://purl.obolibrary.org/obo/OBI_0001520 cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection http://purl.obolibrary.org/obo/OBI_0001992 assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex A cell bound MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. http://purl.obolibrary.org/obo/OBI_0001521 ELISA measuring epitope specific granulocyte colony stimulating factor production by T cells http://purl.obolibrary.org/obo/OBI_0001600 biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001522 sequence assembly algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm An algorithm used to assemble individual sequence reads into larger contiguous sequences (contigs). Assembly details include but are not limited to assembler type (overlap-layout-consensus, deBruijn), assembler version, and any relevant quality control information such as per cent known genes/ESTs captured. http://purl.obolibrary.org/obo/OBI_0001523 cytometric bead array assay measuring epitope specific interleukin-17F production by T cells http://purl.obolibrary.org/obo/OBI_0001772 biological activity assay measuring epitope specific interleukin-17F production by T cells A T cell epitope specific interleukin-17F production assay that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001524 cell bound MHC direct binding assay measuring equilibrium association constant [KA] of a MHC:ligand complex using fluorescence detection http://purl.obolibrary.org/obo/OBI_0001987 assay measuring the association constant [KA] of a MHC:ligand complex A cell bound MHC ligand binding equilibrium association constant (KA) determination assay that uses fluorescence detection to detect direct binding. http://purl.obolibrary.org/obo/OBI_0001525 PDB file http://purl.obolibrary.org/obo/OBI_0001155 3D structural organization datum A 3d structural organization datum capturing the results of X-ray crystallography or NMR experiment that is formatted as specified by the Protein Databank (http://www.wwpdb.org/docs.html). A PDB file can describe the structure of multiple molecules, each of which has a different chain identifier assigned. http://purl.obolibrary.org/obo/OBI_0001526 epitope specific interleukin-17A production by T cells http://purl.obolibrary.org/obo/GO_0097087 interleukin-17A production A process of interleukin-17A production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001527 support service http://purl.obolibrary.org/obo/OBI_0001173 service A service in which the service provider assists the consumer in activities directly or indirectly associated with the production and analysis of experimental research data. http://purl.obolibrary.org/obo/OBI_0001528 material service http://purl.obolibrary.org/obo/OBI_0001173 service A service which has a material entity as specified input and/or specified output. http://purl.obolibrary.org/obo/OBI_0001529 data analysis service http://purl.obolibrary.org/obo/OBI_0001530 data service A service in which a service consumer provides some input data and a service provider transforms, models, or interprets the input data and returns this generated data as output. http://purl.obolibrary.org/obo/OBI_0001530 data service http://purl.obolibrary.org/obo/OBI_0001173 service A service that has some information content entity as input and output. http://purl.obolibrary.org/obo/OBI_0001531 purified MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection http://purl.obolibrary.org/obo/OBI_0001990 assay measuring the half life of a MHC:ligand complex A purified MHC ligand half life of binding determination assay that uses fluorescence detection to measure direct ligand binding. http://purl.obolibrary.org/obo/OBI_0001532 cytometric bead array assay measuring epitope specific interleukin-9 production by T cells http://purl.obolibrary.org/obo/OBI_0001253 biological activity assay measuring interleukin-9 production by T cells An assay of epitope specific interleukin-9 production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001533 data storage service http://purl.obolibrary.org/obo/OBI_0001530 data service A storage service in which a service consumer provides data as input which a service provider stores and returns as output in its original form. http://purl.obolibrary.org/obo/OBI_0001534 purified MHC competitive binding assay measuring binding of a MHC:ligand complex using fluorescence detection http://purl.obolibrary.org/obo/OBI_0001555 purified MHC binding assay measuring binding of a MHC:ligand complex A purified MHC binding assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. http://purl.obolibrary.org/obo/OBI_0001535 epitope specific interleukin-7 production by T cells http://purl.obolibrary.org/obo/GO_0032636 interleukin-7 production A process of interleukin-7 production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001536 equilibrium dissociation constant (KD) http://purl.obolibrary.org/obo/OBI_0001144 binding constant A binding constant defined as the ratio of kon over koff (on-rate of binding divided by off-rate) http://purl.obolibrary.org/obo/OBI_0001537 purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection http://purl.obolibrary.org/obo/OBI_0001988 assay measuring the dissociation constant [KD] of a MHC:ligand complex A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. http://purl.obolibrary.org/obo/OBI_0001538 training service http://purl.obolibrary.org/obo/OBI_0001173 service A service in which the service provider offers educational materials or events, such as courses, workshops or graduate programs, to the service consumer. http://purl.obolibrary.org/obo/OBI_0001539 cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection http://purl.obolibrary.org/obo/OBI_0001988 assay measuring the dissociation constant [KD] of a MHC:ligand complex A cell bound MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. http://purl.obolibrary.org/obo/OBI_0001540 obsolete T cell recognition of eluted MHC ligand assay http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class An assay that identifies an MHC ligand using a T cell response assay as a readout http://purl.obolibrary.org/obo/OBI_0001541 purified MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detection http://purl.obolibrary.org/obo/OBI_0001994 assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complex A purified MHC ligand binding on rate (kon) determination assay that uses fluorescence detection to measure direct ligand binding. http://purl.obolibrary.org/obo/OBI_0001542 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-13 production by T cells http://purl.obolibrary.org/obo/OBI_0001251 biological activity assay measuring epitope specific interleukin-13 production by T cells An assay of epitope specific interleukin-13 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001543 purified MHC direct binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by EC50 using fluorescence detection http://purl.obolibrary.org/obo/OBI_0001988 assay measuring the dissociation constant [KD] of a MHC:ligand complex A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses fluorescence detection to measure direct ligand binding and provides EC50 values determined under assay conditions where the EC50 approximates a KD value. http://purl.obolibrary.org/obo/OBI_0001544 cell lysate MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection http://purl.obolibrary.org/obo/OBI_0001988 assay measuring the dissociation constant [KD] of a MHC:ligand complex A cell lysate MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. http://purl.obolibrary.org/obo/OBI_0001545 intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells http://purl.obolibrary.org/obo/OBI_0001333 biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001546 comparative phenotypic assessment http://purl.obolibrary.org/obo/OBI_0001834 drawing a conclusion Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms to make a conclusion about a phenotypic difference http://purl.obolibrary.org/obo/OBI_0001547 material analysis service http://purl.obolibrary.org/obo/OBI_0001528 material service A service in which a service consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer. http://purl.obolibrary.org/obo/OBI_0001548 equilibrium association constant (KA) http://purl.obolibrary.org/obo/OBI_0001144 binding constant A binding constant defined as the ratio of koff over kon (off-rate of binding divided by on-rate) http://purl.obolibrary.org/obo/OBI_0001549 cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection http://purl.obolibrary.org/obo/OBI_0001988 assay measuring the dissociation constant [KD] of a MHC:ligand complex A cell bound MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. http://purl.obolibrary.org/obo/OBI_0001550 cell bound MHC binding assay measuring binding of a MHC:ligand complex http://purl.obolibrary.org/obo/OBI_0002072 assay measuring qualitiative binding of a MHC:ligand complex A MHC binding qualitative binding to ligand assay measuring MHC ligand binding using MHC present on cells. http://purl.obolibrary.org/obo/OBI_0001551 access service http://purl.obolibrary.org/obo/OBI_0001173 service A service in which a service consumer receives the right to use a resource (instrument, database, software, etc) that is owned or managed by a service provider. Ownership of the accessed resource remains with the service provider during and after provision of service. http://purl.obolibrary.org/obo/OBI_0001552 intracellular cytokine staining assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells http://purl.obolibrary.org/obo/OBI_0001607 biological activity assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells A T cell epitope specific tumor necrosis factor (ligand) superfamily member 11 production assay that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001553 assay measuring a binding constant of a MHC:ligand complex http://purl.obolibrary.org/obo/OBI_1110126 assay measuring binding of a MHC:ligand complex A MHC:ligand binding assay that measures a binding constant. http://purl.obolibrary.org/obo/OBI_0001554 rate measurement datum http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum A scalar measurement datum that represents the number of events occuring over a time interval http://purl.obolibrary.org/obo/OBI_0001555 purified MHC binding assay measuring binding of a MHC:ligand complex http://purl.obolibrary.org/obo/OBI_0002072 assay measuring qualitiative binding of a MHC:ligand complex A MHC binding qualitative binding to ligand assay using MHC in a purified MHC molecule preparation. http://purl.obolibrary.org/obo/OBI_0001556 cell lysate MHC direct binding assay of a MHC:ligand complex using radioactivity detection http://purl.obolibrary.org/obo/OBI_0001579 cell lysate MHC binding assay measuring binding of a MHC:ligand complex A cell lysate MHC binding assay that uses radioactivity detection to detect direct binding. http://purl.obolibrary.org/obo/OBI_0001557 material storage service http://purl.obolibrary.org/obo/OBI_0001515 material maintenance service A storage service in which a service consumer provides some material as input which a service provider stores and returns as output. http://purl.obolibrary.org/obo/OBI_0001558 cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection http://purl.obolibrary.org/obo/OBI_0001990 assay measuring the half life of a MHC:ligand complex A cell bound MHC ligand half life of binding determination assay that uses radioactivity detection to measure direct ligand binding. http://purl.obolibrary.org/obo/OBI_0001559 cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection http://purl.obolibrary.org/obo/OBI_0001990 assay measuring the half life of a MHC:ligand complex A cell bound MHC ligand half life of binding determination assay that uses fluorescence detection to measure direct ligand binding. http://purl.obolibrary.org/obo/OBI_0001560 obsolete cell lysate MHC binding constant determination assay http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class An assay that measures the affinity of a ligand to a MHC in a cell lysate preparation and that quantifies the affinity with a binding constant. http://purl.obolibrary.org/obo/OBI_0001561 cell bound MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection http://purl.obolibrary.org/obo/OBI_0001991 assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex A cell bound MHC ligand binding half maximal effective concentration (EC50) determination assay that uses fluorescence detection to measure direct ligand binding. http://purl.obolibrary.org/obo/OBI_0001562 intracellular cytokine staining assay measuring epitope specific interleukin-17F production by T cells http://purl.obolibrary.org/obo/OBI_1110178 intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells A T cell epitope specific interleukin-17F production assay that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001563 material processing service http://purl.obolibrary.org/obo/OBI_0001528 material service A service in which a service provider makes physical changes to a specified input material entity with the objective of producing a new material entity form input materials, or modifying the input material entity, and returning this as output to the service consumer. http://purl.obolibrary.org/obo/OBI_0001564 purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by IC50 using radioactivity detection http://purl.obolibrary.org/obo/OBI_0001989 purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value. http://purl.obolibrary.org/obo/OBI_0001565 cell lysate MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection http://purl.obolibrary.org/obo/OBI_0001990 assay measuring the half life of a MHC:ligand complex A cell lysate MHC ligand half life of binding determination assay that uses radioactivity detection to measure direct ligand binding. http://purl.obolibrary.org/obo/OBI_0001567 cell lysate MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using radioactivity detection http://purl.obolibrary.org/obo/OBI_0001993 assay measuring the off rate measurement [koff] of a MHC:ligand complex A cell lysate MHC ligand binding off rate measurement (koff) determination assay that uses radioactivity detection to measure direct ligand binding. http://purl.obolibrary.org/obo/OBI_0001568 purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection http://purl.obolibrary.org/obo/OBI_0001992 assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex A purified MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. http://purl.obolibrary.org/obo/OBI_0001569 purified MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using fluorescence detection http://purl.obolibrary.org/obo/OBI_0001993 assay measuring the off rate measurement [koff] of a MHC:ligand complex A purified MHC ligand binding off rate measurement (koff) determination assay that uses fluorescence detection to measure direct ligand binding. http://purl.obolibrary.org/obo/OBI_0001570 biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects vascular endothelial growth factor production by T cells. http://purl.obolibrary.org/obo/OBI_0001571 equilibrium dissociation constant (KD) approximated by IC50 http://purl.obolibrary.org/obo/OBI_0001191 half maximal inhibitory concentration (IC50) A measurement of an IC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, there is a single population of sites on the receptor that competitor and ligand are binding to, and the concentration of the receptor must be much less than the KD for the competitor and the ligand. In this case, according to Cheng and Prussoff, KD = IC50 / (1 + Lstot / KDs), in which Lstot is the total concentration of the labeled competitor and KDs is the KD value of that competitor. http://purl.obolibrary.org/obo/OBI_0001572 obsolete cell bound MHC binding constant determination assay http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class An assay that measures the affinity of a ligand to MHC moleculs bound to the cell surface and that quantifies the affinity with a binding constant. http://purl.obolibrary.org/obo/OBI_0001573 DNA sequence data http://purl.obolibrary.org/obo/OBI_0000973 sequence data A sequence data item that is about the primary structure of DNA http://purl.obolibrary.org/obo/OBI_0001574 obsolete cell lysate MHC competitive binding assay using radioactivity detection http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class competitive inhibition of binding assay measuring MHC ligand binding by radioactivity detection using MHC derived from a cell lysate http://purl.obolibrary.org/obo/OBI_0001575 assigning gene property based on phenotypic assessment http://purl.obolibrary.org/obo/OBI_0000338 drawing a conclusion based on data Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms that have a defined genetic difference, and assigning a property to the product of the targeted gene as a result. http://purl.obolibrary.org/obo/OBI_0001576 obsolete purified MHC binding constant determination assay http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class An assay that measures the affinity of a ligand to a purified MHC complex preparation and that quantifies the affinity with a binding constant. http://purl.obolibrary.org/obo/OBI_0001577 cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-22 production by T cells http://purl.obolibrary.org/obo/OBI_0001217 biological activity assay measuring epitope specific interleukin-22 production by T cells An assay of epitope specific interleukin-22 production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001578 ELISA measuring epitope specific vascular endothelial growth factor production by T cells http://purl.obolibrary.org/obo/OBI_0001570 biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells An assay of epitope specific vascular endothelial growth factor production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001579 cell lysate MHC binding assay measuring binding of a MHC:ligand complex http://purl.obolibrary.org/obo/OBI_0002072 assay measuring qualitiative binding of a MHC:ligand complex A MHC binding qualitative binding to ligand assay using MHC in a cell lysate. http://purl.obolibrary.org/obo/OBI_0001580 material transport service http://purl.obolibrary.org/obo/OBI_0001528 material service A service in which a service provider facilitates the transport of some material entity to a specified destination for the service consumer. http://purl.obolibrary.org/obo/OBI_0001581 equilibrium dissociation constant (KD) approximated by EC50 http://purl.obolibrary.org/obo/OBI_0001180 half maximal effective concentration (EC50) A measurement of an EC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, and the concentration of the receptor must be much less than the KD for the ligand. http://purl.obolibrary.org/obo/OBI_0001582 obsolete cell bound MHC direct binding assay http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class direct binding assay measuring MHC ligand binding using MHC derived from a cell http://purl.obolibrary.org/obo/OBI_0001583 half life of binding datum http://purl.obolibrary.org/obo/OBI_0001171 half life datum (t 1/2) A half life datum of the time it takes for 50% of bound complexes in an ensemble to disassociate in absence of re-association. http://purl.obolibrary.org/obo/OBI_0001584 purified MHC direct binding assay measuring binding of a MHC:ligand complex using phage display http://purl.obolibrary.org/obo/OBI_0001555 purified MHC binding assay measuring binding of a MHC:ligand complex A purified MHC binding assay that uses a phage display binding assay to measure direct ligand binding. http://purl.obolibrary.org/obo/OBI_0001585 cytometric bead array assay measuring epitope specific interleukin-7 production by T cells http://purl.obolibrary.org/obo/OBI_0001587 biological activity assay measuring epitope specific interleukin-7 production by T cells An assay of epitope specific interleukin-7 production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001586 purified MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection http://purl.obolibrary.org/obo/OBI_0001990 assay measuring the half life of a MHC:ligand complex A purified MHC ligand half life of binding determination assay that uses radioactivity detection to measure direct ligand binding. http://purl.obolibrary.org/obo/OBI_0001587 biological activity assay measuring epitope specific interleukin-7 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects interleukin-7 production by T cells. http://purl.obolibrary.org/obo/OBI_0001588 binding http://purl.obolibrary.org/obo/GO_0008150 biological_process The process of material entities forming complexes. http://purl.obolibrary.org/obo/OBI_0001589 intracellular cytokine staining assay measuring epitope specific interleukin-17A production by T cells http://purl.obolibrary.org/obo/OBI_1110178 intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells A T cell epitope specific interleukin-17A production assay that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001590 purified MHC direct binding assay measuring binding of a MHC:ligand complex using fluorescence detection http://purl.obolibrary.org/obo/OBI_0001555 purified MHC binding assay measuring binding of a MHC:ligand complex A purified MHC binding assay that uses fluorescence detection to measure direct ligand binding. http://purl.obolibrary.org/obo/OBI_0001591 direct binding assay http://purl.obolibrary.org/obo/OBI_0001146 binding assay A binding assay that measures the formation or disassociation of a complex of 2 material entities directly without use of a competitve ligand. http://purl.obolibrary.org/obo/OBI_0001592 purified MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection http://purl.obolibrary.org/obo/OBI_0001991 assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex A purified MHC ligand binding half maximal effective concentration (EC50) determination assay that uses fluorescence detection to measure direct ligand binding. http://purl.obolibrary.org/obo/OBI_0001593 competitive inhibition of binding assay http://purl.obolibrary.org/obo/OBI_0001146 binding assay A binding assay that detects the inhibition of binding between 2 material entities known to form a complex by the addition of a third material entity of interest. Inhibition of binding between the 2 materials reflects binding by the third material. http://purl.obolibrary.org/obo/OBI_0001594 cell bound MHC competitive binding assay of a MHC:ligand complex using fluorescence detection http://purl.obolibrary.org/obo/OBI_0001550 cell bound MHC binding assay measuring binding of a MHC:ligand complex A cell bound MHC binding assay that uses fluorescence to detect loss of binding of a known reference ligand due to competition by the ligand under investigation http://purl.obolibrary.org/obo/OBI_0001595 X-ray crystallography assay determining the 3D structure of a MHC:ligand complex http://purl.obolibrary.org/obo/OBI_0002050 3D structure determining assay of a MHC:ligand complex A MHC binding 3D structure determination of MHC molecule:epitope complex assay that uses an X-ray crystallography assay. http://purl.obolibrary.org/obo/OBI_0001596 PDB file chain http://purl.obolibrary.org/obo/OBI_0001155 3D structural organization datum A 3D structural organization datum that is part of a PDB file and has a specific chain identifier that identifies the entire information on a subset of the material entities http://purl.obolibrary.org/obo/OBI_0001597 cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using T cell epitope recognition http://purl.obolibrary.org/obo/OBI_0001992 assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex A cell bound MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses a T cell epitope recognition assay to measure ligand binding. http://purl.obolibrary.org/obo/OBI_0001598 data maintenance service http://purl.obolibrary.org/obo/OBI_0001530 data service A maintenance service in which a service provider actively manages or maintains data or a database for the service consumer. Maintenance of the data is performed to maintain its integrity or enhance its quality or utility for the consumer, but new data is not generated as a result of the maintenance. http://purl.obolibrary.org/obo/OBI_0001599 cell bound MHC competitive binding assay of a MHC:ligand complex using radioactivity detection http://purl.obolibrary.org/obo/OBI_0001550 cell bound MHC binding assay measuring binding of a MHC:ligand complex A cell bound MHC binding assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. http://purl.obolibrary.org/obo/OBI_0001600 biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects granulocyte colony stimulating factor production by T cells. http://purl.obolibrary.org/obo/OBI_0001601 cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-21 production by T cells http://purl.obolibrary.org/obo/OBI_0001237 biological activity assay measuring epitope specific interleukin-21 production by T cells An assay of epitope specific interleukin-21 production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001602 cell bound MHC direct binding assay of a MHC:ligand complex using radioactivity detection http://purl.obolibrary.org/obo/OBI_0001550 cell bound MHC binding assay measuring binding of a MHC:ligand complex A cell bound MHC binding assay that uses radioactivity detection to detect direct binding. http://purl.obolibrary.org/obo/OBI_0001603 binding off rate measurement datum (koff) http://purl.obolibrary.org/obo/OBI_0001554 rate measurement datum A rate measurement datum of how quickly bound complexes disassociate http://purl.obolibrary.org/obo/OBI_0001604 purified MHC direct binding assay measuring 50% dissociation of binding temperature [Tm] of a MHC:ligand complex using fluorescence detection http://purl.obolibrary.org/obo/OBI_0001555 purified MHC binding assay measuring binding of a MHC:ligand complex A purified MHC binding assay that uses fluorescence detection to measure the 50% dissociation of binding temperature of direct ligand binding. http://purl.obolibrary.org/obo/OBI_0001605 binding on rate measurement datum (kon) http://purl.obolibrary.org/obo/OBI_0001554 rate measurement datum A rate measurement datum of how quickly bound complexes form http://purl.obolibrary.org/obo/OBI_0001606 cell bound MHC direct binding assay of a MHC:ligand complex using fluorescence detection http://purl.obolibrary.org/obo/OBI_0001550 cell bound MHC binding assay measuring binding of a MHC:ligand complex A cell bound MHC binding assay that uses fluorescence detection to detect direct binding. http://purl.obolibrary.org/obo/OBI_0001607 biological activity assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells http://purl.obolibrary.org/obo/OBI_0001400 biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells An assay of epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells that detects tumor necrosis factor production. http://purl.obolibrary.org/obo/OBI_0001608 purified MHC direct binding assay of a MHC:ligand complex using radioactivity detection http://purl.obolibrary.org/obo/OBI_0001555 purified MHC binding assay measuring binding of a MHC:ligand complex A purified MHC binding assay that uses radioactivity detection to measure direct ligand binding. http://purl.obolibrary.org/obo/OBI_0001609 intracellular cytokine staining assay measuring epitope specific interleukin-8 production by T cells http://purl.obolibrary.org/obo/OBI_0001218 biological activity assay measuring epitope specific interleukin-8 production by T cells An assay of epitope specific interleukin-8 production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001610 cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-223 production by T cells http://purl.obolibrary.org/obo/OBI_0001363 biological activity assay measuring epitope specific interleukin-23 production by T cells An assay of epitope specific interleukin-23 production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001611 obsolete purified MHC direct binding assay http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class direct binding assay measuring MHC ligand binding using MHC derived from a purified MHC molecule preparation http://purl.obolibrary.org/obo/OBI_0001612 epitope specific vascular endothelial growth factor production by T cells http://purl.obolibrary.org/obo/GO_0010573 vascular endothelial growth factor production A process of vascular endothelial growth factor production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001613 purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection http://purl.obolibrary.org/obo/OBI_0001992 assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex A purified MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. http://purl.obolibrary.org/obo/OBI_0001614 GenBank ID http://purl.obolibrary.org/obo/IAO_0000577 centrally registered identifier symbol A CRID symbol uniquely indentifies the submitted GeneBank sequence record. http://purl.obolibrary.org/obo/OBI_0001615 investigation description http://purl.obolibrary.org/obo/OBI_0001898 comment on investigation A textual entity that describes an investigation. http://purl.obolibrary.org/obo/OBI_0001618 average depth of sequence coverage http://purl.obolibrary.org/obo/OBI_0000679 average value An average value of the depth of sequence coverage based both on external (e.g. Cot-based size estimates) and internal (average coverage in the assembly) measures of genome size. http://purl.obolibrary.org/obo/OBI_0001622 investigation title http://purl.obolibrary.org/obo/OBI_0001898 comment on investigation A textual entity that denotes an investigation. http://purl.obolibrary.org/obo/OBI_0001623 organism identification objective http://purl.obolibrary.org/obo/OBI_0000015 biological feature identification objective A biological feature identification objective to identify the organism species in a specimen. http://purl.obolibrary.org/obo/OBI_0001624 organism identification assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that identifies the organism species in a specimen. http://purl.obolibrary.org/obo/OBI_0001625 sequence annotation algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm An algorithm used to identify sequence features (e.g. protein coding regions) in the assembled contig sequence. This may also include a description of any manual curation that may have generated or validated the annotation. http://purl.obolibrary.org/obo/OBI_0001627 country name http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that denotes a geographic location that is a site or part of a site that is identified as a country in the political geography. http://purl.obolibrary.org/obo/OBI_0001628 investigation identifier http://purl.obolibrary.org/obo/IAO_0000577 centrally registered identifier symbol A CRID symbol used to identify an investigation. http://purl.obolibrary.org/obo/OBI_0001629 grant identifier http://purl.obolibrary.org/obo/IAO_0000577 centrally registered identifier symbol A CRID symbol used to identify a grant. http://purl.obolibrary.org/obo/OBI_0001630 analytical chromatography http://purl.obolibrary.org/obo/OBI_0000443 analyte assay An analyte assay that uses a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials and thereby detect its presence in an input material. http://purl.obolibrary.org/obo/OBI_0001631 electron microscopy imaging assay http://purl.obolibrary.org/obo/OBI_0002119 microscopy assay An imaging assay in which an electrons are used to probe the density, shape and composition of an input material which are detected in an electron microscope and utilized to produce an image of the material. http://purl.obolibrary.org/obo/OBI_0001632 immuno staining assay http://purl.obolibrary.org/obo/OBI_0600017 assay detecting a molecular label A assay detecting a molecular label assay in which the label is attached to an antibody so that substances are marked based on the antibody's binding specificity. http://purl.obolibrary.org/obo/OBI_0001633 purified material http://purl.obolibrary.org/obo/OBI_0000047 processed material A material entity that is generated by a purification process in which an input material is separated to obtain a fraction with a higher concentration of a desired component http://purl.obolibrary.org/obo/OBI_0001634 calorimetric binding assay http://purl.obolibrary.org/obo/OBI_0001146 binding assay A binding assay in which the heat generated or absorbed during a binding event is measured, which allows determination of binding constants, reaction stoichiometry, enthalpy and entropy. http://purl.obolibrary.org/obo/OBI_0001635 antibody binding detection by fluorescence quenching http://purl.obolibrary.org/obo/OBI_0001979 fluorescence quenching binding assay A binding assay in which affinity is measured by detecting a change in fluorescence (usually quenching) that occurs upon binding of the antibody to the ligand. The fluorescent signal that is affected by binding is either from an exogenous fluorophore attached to the ligand, or is the intrisic fluorescence of aromatic (tryptophan) residues on the binding site of the antibody (no conjugated fluorophore necessary) or, less commonly, on the ligand binding region (epitope). http://purl.obolibrary.org/obo/OBI_0001636 grant http://purl.obolibrary.org/obo/IAO_0000104 plan specification A plan specification of organization A to give money to organization B so that B conducts investigations. Organization A has funder role and Organization B has research organization role. http://purl.obolibrary.org/obo/OBI_0001638 antigen inhibition assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex approximated by IC50 http://purl.obolibrary.org/obo/OBI_0001708 assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex A B cell epitope equilibrium dissociation constant (KD) assay that provides IC50 values determined under assay conditions where the IC50 approximates a KD value using a B cell epitope antigen inhibition of binding assay. http://purl.obolibrary.org/obo/OBI_0001639 biological activity assay measuring epitope specific Ig-mediated histamine release http://purl.obolibrary.org/obo/OBI_0001704 biological activity assay measuring epitope specific activation of additional immune response in vitro A B cell epitope specific activation of additional immune response in vitro assay that detects histamine release. http://purl.obolibrary.org/obo/OBI_0001640 biological activity assay measuring epitope specific immunoglobulin-mediated antigen activation http://purl.obolibrary.org/obo/OBI_0001706 assay measuring B cell epitope specific biological activity A B cell epitope dependent biological activity determination assay that detects antigen activation. http://purl.obolibrary.org/obo/OBI_0001641 biological activity assay measuring epitope specific complement-dependent cytotoxicity http://purl.obolibrary.org/obo/OBI_0001704 biological activity assay measuring epitope specific activation of additional immune response in vitro A B cell epitope specific activation of additional immune response in vitro assay that detects complement-dependent cytotoxicity. http://purl.obolibrary.org/obo/OBI_0001642 biological activity assay measuring epitope specific antibody-dependent cellular cytotoxicity http://purl.obolibrary.org/obo/OBI_0001704 biological activity assay measuring epitope specific activation of additional immune response in vitro A B cell epitope specific activation of additional immune response in vitro assay that detects antibody-dependent cellular cytotoxicity. http://purl.obolibrary.org/obo/OBI_0001643 biological activity assay measuring epitope specific immunoglobulin-mediated neutralization http://purl.obolibrary.org/obo/OBI_0001706 assay measuring B cell epitope specific biological activity A B cell epitope dependent biological activity determination assay that detects neutralization of the antigen. http://purl.obolibrary.org/obo/OBI_0001644 biological activity assay measuring epitope specific opsonization http://purl.obolibrary.org/obo/OBI_0001704 biological activity assay measuring epitope specific activation of additional immune response in vitro A B cell epitope specific activation of additional immune response in vitro assay that detects opsonization. http://purl.obolibrary.org/obo/OBI_0001645 calorimetry assay measuring binding of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001703 assay measuring qualitiative binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a calorimetric binding assay. http://purl.obolibrary.org/obo/OBI_0001646 electron microscopy assay determining the 3D structure of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001721 3D structure determining assay of a 3D B cell epitope:antibody complex A B cell epitope 3D structure determination assay that uses an electron microscopy imaging assay. http://purl.obolibrary.org/obo/OBI_0001647 NMR assay determining the 3D structure of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001721 3D structure determining assay of a 3D B cell epitope:antibody complex A B cell epitope 3D structure determination assay that uses a nuclear magnetic resonance assay. http://purl.obolibrary.org/obo/OBI_0001648 cross blocking assay measuring binding of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001703 assay measuring qualitiative binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an antibody cross-blocking assay. http://purl.obolibrary.org/obo/OBI_0001649 RIA measuring binding of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001703 assay measuring qualitiative binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a radio immuno assay. http://purl.obolibrary.org/obo/OBI_0001650 immunoblot assay measuring binding of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001703 assay measuring qualitiative binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an immunoblot assay. http://purl.obolibrary.org/obo/OBI_0001651 plasmon resonance assay measuring binding of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001703 assay measuring qualitiative binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a surface plasmon resonance assay. http://purl.obolibrary.org/obo/OBI_0001652 immuno staining assay measuring binding of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001703 assay measuring qualitiative binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an immuno staining assay. http://purl.obolibrary.org/obo/OBI_0001653 immunoprecipitation assay measuring binding of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001703 assay measuring qualitiative binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an immunoprecipitation assay. http://purl.obolibrary.org/obo/OBI_0001654 mass spectrometry assay measuring binding of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001703 assay measuring qualitiative binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a mass spectrometry assay. http://purl.obolibrary.org/obo/OBI_0001655 phage display assay measuring binding of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001703 assay measuring qualitiative binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a phage display binding assay. http://purl.obolibrary.org/obo/OBI_0001656 electron microscopy assay measuring binding of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001703 assay measuring qualitiative binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an electron microscopy imaging assay. http://purl.obolibrary.org/obo/OBI_0001657 ELISA measuring binding of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001703 assay measuring qualitiative binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an enzyme-linked immunosorbent assay. http://purl.obolibrary.org/obo/OBI_0001658 ELISPOT assay measuring binding of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001703 assay measuring qualitiative binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an enzyme-linked immunospot assay. http://purl.obolibrary.org/obo/OBI_0001659 flow cytometry assay measuring binding of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001703 assay measuring qualitiative binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a flow cytometry assay. http://purl.obolibrary.org/obo/OBI_0001660 intracellular material detection assay measuring epitope specific granzyme A release by T cells http://purl.obolibrary.org/obo/OBI_0001809 biological activity assay measuring epitope specific granzyme A release by T cells A T cell epitope specific granzyme A release assay that uses an intracellular material detection by flow cytometry assay. http://purl.obolibrary.org/obo/OBI_0001661 chromatography assay measuring binding of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001703 assay measuring qualitiative binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an analytical chromatography assay. http://purl.obolibrary.org/obo/OBI_0001662 NMR assay measuring binding of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001703 assay measuring qualitiative binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a nuclear magnetic resonance assay. http://purl.obolibrary.org/obo/OBI_0001663 ELISA measuring epitope specific granulysin release by T cells http://purl.obolibrary.org/obo/OBI_0001810 biological activity assay measuring epitope specific granulysin release by T cells A T cell epitope specific granulysin release assay that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001664 intracellular material detection assay measuring epitope specific granulysin release by T cells http://purl.obolibrary.org/obo/OBI_0001810 biological activity assay measuring epitope specific granulysin release by T cells A T cell epitope specific granulysin release assay that uses an intracellular material detection by flow cytometry assay. http://purl.obolibrary.org/obo/OBI_0001665 cell bound MHC direct binding assay measuring the off rate [koff] of a MHC:ligand complex using fluorescence detection http://purl.obolibrary.org/obo/OBI_0001993 assay measuring the off rate measurement [koff] of a MHC:ligand complex A cell bound MHC ligand binding off rate measurement (koff) determination assay that uses fluorescence detection to measure direct ligand binding. http://purl.obolibrary.org/obo/OBI_0001666 cell bound MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detection http://purl.obolibrary.org/obo/OBI_0001994 assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complex A cell bound MHC ligand binding on rate (kon) determination assay that uses fluorescence detection to measure direct ligand binding. http://purl.obolibrary.org/obo/OBI_0001667 purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by IC50 using fluorescence detection http://purl.obolibrary.org/obo/OBI_0001537 purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value. http://purl.obolibrary.org/obo/OBI_0001668 split-ubiquitin assay http://purl.obolibrary.org/obo/OBI_0001146 binding assay A binding assay that screens membrane soluble proteins by fusion of two integral membrane proteins (bait and prey) to two different ubiquitin moieties. One moiety is also fused to a transcription factor (TF) that can be cleaved off by ubiquitin specific proteases. Upon bait and prey interaction, Nub and Cub-moieties assemble, reconstituting the split-ubiquitin. The reconstituted split-ubiquitin molecule is recognized by ubiquitin specific proteases, which cleave off the reporter protein, allowing it to induce the transcription of reporter genes. http://purl.obolibrary.org/obo/OBI_0001669 far-Western blot assay http://purl.obolibrary.org/obo/OBI_0001146 binding assay An assay that measures protein-protein interactions by separating target proteins on an SDS-PAGE gel, transfering them to a solid substrate, hybridizing with a protein probe and visualizing bound proteins using a probe-directed antibody. This is a adaptation on the western blot assay. http://purl.obolibrary.org/obo/OBI_0001672 gene knock-down assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay which transiently disrupts gene transcripts by expressing antisense RNA constructs or delivering RNA interfering molecules in cells. http://purl.obolibrary.org/obo/OBI_0001675 ELISA measuring epitope specific interleukin-17A production by T cells http://purl.obolibrary.org/obo/OBI_1110162 ELISA measuring epitope specific interleukin-17 production by T cells A T cell epitope specific interleukin-17A production assay that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001676 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-7 production by T cells http://purl.obolibrary.org/obo/OBI_0001587 biological activity assay measuring epitope specific interleukin-7 production by T cells An assay of epitope specific interleukin-7 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001677 epitope specific granulysin production by T cells http://purl.obolibrary.org/obo/GO_0036262 granulysin production A process of granulysin production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001678 epitope specific granzyme A production by T cells http://purl.obolibrary.org/obo/GO_0035746 granzyme A production A process of granzyme A production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001687 contact representative role http://purl.obolibrary.org/obo/BFO_0000023 role A role inhering in a person who represents an institution, organization, or service provider and realized when communication is directed at them about the entity they represent. http://purl.obolibrary.org/obo/OBI_0001689 cytochalasin-induced inhibition of actin polymerization assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay which uses compound cytochalasin (CHEBI: 23528) to block actin polymerization-dependent cell motility (GO:0070358) and actin filament polymerization (GO:0030041). http://purl.obolibrary.org/obo/OBI_0001690 molecular function identification objective http://purl.obolibrary.org/obo/OBI_0000015 biological feature identification objective is an objective specification which aims to discover molecular function realized by a molecular entity http://purl.obolibrary.org/obo/OBI_0001691 cellular structure feature identification objective http://purl.obolibrary.org/obo/OBI_0000015 biological feature identification objective is an objective specification which aims to discover cellular structure properties http://purl.obolibrary.org/obo/OBI_0001692 in vivo assay measuring B cell epitope specific protection from fertility http://purl.obolibrary.org/obo/OBI_0001698 biological activity assay measuring B cell epitope specific in vivo activity An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment based on reduction of fertility. http://purl.obolibrary.org/obo/OBI_0001693 in vivo assay measuring B cell epitope specific tolerance induction http://purl.obolibrary.org/obo/OBI_0001698 biological activity assay measuring B cell epitope specific in vivo activity An efficacy of B cell epitope intervention experiment that uses a tolerance induction intervention experiment. http://purl.obolibrary.org/obo/OBI_0001694 in vivo assay measuring B cell epitope specific induction of hypersensitivity http://purl.obolibrary.org/obo/OBI_0001698 biological activity assay measuring B cell epitope specific in vivo activity An efficacy of B cell epitope intervention experiment that detects a hypersensitivity response by monitoring skin reactions. http://purl.obolibrary.org/obo/OBI_0001695 biological activity assay measuring epitope specific immune complex formation http://purl.obolibrary.org/obo/OBI_0001704 biological activity assay measuring epitope specific activation of additional immune response in vitro A B cell epitope specific activation of additional immune response in vitro assay that detects agglutination. http://purl.obolibrary.org/obo/OBI_0001696 in vivo assay measuring B cell epitope specific protection based on survival http://purl.obolibrary.org/obo/OBI_0001710 in vivo assay measuring B cell epitope specific protection from challenge A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on survival. http://purl.obolibrary.org/obo/OBI_0001697 in vivo assay measuring B cell epitope specific treatment of disease http://purl.obolibrary.org/obo/OBI_0001698 biological activity assay measuring B cell epitope specific in vivo activity An efficacy of B cell epitope intervention experiment that detects a decrease in disease. http://purl.obolibrary.org/obo/OBI_0001698 biological activity assay measuring B cell epitope specific in vivo activity http://purl.obolibrary.org/obo/OBI_0001706 assay measuring B cell epitope specific biological activity A B cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment. http://purl.obolibrary.org/obo/OBI_0001700 immunoprecipitation assay http://purl.obolibrary.org/obo/OBI_0000443 analyte assay An analyte assay in which an input material is mixed with antibodies and bound antigen:antibody complexes are separated out using immunoprecipitation. Either the antibody has known specificy, and the antigen mixture is tested for the presence of a specific antigen, or the antigen solution is well defined and the antibody solution is tested for the presence of antigen specific antibodies. http://purl.obolibrary.org/obo/OBI_0001701 antigen inhibition assay measuring binding of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001703 assay measuring qualitiative binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that measures the ability of an antigen to inhibit antibody binding to a known ligand. http://purl.obolibrary.org/obo/OBI_0001702 immunoglobulin binding to epitope http://purl.obolibrary.org/obo/OBI_1110014 epitope binding by adaptive immune receptor a process of an immunoglobulin complex binding to a material entity at the immunoglobulin complementarity determining region (CDR). http://purl.obolibrary.org/obo/OBI_0001703 assay measuring qualitiative binding of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_1110127 assay measuring binding of a B cell epitope:antibody complex A B cell epitope recognition assay that detects qualitative binding. http://purl.obolibrary.org/obo/OBI_0001704 biological activity assay measuring epitope specific activation of additional immune response in vitro http://purl.obolibrary.org/obo/OBI_0001706 assay measuring B cell epitope specific biological activity A B cell epitope dependent biological activity determination assay that detects secondary in vitro activity. http://purl.obolibrary.org/obo/OBI_0001705 biological activity assay measuring epitope specific antigen inhibition of antibody activity http://purl.obolibrary.org/obo/OBI_0001706 assay measuring B cell epitope specific biological activity A B cell epitope dependent biological activity determination assay that detects inhibition of the antibody's activity by the antigen. http://purl.obolibrary.org/obo/OBI_0001706 assay measuring B cell epitope specific biological activity http://purl.obolibrary.org/obo/OBI_1110127 assay measuring binding of a B cell epitope:antibody complex A B cell epitope recognition assay that detects biological activity. http://purl.obolibrary.org/obo/OBI_0001707 immunoglobulin mediated histamine release http://purl.obolibrary.org/obo/GO_0008150 biological_process The release of histamine by cells stimulated through their Fc receptors which are loaded with immunoglobulins. http://purl.obolibrary.org/obo/OBI_0001708 assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001709 assay measuring a binding constant of a B cell epitope:antibody complex A B cell epitope binding constant determination assay that measures the dissociation constant KD. http://purl.obolibrary.org/obo/OBI_0001709 assay measuring a binding constant of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_1110127 assay measuring binding of a B cell epitope:antibody complex A B cell epitope recognition assay that quantitavely characterizes the binding of an antibody / BCR with a ligand by determining a binding constant. http://purl.obolibrary.org/obo/OBI_0001710 in vivo assay measuring B cell epitope specific protection from challenge http://purl.obolibrary.org/obo/OBI_0001698 biological activity assay measuring B cell epitope specific in vivo activity An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment. http://purl.obolibrary.org/obo/OBI_0001711 in vivo assay measuring B cell epitope specific disease exacerbation http://purl.obolibrary.org/obo/OBI_0001698 biological activity assay measuring B cell epitope specific in vivo activity An efficacy of B cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment. http://purl.obolibrary.org/obo/OBI_0001712 obsolete B cell epitope direct binding assay http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class A direct binding assay using a assay http://purl.obolibrary.org/obo/OBI_0001713 B cell epitope specific opsonization http://purl.obolibrary.org/obo/GO_0008228 opsonization opsonization resulting from antibody binding to epitope http://purl.obolibrary.org/obo/OBI_0001714 B cell epitope specific immunoglobulin-mediated neutralization http://purl.obolibrary.org/obo/GO_0097282 immunoglobulin-mediated neutralization immunoglobulin-mediated neutralization resulting from antibody binding to epitope http://purl.obolibrary.org/obo/OBI_0001715 obsolete B cell epitope competitive binding assay http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class A competitive inhibition of binding assay using a assay http://purl.obolibrary.org/obo/OBI_0001716 B cell epitope specific complement-dependent cytotoxicity http://purl.obolibrary.org/obo/GO_0097278 complement-dependent cytotoxicity complement-dependent cytotoxicity resulting from antibody binding to epitope http://purl.obolibrary.org/obo/OBI_0001717 B cell epitope specific antibody-dependent cellular cytotoxicity http://purl.obolibrary.org/obo/GO_0001788 antibody-dependent cellular cytotoxicity antibody-dependent cellular cytotoxicity resulting from antibody binding to epitope http://purl.obolibrary.org/obo/OBI_0001718 assay measuring the on rate [kon] of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001709 assay measuring a binding constant of a B cell epitope:antibody complex A B cell epitope binding constant determination assay that measures the on rate. http://purl.obolibrary.org/obo/OBI_0001719 assay measuring the association constant [KA] of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001709 assay measuring a binding constant of a B cell epitope:antibody complex A B cell epitope binding constant determination assay that measures the association constant KA. http://purl.obolibrary.org/obo/OBI_0001720 B cell epitope specific immune complex formation http://purl.obolibrary.org/obo/GO_0097281 immune complex formation immune complex formation resulting from antibody binding to epitope http://purl.obolibrary.org/obo/OBI_0001721 3D structure determining assay of a 3D B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_1110127 assay measuring binding of a B cell epitope:antibody complex A B cell epitope recognition assay that characterizes the 3D structure of an antibody / BCR with a ligand. http://purl.obolibrary.org/obo/OBI_0001722 B cell epitope specific hypersensitivity http://purl.obolibrary.org/obo/GO_0002524 hypersensitivity hypersensitivity resulting from antibody binding to epitope http://purl.obolibrary.org/obo/OBI_0001723 assay measuring the off rate [koff] of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001709 assay measuring a binding constant of a B cell epitope:antibody complex A B cell epitope binding constant determination assay that measures the off rate. http://purl.obolibrary.org/obo/OBI_0001724 biological activity assay measuring epitope specific hemagglutination inhibition http://purl.obolibrary.org/obo/OBI_0001703 assay measuring qualitiative binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a viral hemagglutination inhibition assay. http://purl.obolibrary.org/obo/OBI_0001725 B cell epitope specific histamine secretion mediated by immunoglobulin http://purl.obolibrary.org/obo/GO_0097280 histamine secretion mediated by immunoglobulin histamine secretion mediated by immunoglobulin resulting from antibody binding to epitope http://purl.obolibrary.org/obo/OBI_0001726 quenching assay measuring binding of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001703 assay measuring qualitiative binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an antibody binding detection by fluorescence quenching. http://purl.obolibrary.org/obo/OBI_0001727 RIA measuring the dissociation constant [KD] of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001708 assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a radio immuno assay. http://purl.obolibrary.org/obo/OBI_0001728 ELISA measuring the dissociation constant [KD] of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001708 assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex A B cell epitope equilibrium dissociation constant (KD) determination assay that uses an enzyme-linked immunosorbent assay. http://purl.obolibrary.org/obo/OBI_0001729 quenching assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001708 assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex A B cell epitope equilibrium dissociation constant (KD) determination assay that uses an antibody binding detection by fluorescence quenching assay. http://purl.obolibrary.org/obo/OBI_0001730 surface plasmon resonance assay measuring the association constant [KA] of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001719 assay measuring the association constant [KA] of a B cell epitope:antibody complex A B cell epitope equilibrium association constant (KA) determination assay that uses a surface plasmon resonance assay. http://purl.obolibrary.org/obo/OBI_0001731 surface plasmon resonance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001708 assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a surface plasmon resonance assay. http://purl.obolibrary.org/obo/OBI_0001732 quenching assay measuring the association constant [KA] of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001719 assay measuring the association constant [KA] of a B cell epitope:antibody complex A B cell epitope equilibrium association constant (KA) determination assay that uses an antibody binding detection by fluorescence quenching assay. http://purl.obolibrary.org/obo/OBI_0001733 calorimetry assay measuring the association constant [KA] of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001719 assay measuring the association constant [KA] of a B cell epitope:antibody complex A B cell epitope equilibrium association constant (KA) determination assay that uses a calorimetric binding assay. http://purl.obolibrary.org/obo/OBI_0001734 calorimetry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001708 assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a calorimetric binding assay. http://purl.obolibrary.org/obo/OBI_0001735 ELISA measuring the association constant [KA] of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001719 assay measuring the association constant [KA] of a B cell epitope:antibody complex A B cell epitope equilibrium association constant (KA) determination assay that uses an enzyme-linked immunosorbent assay. http://purl.obolibrary.org/obo/OBI_0001736 RIA measuring the association constant [KA] of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001719 assay measuring the association constant [KA] of a B cell epitope:antibody complex A B cell epitope equilibrium association constant (KA) determination assay that uses a radio immuno assay. http://purl.obolibrary.org/obo/OBI_0001737 obsolete B cell epitope specific X-ray crystallography assay http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class A X-ray crystallography assay measuring epitope specfic antibody binding event in angstroms http://purl.obolibrary.org/obo/OBI_0001738 X-ray crystallography assay determining the 3D structure of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001721 3D structure determining assay of a 3D B cell epitope:antibody complex A B cell epitope 3D structure determination assay that uses an X-ray crystallography assay. http://purl.obolibrary.org/obo/OBI_0001739 surface plasmon resonance assay measuring the off rate [koff] of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001723 assay measuring the off rate [koff] of a B cell epitope:antibody complex A B cell epitope binding off rate measurement (koff) determination assay that uses a surface plasmon resonance assay. http://purl.obolibrary.org/obo/OBI_0001740 quenching assay measuring the off rate [koff] of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001723 assay measuring the off rate [koff] of a B cell epitope:antibody complex A B cell epitope binding off rate measurement (koff) determination assay that uses an antibody binding detection by fluorescence quenching assay. http://purl.obolibrary.org/obo/OBI_0001741 surface plasmon resonance assay measuring the on rate [kon] of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001718 assay measuring the on rate [kon] of a B cell epitope:antibody complex A B cell epitope on rate measurement (kon) determination assay that uses a surface plasmon resonance assay. http://purl.obolibrary.org/obo/OBI_0001742 quenching assay measuring the on rate [kon] of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001718 assay measuring the on rate [kon] of a B cell epitope:antibody complex A B cell epitope on rate measurement (kon) determination assay that uses an antibody binding detection by fluorescence quenching assay. http://purl.obolibrary.org/obo/OBI_0001743 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 beta production by T cells http://purl.obolibrary.org/obo/OBI_0001449 biological activity assay measuring epitope specific interleukin-1 beta production by T cells An assay of epitope specific interleukin-1 beta production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001744 intracellular cytokine staining assay measuring epitope specific interleukin-1 alpha production by T cells http://purl.obolibrary.org/obo/OBI_0001388 biological activity assay measuring epitope specific interleukin-1 alpha production by T cells An assay of epitope specific interleukin-1 alpha production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001745 ELISPOT assay measuring epitope specific interleukin-1 alpha production by T cells http://purl.obolibrary.org/obo/OBI_0001388 biological activity assay measuring epitope specific interleukin-1 alpha production by T cells An assay of epitope specific interleukin-1 alpha production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001746 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 alpha production by T cells http://purl.obolibrary.org/obo/OBI_0001388 biological activity assay measuring epitope specific interleukin-1 alpha production by T cells An assay of epitope specific interleukin-1 alpha production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001747 cytometric bead array assay measuring epitope specific interleukin-1 alpha production by T cells http://purl.obolibrary.org/obo/OBI_0001388 biological activity assay measuring epitope specific interleukin-1 alpha production by T cells An assay of epitope specific interleukin-1 alpha production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001748 ELISPOT assay measuring epitope specific interferon-beta production by T cells http://purl.obolibrary.org/obo/OBI_0001390 biological activity assay measuring epitope specific interferon-beta production by T cells An assay of epitope specific interferon-beta production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001749 intracellular cytokine staining assay measuring epitope specific interferon-beta production by T cells http://purl.obolibrary.org/obo/OBI_0001390 biological activity assay measuring epitope specific interferon-beta production by T cells An assay of epitope specific interferon-beta production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001750 intracellular cytokine staining assay measuring epitope specific granulocyte colony stimulating factor production by T cells http://purl.obolibrary.org/obo/OBI_0001600 biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001751 ELISA measuring epitope specific interferon-beta production by T cells http://purl.obolibrary.org/obo/OBI_0001390 biological activity assay measuring epitope specific interferon-beta production by T cells An assay of epitope specific interferon-beta production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001752 detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte colony stimulating factor production by T cells http://purl.obolibrary.org/obo/OBI_0001600 biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001753 ELISPOT assay measuring epitope specific granulocyte colony stimulating factor production by T cells http://purl.obolibrary.org/obo/OBI_0001600 biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001754 cytometric bead array assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells http://purl.obolibrary.org/obo/OBI_0001459 biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001756 ELISPOT assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells http://purl.obolibrary.org/obo/OBI_0001459 biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001757 detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells http://purl.obolibrary.org/obo/OBI_0001459 biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001758 ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells http://purl.obolibrary.org/obo/OBI_0001345 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001759 detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells http://purl.obolibrary.org/obo/OBI_0001776 biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells An assay of epitope specific chemokine (C-X-C motif) ligand 12 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001760 detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells http://purl.obolibrary.org/obo/OBI_0001779 biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells An assay of epitope specific chemokine (C-X-C motif) ligand 13 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001761 detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells http://purl.obolibrary.org/obo/OBI_0001778 biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells An assay of epitope specific chemokine (C-X-C motif) ligand 16 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001762 detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells http://purl.obolibrary.org/obo/OBI_0001774 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 21 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001763 detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells http://purl.obolibrary.org/obo/OBI_0001777 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 22 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001764 cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells http://purl.obolibrary.org/obo/OBI_0001345 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001765 detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells http://purl.obolibrary.org/obo/OBI_0001345 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001766 detection of specific nucleic acids with complementary probes assay measuring epitope specific vascular endothelial growth factor production by T cells http://purl.obolibrary.org/obo/OBI_0001570 biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells An assay of epitope specific vascular endothelial growth factor production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001767 detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells http://purl.obolibrary.org/obo/OBI_0001775 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 19 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001768 intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells http://purl.obolibrary.org/obo/OBI_0001276 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001769 specimen collector role http://purl.obolibrary.org/obo/OBI_0000202 investigation agent role An Investigation agent role borne by a person or organization which is realized in a specimen collection process. http://purl.obolibrary.org/obo/OBI_0001770 intracellular cytokine staining assay measuring epitope specific vascular endothelial growth factor production by T cells http://purl.obolibrary.org/obo/OBI_0001570 biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells An assay of epitope specific vascular endothelial growth factor production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001771 ELISPOT assay measuring epitope specific vascular endothelial growth factor production by T cells http://purl.obolibrary.org/obo/OBI_0001570 biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells An assay of epitope specific vascular endothelial growth factor production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001772 biological activity assay measuring epitope specific interleukin-17F production by T cells http://purl.obolibrary.org/obo/OBI_0001295 biological activity assay measuring epitope specific interleukin-17 production by T cells An assay of epitope specific interleukin-17 production by T cells that detects interleukin-17F production. http://purl.obolibrary.org/obo/OBI_0001773 biological activity assay measuring epitope specific interleukin-17A production by T cells http://purl.obolibrary.org/obo/OBI_0001295 biological activity assay measuring epitope specific interleukin-17 production by T cells An assay of epitope specific interleukin-17 production by T cells that detects interleukin-17A production. http://purl.obolibrary.org/obo/OBI_0001774 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 21 production by T cells. http://purl.obolibrary.org/obo/OBI_0001775 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 19 production by T cells. http://purl.obolibrary.org/obo/OBI_0001776 biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 12 production by T cells. http://purl.obolibrary.org/obo/OBI_0001777 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 22 production by T cells. http://purl.obolibrary.org/obo/OBI_0001778 biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 16 production by T cells. http://purl.obolibrary.org/obo/OBI_0001779 biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 13 production by T cells. http://purl.obolibrary.org/obo/OBI_0001780 ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells http://purl.obolibrary.org/obo/OBI_0001333 biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001781 cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells http://purl.obolibrary.org/obo/OBI_0001456 biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001782 detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells http://purl.obolibrary.org/obo/OBI_0001456 biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001783 intracellular cytokine staining assay measuring epitope specific monocyte chemotactic protein-1 production by T cells http://purl.obolibrary.org/obo/OBI_0001465 biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001784 ELISPOT assay measuring epitope specific monocyte chemotactic protein-1 production by T cells http://purl.obolibrary.org/obo/OBI_0001465 biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001785 intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells http://purl.obolibrary.org/obo/OBI_0001456 biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001786 ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells http://purl.obolibrary.org/obo/OBI_0001456 biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001787 cytometric bead array assay measuring epitope specific vascular endothelial growth factor production by T cells http://purl.obolibrary.org/obo/OBI_0001570 biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells An assay of epitope specific vascular endothelial growth factor production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001788 detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells http://purl.obolibrary.org/obo/OBI_0001400 biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001789 intracellular cytokine staining assay measuring epitope specific RANTES production by T cells http://purl.obolibrary.org/obo/OBI_0001232 biological activity assay measuring epitope specific RANTES production by T cells An assay of epitope specific RANTES production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001790 ELISPOT assay measuring epitope specific RANTES production by T cells http://purl.obolibrary.org/obo/OBI_0001232 biological activity assay measuring epitope specific RANTES production by T cells An assay of epitope specific RANTES production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001791 ELISPOT assay measuring epitope specific lymphotoxin A production by T cells http://purl.obolibrary.org/obo/OBI_0001327 biological activity assay measuring epitope specific lymphotoxin A production by T cells An assay of epitope specific lymphotoxin A production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001792 detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells http://purl.obolibrary.org/obo/OBI_0001333 biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001793 cytometric bead array assay measuring epitope specific lymphotoxin A production by T cells http://purl.obolibrary.org/obo/OBI_0001368 cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells An assay of epitope specific lymphotoxin A production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001794 detection of specific nucleic acids with complementary probes assay measuring epitope specific lymphotoxin A production by T cells http://purl.obolibrary.org/obo/OBI_0001788 detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells An assay of epitope specific lymphotoxin A production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001795 ELISPOT assay measuring epitope specific IP-10 production by T cells http://purl.obolibrary.org/obo/OBI_0001308 biological activity assay measuring epitope specific IP-10 production by T cells An assay of epitope specific IP-10 production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001796 intracellular cytokine staining assay measuring epitope specific IP-10 production by T cells http://purl.obolibrary.org/obo/OBI_0001308 biological activity assay measuring epitope specific IP-10 production by T cells An assay of epitope specific IP-10 production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001797 ELISPOT assay measuring epitope specific interleukin-9 production by T cells http://purl.obolibrary.org/obo/OBI_0001253 biological activity assay measuring interleukin-9 production by T cells An assay of epitope specific interleukin-9 production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001798 intracellular cytokine staining assay measuring epitope specific interleukin-9 production by T cells http://purl.obolibrary.org/obo/OBI_0001253 biological activity assay measuring interleukin-9 production by T cells An assay of epitope specific interleukin-9 production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001799 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-9 production by T cells http://purl.obolibrary.org/obo/OBI_0001253 biological activity assay measuring interleukin-9 production by T cells An assay of epitope specific interleukin-9 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001800 ELISPOT assay measuring epitope specific interleukin-8 production by T cells http://purl.obolibrary.org/obo/OBI_0001218 biological activity assay measuring epitope specific interleukin-8 production by T cells An assay of epitope specific interleukin-8 production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001801 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-8 production by T cells http://purl.obolibrary.org/obo/OBI_0001218 biological activity assay measuring epitope specific interleukin-8 production by T cells An assay of epitope specific interleukin-8 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001802 ELISPOT assay measuring epitope specific interleukin-3 production by T cells http://purl.obolibrary.org/obo/OBI_0001406 biological activity assay measuring epitope specific interleukin-3 production by T cells An assay of epitope specific interleukin-3 production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001803 ELISA measuring epitope specific interleukin-7 production by T cells http://purl.obolibrary.org/obo/OBI_0001587 biological activity assay measuring epitope specific interleukin-7 production by T cells An assay of epitope specific interleukin-7 production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001804 ELISPOT assay measuring epitope specific interleukin-7 production by T cells http://purl.obolibrary.org/obo/OBI_0001587 biological activity assay measuring epitope specific interleukin-7 production by T cells An assay of epitope specific interleukin-7 production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001805 intracellular cytokine staining assay measuring epitope specific interleukin-7 production by T cells http://purl.obolibrary.org/obo/OBI_0001587 biological activity assay measuring epitope specific interleukin-7 production by T cells An assay of epitope specific interleukin-7 production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001806 intracellular cytokine staining assay measuring epitope specific interleukin-27 production by T cells http://purl.obolibrary.org/obo/OBI_0001198 biological activity assay measuring epitope specific interleukin-27 production by T cells An assay of epitope specific interleukin-27 production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001807 cytometric bead array assay measuring epitope specific interleukin-3 production by T cells http://purl.obolibrary.org/obo/OBI_0001406 biological activity assay measuring epitope specific interleukin-3 production by T cells An assay of epitope specific interleukin-3 production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001808 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-3 production by T cells http://purl.obolibrary.org/obo/OBI_0001406 biological activity assay measuring epitope specific interleukin-3 production by T cells An assay of epitope specific interleukin-3 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001809 biological activity assay measuring epitope specific granzyme A release by T cells http://purl.obolibrary.org/obo/OBI_0001269 biological activity assay measuring epitope specific cytotoxic T cell degranulation A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme A release by T cells. http://purl.obolibrary.org/obo/OBI_0001810 biological activity assay measuring epitope specific granulysin release by T cells http://purl.obolibrary.org/obo/OBI_0001269 biological activity assay measuring epitope specific cytotoxic T cell degranulation A T cell epitope specific cytotoxic T cell degranulation assay that detects granulysin release by T cells. http://purl.obolibrary.org/obo/OBI_0001811 cytometric bead array assay measuring epitope specific interleukin-27 production by T cells http://purl.obolibrary.org/obo/OBI_0001198 biological activity assay measuring epitope specific interleukin-27 production by T cells An assay of epitope specific interleukin-27 production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001812 intracellular cytokine staining assay measuring epitope specific interleukin-23 production by T cells http://purl.obolibrary.org/obo/OBI_0001363 biological activity assay measuring epitope specific interleukin-23 production by T cells An assay of epitope specific interleukin-23 production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001813 ELISPOT assay measuring epitope specific interleukin-27 production by T cells http://purl.obolibrary.org/obo/OBI_0001198 biological activity assay measuring epitope specific interleukin-27 production by T cells An assay of epitope specific interleukin-27 production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001814 ELISA measuring epitope specific interleukin-27 production by T cells http://purl.obolibrary.org/obo/OBI_0001198 biological activity assay measuring epitope specific interleukin-27 production by T cells An assay of epitope specific interleukin-27 production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001815 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-18 production by T cells http://purl.obolibrary.org/obo/OBI_0001380 biological activity assay measuring epitope specific interleukin-18 production by T cells An assay of epitope specific interleukin-18 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001816 epitope specific chemokine (C-X-C motif) ligand 13 production by T cells http://purl.obolibrary.org/obo/GO_0097391 chemokine (C-X-C motif) ligand 13 production A process of chemokine (C-X-C motif) ligand 13 production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001817 ELISPOT assay measuring epitope specific interleukin-18 production by T cells http://purl.obolibrary.org/obo/OBI_0001380 biological activity assay measuring epitope specific interleukin-18 production by T cells An assay of epitope specific interleukin-18 production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001818 epitope specific chemokine (C-X-C motif) ligand 12 production by T cells http://purl.obolibrary.org/obo/GO_0097390 chemokine (C-X-C motif) ligand 12 production A process of chemokine (C-X-C motif) ligand 12 production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001819 epitope specific chemokine (C-C motif) ligand 22 production by T cells http://purl.obolibrary.org/obo/GO_0071924 chemokine (C-C motif) ligand 22 production A process of chemokine (C-C motif) ligand 22 production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001820 epitope specific chemokine (C-X-C motif) ligand 16 production by T cells http://purl.obolibrary.org/obo/GO_0097392 chemokine (C-X-C motif) ligand 16 production A process of chemokine (C-X-C motif) ligand 16 production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001821 ELISPOT assay measuring epitope specific interleukin-22 production by T cells http://purl.obolibrary.org/obo/OBI_0001217 biological activity assay measuring epitope specific interleukin-22 production by T cells An assay of epitope specific interleukin-22 production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001822 ELISPOT assay measuring epitope specific interleukin-23 production by T cells http://purl.obolibrary.org/obo/OBI_0001363 biological activity assay measuring epitope specific interleukin-23 production by T cells An assay of epitope specific interleukin-23 production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001823 epitope specific chemokine (C-C motif) ligand 21 production by T cells http://purl.obolibrary.org/obo/GO_0097389 chemokine (C-C motif) ligand 21 production A process of chemokine (C-C motif) ligand 21 production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001824 intracellular cytokine staining assay measuring epitope specific interleukin-18 production by T cells http://purl.obolibrary.org/obo/OBI_0001380 biological activity assay measuring epitope specific interleukin-18 production by T cells An assay of epitope specific interleukin-18 production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001825 epitope specific chemokine (C-C motif) ligand 19 production by T cells http://purl.obolibrary.org/obo/GO_0097388 chemokine (C-C motif) ligand 19 production A process of chemokine (C-C motif) ligand 19 production by T cells resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_0001826 ELISPOT assay measuring epitope specific interleukin-21 production by T cells http://purl.obolibrary.org/obo/OBI_0001237 biological activity assay measuring epitope specific interleukin-21 production by T cells An assay of epitope specific interleukin-21 production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001827 detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells http://purl.obolibrary.org/obo/OBI_0001276 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001828 cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells http://purl.obolibrary.org/obo/OBI_0001276 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001829 ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells http://purl.obolibrary.org/obo/OBI_0001276 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001830 ELISPOT assay measuring epitope specific interleukin-17F production by T cells http://purl.obolibrary.org/obo/OBI_0001772 biological activity assay measuring epitope specific interleukin-17F production by T cells A T cell epitope specific interleukin-17F production assay that uses an ELISPOT. http://purl.obolibrary.org/obo/OBI_0001831 ELISA measuring epitope specific interleukin-17F production by T cells http://purl.obolibrary.org/obo/OBI_1110162 ELISA measuring epitope specific interleukin-17 production by T cells A T cell epitope specific interleukin-17F production assay that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001832 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17F production by T cells http://purl.obolibrary.org/obo/OBI_0001772 biological activity assay measuring epitope specific interleukin-17F production by T cells A T cell epitope specific interleukin-17F production assay that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001833 ELISPOT assay measuring epitope specific interleukin-17A production by T cells http://purl.obolibrary.org/obo/OBI_0001773 biological activity assay measuring epitope specific interleukin-17A production by T cells A T cell epitope specific interleukin-17A production assay that uses an ELISPOT. http://purl.obolibrary.org/obo/OBI_0001834 drawing a conclusion http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process in which new information is inferred from existing information. http://purl.obolibrary.org/obo/OBI_0001835 cytometric bead array assay measuring epitope specific interleukin-18 production by T cells http://purl.obolibrary.org/obo/OBI_0001380 biological activity assay measuring epitope specific interleukin-18 production by T cells An assay of epitope specific interleukin-18 production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0001836 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-16 production by T cells http://purl.obolibrary.org/obo/OBI_0001280 biological activity assay measuring epitope specific interleukin-16 production by T cells An assay of epitope specific interleukin-16 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001837 ELISA measuring epitope specific interleukin-16 production by T cells http://purl.obolibrary.org/obo/OBI_0001280 biological activity assay measuring epitope specific interleukin-16 production by T cells An assay of epitope specific interleukin-16 production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0001838 ELISPOT assay measuring epitope specific interleukin-16 production by T cells http://purl.obolibrary.org/obo/OBI_0001280 biological activity assay measuring epitope specific interleukin-16 production by T cells An assay of epitope specific interleukin-16 production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001839 intracellular cytokine staining assay measuring epitope specific interleukin-16 production by T cells http://purl.obolibrary.org/obo/OBI_0001280 biological activity assay measuring epitope specific interleukin-16 production by T cells An assay of epitope specific interleukin-16 production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001840 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17A production by T cells http://purl.obolibrary.org/obo/OBI_0001773 biological activity assay measuring epitope specific interleukin-17A production by T cells A T cell epitope specific interleukin-17A production assay that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001841 intracellular cytokine staining assay measuring epitope specific interleukin-1 beta production by T cells http://purl.obolibrary.org/obo/OBI_0001449 biological activity assay measuring epitope specific interleukin-1 beta production by T cells An assay of epitope specific interleukin-1 beta production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001842 ELISPOT assay measuring epitope specific interleukin-1 beta production by T cells http://purl.obolibrary.org/obo/OBI_0001449 biological activity assay measuring epitope specific interleukin-1 beta production by T cells An assay of epitope specific interleukin-1 beta production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001843 detection of specific nucleic acids with complementary probes measuring epitope specific interleukin-15 production by T cells http://purl.obolibrary.org/obo/OBI_0001292 biological activity assay measuring epitope specific interleukin-15 production by T cells An assay of epitope specific interleukin-15 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0001844 ELISPOT assay measuring epitope specific interleukin-12 production by T cells http://purl.obolibrary.org/obo/OBI_0001391 biological activity assay measuring epitope specific interleukin-12 production by T cells An assay of epitope specific interleukin-12 production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001845 intracellular cytokine staining assay measuring epitope specific interleukin-15 production by T cells http://purl.obolibrary.org/obo/OBI_0001292 biological activity assay measuring epitope specific interleukin-15 production by T cells An assay of epitope specific interleukin-15 production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_0001846 ELISPOT assay measuring epitope specific interleukin-15 production by T cells http://purl.obolibrary.org/obo/OBI_0001292 biological activity assay measuring epitope specific interleukin-15 production by T cells An assay of epitope specific interleukin-15 production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0001851 transcription start site identification objective http://purl.obolibrary.org/obo/OBI_0001331 transcription profiling identification objective A transcription profiling identification objective that aims to characterize the transcription start sites of genes. http://purl.obolibrary.org/obo/OBI_0001852 paired-end library preparation http://purl.obolibrary.org/obo/OBI_0000711 library preparation A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process. http://purl.obolibrary.org/obo/OBI_0001853 DNase I hypersensitive sites sequencing assay http://purl.obolibrary.org/obo/OBI_0000626 DNA sequencing assay An assay that identifies the location of regulatory regions, based on the genome-wide sequencing of regions super sensitive to cleavage by DNase I. http://purl.obolibrary.org/obo/OBI_0001854 protein and RNA interaction identification objective http://purl.obolibrary.org/obo/OBI_0000113 sequence feature identification objective A sequence feature identification objective that aims to characterize the interactions between protein and RNA. http://purl.obolibrary.org/obo/OBI_0001865 assay array http://purl.obolibrary.org/obo/OBI_0000968 device A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface. http://purl.obolibrary.org/obo/OBI_0001866 secondary cultured cell http://purl.obolibrary.org/obo/CL_0000010 cultured cell A cultured cell that has been passaged or derives from a cell that has been passaged in culture. http://purl.obolibrary.org/obo/OBI_0001867 establishing cell line http://purl.obolibrary.org/obo/OBI_0600036 establishing cell culture a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset). http://purl.obolibrary.org/obo/OBI_0001869 Illumina BeadChip http://purl.obolibrary.org/obo/OBI_0001865 assay array An array that consists of 3-micron silica beads that self assemble in microwells on either of two materials: fiber optic bundles or planar silica slides. http://purl.obolibrary.org/obo/OBI_0001870 Illumina methylation BeadChip http://purl.obolibrary.org/obo/OBI_0001869 Illumina BeadChip A BeadChip made for an analyte assay that generates information about DNA methylation. http://purl.obolibrary.org/obo/OBI_0001871 LSRFortessa X-20 http://purl.obolibrary.org/obo/OBI_0400008 flow cytometer analyzer A flow cytometer analyzer manifactured by Becton ans Dickinson. Can be configured with up to 5 lasers, 488nm, 532 or 561 nm, 640 nm, 405 nm, 355 nm for measuring up to 20 parameters simultaneously. http://purl.obolibrary.org/obo/OBI_0001872 sequence assembly process http://purl.obolibrary.org/obo/OBI_0200000 data transformation A data transformation that assembles two or more individual sequence reads into contiguous sequences (i.e., contigs). http://purl.obolibrary.org/obo/OBI_0001873 number of errors http://purl.obolibrary.org/obo/OBI_0001933 value specification a data item that is the number of times that a given process failed, as an integer http://purl.obolibrary.org/obo/OBI_0001874 random access memory size http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum random access memory size is a scalar measurement datum which denotes the amount of physical memory know as random access memory present of a computer or required by a computational process or data transformation http://purl.obolibrary.org/obo/OBI_0001876 cell culture http://purl.obolibrary.org/obo/OBI_0000047 processed material A material entity comprised of cultured cells and the media in which they are being propagated or stored. http://purl.obolibrary.org/obo/OBI_0001878 establishing primary cell culture http://purl.obolibrary.org/obo/OBI_0600036 establishing cell culture an establishing cell culture process whereby cells explanted directly from an organismal source or specimen, and placed in culture for maintenance or propagation as a primary cell culture http://purl.obolibrary.org/obo/OBI_0001879 reagent http://purl.obolibrary.org/obo/OBI_0000047 processed material A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output. http://purl.obolibrary.org/obo/OBI_0001880 organization of specimen provider principal investigator http://purl.obolibrary.org/obo/OBI_0000245 organization An organization that is the affiliation of the principal investigator providing the specimens for the investigation http://purl.obolibrary.org/obo/OBI_0001881 organization of Bioinformatics Resource Center contact person http://purl.obolibrary.org/obo/OBI_0000245 organization An organization that is the affiliation of the person who is contact representative of a Bioinformatics Resource Center http://purl.obolibrary.org/obo/OBI_0001882 target material in specimen specification http://purl.obolibrary.org/obo/IAO_0000104 plan specification A plan specification which specifies the type of material that will be assayed in an investigation. http://purl.obolibrary.org/obo/OBI_0001883 Bioinformatics Resource Center contact person http://purl.obolibrary.org/obo/NCBITaxon_9606 Homo sapiens A person who is the contact representative of a Bioinformatics Resource Center http://purl.obolibrary.org/obo/OBI_0001884 specimen-based scope of investigation specification http://purl.obolibrary.org/obo/IAO_0000104 plan specification A plan specification which specifies the scope of an investigation based on the heterogeneity of organisms or type of material that are the specified input of specimen collection. http://purl.obolibrary.org/obo/OBI_0001885 specimen repository organization http://purl.obolibrary.org/obo/OBI_0000245 organization An organization that provides a service to store and distribute specimens http://purl.obolibrary.org/obo/OBI_0001887 email address of Bioinformatics Resource Center contact person http://purl.obolibrary.org/obo/IAO_0000429 email address An email address of the person who is contact representative of a Bioinformatics Resource Center http://purl.obolibrary.org/obo/OBI_0001888 sequencing facility contact person http://purl.obolibrary.org/obo/NCBITaxon_9606 Homo sapiens A person who is the contact representative at the sequencing facility http://purl.obolibrary.org/obo/OBI_0001889 specimen provider principal investigator http://purl.obolibrary.org/obo/NCBITaxon_9606 Homo sapiens A person who is a principal investigator and provides the specimen http://purl.obolibrary.org/obo/OBI_0001890 email address of specimen collector http://purl.obolibrary.org/obo/IAO_0000429 email address An email address of the person collecting the specimen http://purl.obolibrary.org/obo/OBI_0001891 sequencing facility organization http://purl.obolibrary.org/obo/OBI_0002198 molecular analysis facility organization An organization that provides sequence determination service http://purl.obolibrary.org/obo/OBI_0001892 specification of data to be generated in an investigation http://purl.obolibrary.org/obo/IAO_0000005 objective specification An objective specification which indicates the type of data that will be generated and submitted to a database. http://purl.obolibrary.org/obo/OBI_0001893 organization of specimen collector http://purl.obolibrary.org/obo/OBI_0000245 organization An organization that is the affiliation of the person collecting the specimen http://purl.obolibrary.org/obo/OBI_0001894 email address of sequencing facility contact person http://purl.obolibrary.org/obo/IAO_0000429 email address An email address of the contact representative at the sequencing facility http://purl.obolibrary.org/obo/OBI_0001895 specimen collector http://purl.obolibrary.org/obo/NCBITaxon_9606 Homo sapiens A person who collects the specimen http://purl.obolibrary.org/obo/OBI_0001896 investigation assay specification http://purl.obolibrary.org/obo/IAO_0000104 plan specification A plan specification which indicates the assay type used to obtain data. http://purl.obolibrary.org/obo/OBI_0001897 organization of sequencing facility contact person http://purl.obolibrary.org/obo/OBI_0000245 organization An organization that is the affiliation of the contact representative at the sequencing facility http://purl.obolibrary.org/obo/OBI_0001898 comment on investigation http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that is about any of the aspects of an investigation worth noting http://purl.obolibrary.org/obo/OBI_0001899 target capture specification http://purl.obolibrary.org/obo/IAO_0000104 plan specification A plan specification which specifies how the material enrichment procedure will influence the scale, or type of material that will be assayed in the specimen. http://purl.obolibrary.org/obo/OBI_0001900 specimen identifier assigned by specimen repository http://purl.obolibrary.org/obo/OBI_0001616 specimen identifier A specimen identifier which is assigned by a specimen repository http://purl.obolibrary.org/obo/OBI_0001901 specimen identifier assigned by sequencing facility http://purl.obolibrary.org/obo/OBI_0001616 specimen identifier A specimen identifier which is assigned by a sequencing facility http://purl.obolibrary.org/obo/OBI_0001902 sample preparation for sequencing assay http://purl.obolibrary.org/obo/OBI_0000073 sample preparation for assay A sample preparation for assay that preparation of nucleic acids for a sequencing assay http://purl.obolibrary.org/obo/OBI_0001903 email address of specimen provider principal investigator http://purl.obolibrary.org/obo/IAO_0000429 email address An email address of the principal investigator providing the specimens for the investigation http://purl.obolibrary.org/obo/OBI_0001904 sequencing service http://purl.obolibrary.org/obo/OBI_0001547 material analysis service A service provides sequencing service which is the realization of some sequencing such as RNA and DNA sequencing in which the service provider role is realized. http://purl.obolibrary.org/obo/OBI_0001906 cancer cell line http://purl.obolibrary.org/obo/CLO_0009828 immortal cell line An immortal cell line derived from a transformed cell that was part of a malignant tumor. http://purl.obolibrary.org/obo/OBI_0001907 immortalizing cell line transformation http://purl.obolibrary.org/obo/OBI_0600043 genetic transformation a genetic transformation of a cell line cell with transgenic constructs intended to confer the capability for indefinite propagation in culture http://purl.obolibrary.org/obo/OBI_0001909 conclusion based on data http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity that is inferred from data. http://purl.obolibrary.org/obo/OBI_0001910 primary cell culture http://purl.obolibrary.org/obo/OBI_0001876 cell culture A cell culture comprised of primary cultured cells and the media in which they are being actively propaged or quiescently stored. http://purl.obolibrary.org/obo/OBI_0001911 cell line culture http://purl.obolibrary.org/obo/OBI_0001876 cell culture A cell culture comprised of cell line cells and the media in which they are being actively propagated or quiescently stored. http://purl.obolibrary.org/obo/OBI_0001912 cell freezing medium http://purl.obolibrary.org/obo/OBI_0000047 processed material A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles. http://purl.obolibrary.org/obo/OBI_0001916 DNA replication identification objective http://purl.obolibrary.org/obo/OBI_0000131 molecular feature identification objective A molecular feature identification objective that aims to examine charateristics of DNA replication, such as replication time. http://purl.obolibrary.org/obo/OBI_0001917 chromosome conformation identification objective http://purl.obolibrary.org/obo/OBI_0000131 molecular feature identification objective A molecular feature identification objective that aims to determine spatial organization of chromatin. http://purl.obolibrary.org/obo/OBI_0001921 RNA-binding protein immunoprecipitation tiling array profiling assay http://purl.obolibrary.org/obo/OBI_0001918 RNA-binding protein immunoprecipitation array profiling assay An RNA-binding protein immunoprecipitation array profiling assay that combines immunoprecipitation of an RNA-binding protein and RNA tiling array to identify mRNAs associated with selected RNA binding proteins (RBPs). http://purl.obolibrary.org/obo/OBI_0001923 protein sequencing by tandem mass spectrometry assay http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay A sequencing assay that detremines amino acid sequences of proteins using multiple rounds of mass spectrometry and molecule fragmentation. http://purl.obolibrary.org/obo/OBI_0001929 mass value specification http://purl.obolibrary.org/obo/OBI_0001931 scalar value specification A value specification that specifies the mass of some thing. http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification http://purl.obolibrary.org/obo/OBI_0001933 value specification A value specification that is specifies one category out of a fixed number of nominal categories http://purl.obolibrary.org/obo/OBI_0001931 scalar value specification http://purl.obolibrary.org/obo/OBI_0001933 value specification A value specification that consists of two parts: a numeral and a unit label http://purl.obolibrary.org/obo/OBI_0001932 comparing prediction to measurement http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process in which predicted values for some thing are compared to measured values for that thing. http://purl.obolibrary.org/obo/OBI_0001933 value specification http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity that specifies a value within a classification scheme or on a quantitative scale. http://purl.obolibrary.org/obo/OBI_0001934 predicted value http://purl.obolibrary.org/obo/IAO_0000030 information content entity an information content entity that has been generated by a prediction process in which an estimate of a value of an entity is made which can be measured but without performing such a measurement. The value specification is intended to be close to the value a measurement process would produce modulo a prediction error. http://purl.obolibrary.org/obo/OBI_0001935 predicted mass value http://purl.obolibrary.org/obo/OBI_0001934 predicted value A predicted value where the prediction specifies the mass of some thing. http://purl.obolibrary.org/obo/OBI_0001936 molecular-labeled material http://purl.obolibrary.org/obo/OBI_0000047 processed material a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay http://purl.obolibrary.org/obo/OBI_0001939 genome coverage http://purl.obolibrary.org/obo/IAO_0000027 data item A data item that is the total number of bases in reads, divided by genome size, assumed to be the reference size (for instance of 3.10 Gb for human and 2.73 Gb for mouse) and refers to the percentage of the genome that is contained in the assembly based on size estimates; these are usually based on cytological techniques. Genome coverage of 90–95% is generally considered to be good, as most genomes contain a considerable fraction of repetitive regions that are difficult to sequence. So it is not a cause for concern if the genome coverage of an assembly is a bit less than 100%. http://purl.obolibrary.org/obo/OBI_0001941 contig N50 http://purl.obolibrary.org/obo/OBI_0001940 N50 N50 statistic computed for the contigs produced by the assembly process. A contig N50 is calculated by first ordering every contig by length from longest to shortest. Next, starting from the longest contig, the lengths of each contig are summed, until this running sum equals one-half of the total length of all contigs in the assembly. The contig N50 of the assembly is the length of the shortest contig in this list. http://purl.obolibrary.org/obo/OBI_0001943 software pipeline http://purl.obolibrary.org/obo/IAO_0000104 plan specification A plan specification that specifies a chain encoded in software of processing elements (processes, threads, coroutines, etc.), arranged so that the output of each element is the input of the next. Usually some amount of buffering is provided between consecutive elements. http://purl.obolibrary.org/obo/OBI_0001944 sequence annotation http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process that identifies and reports sequence features (e.g. protein coding regions) in sequence data. http://purl.obolibrary.org/obo/OBI_0001945 scaffold N50 http://purl.obolibrary.org/obo/OBI_0001940 N50 N50 statistic computed for the scaffold produced by the assembly process. The method for computing the value is similar to that of contig N50 but uses scaffold information instead of contig information http://purl.obolibrary.org/obo/OBI_0001947 sequence annotation provider http://purl.obolibrary.org/obo/BFO_0000040 material entity A person or organization reporting the feature annotation results from the analysis of a macromolecular sequence. http://purl.obolibrary.org/obo/OBI_0001948 sequence assembly name http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that is used to denote a sequence assembly. http://purl.obolibrary.org/obo/OBI_0001949 sequence annotation reporting role http://purl.obolibrary.org/obo/OBI_0000068 reporting party role A reporting party role that is realized by a person or organization who reports the feature annotation results from the analysis of a macromolecular sequence. http://purl.obolibrary.org/obo/OBI_0001952 flash freezing http://purl.obolibrary.org/obo/OBI_0001953 freezing A freezing process by which material entities are quickly frozen by subjecting them to cryogenic temperatures, or in direct contact with Liquid nitrogen at -320.8F or -196°C. http://purl.obolibrary.org/obo/OBI_0001953 freezing http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process in which a material entity has it's temperature lowered to below the freezing point in order to bring it to a state in which it can be maintained at this lower temperature in order to preserve some of its qualities. http://purl.obolibrary.org/obo/OBI_0001955 competitive binding reference ligand role http://purl.obolibrary.org/obo/OBI_0000064 positive reference substance role A positive reference substance role that inheres in a material entity that is known to bind to a target entity, and that is realized in a competitive binding assay that has as specified input the target entity, an evaluant and the positive reference substance, where the binding of the evaluant to the target is measured based on the evaluant's ability to compete with the positive reference substance for binding to the target. http://purl.obolibrary.org/obo/OBI_0001956 assay using chromatin immunoprecipitation http://purl.obolibrary.org/obo/OBI_0001700 immunoprecipitation assay An assay that produces data about protein-DNA interaction or DNA epigenetic modification using immunoprecipitation http://purl.obolibrary.org/obo/OBI_0001957 hardware testing design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that aims to compare different types of hardware for performance, reproducibility, accuracy and precision. http://purl.obolibrary.org/obo/OBI_0001958 systematic review study design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design for identifying in the literature prior studies of a pre-determined phenomenon or set of related phenomena according to certain criteria, extracting findings from these studies, and summarizing these findings and/or attempting to draw new conclusions from them which were not justified by any of the individual, prior studies. Many systematic reviews also assess the quality of the studies so reviewed. http://purl.obolibrary.org/obo/OBI_0001959 multiplexed nucleotide library sequencing http://purl.obolibrary.org/obo/OBI_0000094 material processing A planned process which consists in running a set of samples as a pool on a sequencing instrument, while retaining the ability to associate individual results to each of the individual input samples through the use of a ligated oligonucleotide (the "multiplex identifier sequence"). This oligonucleotide is introduced during the sequence library preparation, and is unique to and specific for all library fragments derived from each sample in a sample pool. http://purl.obolibrary.org/obo/OBI_0001961 PCR program http://purl.obolibrary.org/obo/IAO_0000104 plan specification a PCR program is a plan specification which is executed during a polymerase chain reaction (PCR) by a thermocycler instrument that will iterate through the changes in temperature and duration of each of the annealing, denaturation, elongation steps for as many times as specified by the program. http://purl.obolibrary.org/obo/OBI_0001962 target gene specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity is a directive information specifying a coding genomic region which is the focus of a planned process such as an assay, for instance in a environmental gene survey http://purl.obolibrary.org/obo/OBI_0001963 target subfragment specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity is a directive information specifying a genomic region, possibly located in a coding genomic region, which is the focus of a planned process such as an assay, for instance in a environmental gene survey http://purl.obolibrary.org/obo/OBI_0001965 decision analysis study design http://purl.obolibrary.org/obo/OBI_0500000 study design a study design that has a decision analysis objective specification as part http://purl.obolibrary.org/obo/OBI_0001966 sequence library data demultiplexing http://purl.obolibrary.org/obo/OBI_0200187 sequence analysis data transformation is a data transformation which uses sequence alignment and 'multiplex identifier sequence' information to separate all reads belonging to a given single sample following the sequencing of a multiplexed library http://purl.obolibrary.org/obo/OBI_0001967 multiplexing sequence identifier http://purl.obolibrary.org/obo/CHEBI_16991 deoxyribonucleic acid A multiplexing sequence identifier is a nucleic acid sequence which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library http://purl.obolibrary.org/obo/OBI_0001968 operational taxonomic unit matrix http://purl.obolibrary.org/obo/IAO_0000027 data item Operational Taxonomic Unit matrix is a data item, organized as a table, where organismal taxonomic units, computed by sequence analysis and genetic distance calculation, are counted in a set of biological or environmental samples. The table is used to appraise biodiversity of a population or community of living organism. http://purl.obolibrary.org/obo/OBI_0001969 biodiversity assessment objective http://purl.obolibrary.org/obo/OBI_0000015 biological feature identification objective biodiversity assessment objective is an objective of a planned process aimed at producing data item whose interpretation should provide insight about variety of biological species found in a biological sample at macroscopic or microscopic level http://purl.obolibrary.org/obo/OBI_0001976 hydrogen/deuterium exchange footprinting assay http://purl.obolibrary.org/obo/OBI_0002162 footprinting assay A footprinting assay that uses a chemical reaction whereby a covalently bonded hydrogen atom is replaced by a deuterium atom, or vice versa in order to gather information about the solvent accessibility of parts of a molecule and thus its tertiary structure. http://purl.obolibrary.org/obo/OBI_0001977 cytometry assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that counts and/or measures characteristics of cells. http://purl.obolibrary.org/obo/OBI_0001978 immunoblot assay http://purl.obolibrary.org/obo/OBI_0000443 analyte assay An analyte assay that detects specific molecules in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules. http://purl.obolibrary.org/obo/OBI_0001979 fluorescence quenching binding assay http://purl.obolibrary.org/obo/OBI_0001146 binding assay A binding assay in which the proximity of two entities is monitored by measuring a fluorescent signal of one of the entities that gets reduced if the two entities are cliose to each other. http://purl.obolibrary.org/obo/OBI_0001980 in vivo intervention experiment http://purl.obolibrary.org/obo/OBI_0000070 assay An assay in which the effect of a targeted process (the intervention) on an organism is tested. http://purl.obolibrary.org/obo/OBI_0001981 disease exacerbation in vivo intervention experiment http://purl.obolibrary.org/obo/OBI_0001980 in vivo intervention experiment An in vivo intervention experiment that tests the ability of the intervention to increase the severity of a disease in the host. http://purl.obolibrary.org/obo/OBI_0001982 protection from challenge in vivo intervention experiment http://purl.obolibrary.org/obo/OBI_0001980 in vivo intervention experiment An in vivo intervention experiment that tests the ability of the intervention to prevent occurrence of a disease in a host. http://purl.obolibrary.org/obo/OBI_0001983 tolerance induction intervention experiment http://purl.obolibrary.org/obo/OBI_0001980 in vivo intervention experiment An in vivo intervention experiment that tests the ability of the intervention to decrease an immune response. http://purl.obolibrary.org/obo/OBI_0001984 treatment intervention experiment http://purl.obolibrary.org/obo/OBI_0001980 in vivo intervention experiment An in vivo intervention experiment in which the ability of the intervention to reduce or cure the effects of a disease are tested. http://purl.obolibrary.org/obo/OBI_0001985 microarray assay http://purl.obolibrary.org/obo/OBI_0000443 analyte assay An analyte assay where binding of the analyte to immobilized matrix is measured. http://purl.obolibrary.org/obo/OBI_0001986 immunohistochemistry http://purl.obolibrary.org/obo/OBI_0001632 immuno staining assay An immunostaining assay to detect and potentially localize antigens within the cells of a tissue section. http://purl.obolibrary.org/obo/OBI_0001987 assay measuring the association constant [KA] of a MHC:ligand complex http://purl.obolibrary.org/obo/OBI_0001553 assay measuring a binding constant of a MHC:ligand complex A MHC binding constant determination assay measuring equilibrium association constant (KA). http://purl.obolibrary.org/obo/OBI_0001988 assay measuring the dissociation constant [KD] of a MHC:ligand complex http://purl.obolibrary.org/obo/OBI_0001553 assay measuring a binding constant of a MHC:ligand complex A MHC binding constant determination assay measuring equilibrium dissociation constant (KD). http://purl.obolibrary.org/obo/OBI_0001989 purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection http://purl.obolibrary.org/obo/OBI_0001988 assay measuring the dissociation constant [KD] of a MHC:ligand complex A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. http://purl.obolibrary.org/obo/OBI_0001990 assay measuring the half life of a MHC:ligand complex http://purl.obolibrary.org/obo/OBI_0001553 assay measuring a binding constant of a MHC:ligand complex A MHC binding constant determination assay measuring half life of binding. http://purl.obolibrary.org/obo/OBI_0001991 assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex http://purl.obolibrary.org/obo/OBI_0001553 assay measuring a binding constant of a MHC:ligand complex A MHC binding constant determination assay measuring half maximal effective concentration (EC50). http://purl.obolibrary.org/obo/OBI_0001992 assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex http://purl.obolibrary.org/obo/OBI_0001553 assay measuring a binding constant of a MHC:ligand complex A MHC binding constant determination assay measuring half maximal inhibitory concentration (IC50). http://purl.obolibrary.org/obo/OBI_0001993 assay measuring the off rate measurement [koff] of a MHC:ligand complex http://purl.obolibrary.org/obo/OBI_0001553 assay measuring a binding constant of a MHC:ligand complex A MHC binding constant determination assay measuring binding off rate measurement data item (koff). http://purl.obolibrary.org/obo/OBI_0001994 assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complex http://purl.obolibrary.org/obo/OBI_0001553 assay measuring a binding constant of a MHC:ligand complex A MHC binding constant determination assay measuring binding on rate (kon). http://purl.obolibrary.org/obo/OBI_0001995 chromatography assay measuring the association constant [KA] of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001719 assay measuring the association constant [KA] of a B cell epitope:antibody complex A B cell epitope equilibrium association constant (KA) determination assay that uses an analytical chromatography assay. http://purl.obolibrary.org/obo/OBI_0001996 chromatography assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001708 assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex A B cell epitope equilibrium dissociation constant (KD) determination assay that uses an analytical chromatography assay. http://purl.obolibrary.org/obo/OBI_0001997 hydrogen/deuterium exchange footprinting assay measuring binding of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0002449 footprinting assay measuring binding of a B cell epitope:antibody complex A footprinting assay that uses hydrogen/deuterium exchange to measure B cell epitope qualitative binding to antibody. http://purl.obolibrary.org/obo/OBI_0001998 immunohistochemistry assay measuring binding of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001652 immuno staining assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses an immunohistochemistry assay. http://purl.obolibrary.org/obo/OBI_0001999 3D structure determining assay of a T cell epitope:MHC:TCR complex http://purl.obolibrary.org/obo/OBI_1110037 assay measuring binding of a T cell epitope:MHC:TCR complex A T cell epitope recognition assay that uses a 3D structure determination of bound complex assay. http://purl.obolibrary.org/obo/OBI_0002013 nCounter Human miRNA Expression array http://purl.obolibrary.org/obo/OBI_0001865 assay array A human array which is manufacutred by NanoString Technologies. Built upon color-coded molecular barcodes technology, the array profiles miRNA with increased specificity and sensitivty than microarrays. http://purl.obolibrary.org/obo/OBI_0002020 epigenetic modification assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that identifies epigenetic modifications including histone modifications, open chromatin, and DNA methylation. http://purl.obolibrary.org/obo/OBI_0002028 SAGE ditag library preparation http://purl.obolibrary.org/obo/OBI_0000711 library preparation A library preparation in which tags identifiying transcripts are created, ligated to form ditags, amplified, concatemerized and ligated into a vector to create a library. http://purl.obolibrary.org/obo/OBI_0002036 array based nucleic acid structure mapping assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay which aims to provide information about the in vivo organization/structure of nucleic acids using chemical or enzymatic probes using a microarray. http://purl.obolibrary.org/obo/OBI_0002037 micrococcal nuclease digestion followed by tiling array assay http://purl.obolibrary.org/obo/OBI_0002036 array based nucleic acid structure mapping assay An array based nucleic acid structure mapping assay that identifies nucleosome positions genome wide, by detection of regions protected by nucleosomes from digestion by micrococal nuclease using tiling array assays http://purl.obolibrary.org/obo/OBI_0002047 enzyme-linked antibody http://purl.obolibrary.org/obo/OBI_0000047 processed material A processed material that is comprised of an antibody that is covalently linked to an enzyme through bioconjugation. The enzyme can be used as a detection method when the enzyme's reaction produces a detectable signal, for example a color change when the substrate is added. http://purl.obolibrary.org/obo/OBI_0002050 3D structure determining assay of a MHC:ligand complex http://purl.obolibrary.org/obo/OBI_1110126 assay measuring binding of a MHC:ligand complex A MHC:ligand binding assay that uses a 3D structure determination of bound complex assay. http://purl.obolibrary.org/obo/OBI_0002051 in vivo assay measuring B cell epitope specific protection from infectious challenge based on pathogen burden http://purl.obolibrary.org/obo/OBI_0001710 in vivo assay measuring B cell epitope specific protection from challenge A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on pathogen burden. http://purl.obolibrary.org/obo/OBI_0002052 in vivo assay measuring B cell epitope specific protection from tumor challenge http://purl.obolibrary.org/obo/OBI_0001710 in vivo assay measuring B cell epitope specific protection from challenge A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on tumor burden. http://purl.obolibrary.org/obo/OBI_0002053 microarray assay measuring binding of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001703 assay measuring qualitiative binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a microarray. http://purl.obolibrary.org/obo/OBI_0002054 NMR assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001708 assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a nuclear magnetic resonance assay. http://purl.obolibrary.org/obo/OBI_0002055 assay measuring T cell epitope specific biological activity http://purl.obolibrary.org/obo/OBI_1110037 assay measuring binding of a T cell epitope:MHC:TCR complex A T cell epitope recognition assay that detects biological activity. http://purl.obolibrary.org/obo/OBI_0002056 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 17 production by T cells. http://purl.obolibrary.org/obo/OBI_0002057 biological activity assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects macrophage migration inhibitory factor (MIF) production by T cells. http://purl.obolibrary.org/obo/OBI_0002058 biological activity assay measuring epitope specific oncostatin M production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects oncostatin M production by T cells. http://purl.obolibrary.org/obo/OBI_0002059 assay measuring a binding constant of a T cell epitope:MHC:TCR complex http://purl.obolibrary.org/obo/OBI_1110037 assay measuring binding of a T cell epitope:MHC:TCR complex A T cell epitope recognition assay that quantitavely characterizes the binding of a TCR with a ligand by determining a binding constant. http://purl.obolibrary.org/obo/OBI_0002060 detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells http://purl.obolibrary.org/obo/OBI_0002056 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 17 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0002061 cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells http://purl.obolibrary.org/obo/OBI_0001777 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 22 production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0002062 in vitro assay measuring epitope specific T cell killing http://purl.obolibrary.org/obo/OBI_1110130 biological activity assay measuring epitope specific T cell killing A T cell epitope specific killing assay that uses an in vitro cell killing assay. http://purl.obolibrary.org/obo/OBI_0002063 cytometric bead array assay measuring epitope specific granzyme A release by T cells http://purl.obolibrary.org/obo/OBI_0001809 biological activity assay measuring epitope specific granzyme A release by T cells A T cell epitope specific granzyme A release assay that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0002064 detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme A release by T cells http://purl.obolibrary.org/obo/OBI_0001809 biological activity assay measuring epitope specific granzyme A release by T cells A T cell epitope specific granzyme A release assay that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0002065 cytometric bead array assay measuring epitope specific granzyme B release by T cells http://purl.obolibrary.org/obo/OBI_0001436 biological activity assay measuring epitope specific granzyme B release by T cells A T cell epitope specific granzyme B release assay that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0002066 detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme B release by T cells http://purl.obolibrary.org/obo/OBI_0001436 biological activity assay measuring epitope specific granzyme B release by T cells A T cell epitope specific granzyme B release assay that uses a detection of specific nucleic acids with complementary probes assay. http://purl.obolibrary.org/obo/OBI_0002067 cytometric bead array assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells http://purl.obolibrary.org/obo/OBI_0002057 biological activity assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells An assay of epitope specific macrophage migration inhibitory factor (MIF) production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0002068 cytometric bead array assay measuring epitope specific oncostatin M production by T cells http://purl.obolibrary.org/obo/OBI_0002058 biological activity assay measuring epitope specific oncostatin M production by T cells An assay of epitope specific oncostatin M production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0002069 ELISPOT assay measuring epitope specific perforin release by T cells http://purl.obolibrary.org/obo/OBI_0001497 biological activity assay measuring epitope specific perforin release by T cells A T cell epitope specific perforin release assay that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_0002070 in vivo assay measuring epitope specific proliferation of T cells http://purl.obolibrary.org/obo/OBI_1110131 biological activity assay measuring epitope specific proliferation of T cells A T cell epitope specific proliferation assay that is performed in vivo. http://purl.obolibrary.org/obo/OBI_0002071 in vitro assay measuring epitope specific proliferation of T cells http://purl.obolibrary.org/obo/OBI_1110131 biological activity assay measuring epitope specific proliferation of T cells A T cell epitope specific proliferation assay that is performed on cells in vitro. http://purl.obolibrary.org/obo/OBI_0002072 assay measuring qualitiative binding of a MHC:ligand complex http://purl.obolibrary.org/obo/OBI_1110126 assay measuring binding of a MHC:ligand complex A MHC:ligand binding assay that detects qualitative binding. http://purl.obolibrary.org/obo/OBI_0002073 in vivo assay measuring T cell epitope specific protection from challenge http://purl.obolibrary.org/obo/OBI_0001484 biological activity assay measuring T cell epitope specific in vivo activity An efficacy of T cell epitope intervention experiment that uses a epitope protection experiment. http://purl.obolibrary.org/obo/OBI_0002074 in vitro assay measuring T cell epitope specific suppression http://purl.obolibrary.org/obo/OBI_0002055 assay measuring T cell epitope specific biological activity T cell epitope dependent biological activity assay that detects suppression of an in vitro response. http://purl.obolibrary.org/obo/OBI_0002075 MHC ligand assay http://purl.obolibrary.org/obo/OBI_1110128 immune epitope assay An immune epitope assay that detects either the processing and presentation of a ligand by an antigen presenting cell or the binding of a ligand to an MHC molecule. http://purl.obolibrary.org/obo/OBI_0002076 collection of specimens http://purl.obolibrary.org/obo/BFO_0000040 material entity A material entity that has two or more specimens as its parts. http://purl.obolibrary.org/obo/OBI_0002078 specimen set collection process http://purl.obolibrary.org/obo/OBI_0000659 specimen collection process A specimen collection process that generates multiple specimens from one source (e.g. one organism) during a time period which for the purpose of the study can be considered to be taken at the same sampling time. http://purl.obolibrary.org/obo/OBI_0002080 human specimen set http://purl.obolibrary.org/obo/OBI_0002079 specimens collected in one encounter A specimen set that is collected from one person during a time period which for the purpose of the study can be considered to be taken at the same sampling time. http://purl.obolibrary.org/obo/OBI_0002081 specimens collected longitudinally http://purl.obolibrary.org/obo/OBI_0002076 collection of specimens A collection of specimens that was derived from the same source material entity at different time points in order to observe changes in that entity. http://purl.obolibrary.org/obo/OBI_0002087 containing a specimen function http://purl.obolibrary.org/obo/OBI_0000370 contain function A contain function that involves physical contact with a specimen. This function is typically performed in such a way that the specimen is usable for an investigation or assay. http://purl.obolibrary.org/obo/OBI_0002088 specimen container http://purl.obolibrary.org/obo/OBI_0000967 container A container with the function of containing a specimen. http://purl.obolibrary.org/obo/OBI_0002089 physical store http://purl.obolibrary.org/obo/OBI_0001034 environmental control device A container with an environmental control function. http://purl.obolibrary.org/obo/OBI_0002095 specimen family creation http://purl.obolibrary.org/obo/OBI_0000094 material processing A material processing that has as its input a specimen and as its output a collection of specimens. http://purl.obolibrary.org/obo/OBI_0002096 carboxyfluorescein succinimidyl ester staining assay measuring epitope specific proliferation of T cells http://purl.obolibrary.org/obo/OBI_0002071 in vitro assay measuring epitope specific proliferation of T cells A T cell epitope specific proliferation assay performed on cells in vitro that uses a CFSE assay. http://purl.obolibrary.org/obo/OBI_0002097 assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex http://purl.obolibrary.org/obo/OBI_0002059 assay measuring a binding constant of a T cell epitope:MHC:TCR complex A T cell epitope binding constant determination assay that measures the dissociation constant KD. http://purl.obolibrary.org/obo/OBI_0002098 assay measuring the on rate [kon] of a T cell epitope:MHC:TCR complex http://purl.obolibrary.org/obo/OBI_0002059 assay measuring a binding constant of a T cell epitope:MHC:TCR complex A T cell epitope binding constant determination assay that measures the on rate. http://purl.obolibrary.org/obo/OBI_0002099 assay measuring the off rate [koff] of a T cell epitope:MHC:TCR complex http://purl.obolibrary.org/obo/OBI_0002059 assay measuring a binding constant of a T cell epitope:MHC:TCR complex A T cell epitope binding constant determination assay that measures the off rate. http://purl.obolibrary.org/obo/OBI_0002100 assay measuring the association constant [KA] of a T cell epitope:MHC:TCR complex http://purl.obolibrary.org/obo/OBI_0002059 assay measuring a binding constant of a T cell epitope:MHC:TCR complex A T cell epitope binding constant determination assay that measures the association constant KA. http://purl.obolibrary.org/obo/OBI_0002101 small-angle scattering assay determining the 3D structure of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001721 3D structure determining assay of a 3D B cell epitope:antibody complex A B cell epitope 3D structure determination assay that uses a small-angle X-ray scattering assay. http://purl.obolibrary.org/obo/OBI_0002102 bio-layer interferometry assay measuring the on rate [kon] of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001718 assay measuring the on rate [kon] of a B cell epitope:antibody complex A B cell epitope assay that measures the on rate using a bio-layer interferometry assay. http://purl.obolibrary.org/obo/OBI_0002103 bio-layer interferometry assay measuring the off rate [koff] of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001723 assay measuring the off rate [koff] of a B cell epitope:antibody complex A B cell epitope assay that measures the off rate using a bio-layer interferometry assay. http://purl.obolibrary.org/obo/OBI_0002104 bio-layer interferometry assay measuring binding of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001703 assay measuring qualitiative binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a bio-layer interferometry assay. http://purl.obolibrary.org/obo/OBI_0002105 bio-layer interferometry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001708 assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a bio-layer interferometry assay. http://purl.obolibrary.org/obo/OBI_0002119 microscopy assay http://purl.obolibrary.org/obo/OBI_0000185 imaging assay An imaging assay that utilizes a microscope to magnify features of the visualized material of interest that are not visible to naked eye. http://purl.obolibrary.org/obo/OBI_0002500 amniotic fluid specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from amniotic fluid. http://purl.obolibrary.org/obo/OBI_0002501 bile specimen http://purl.obolibrary.org/obo/OBI_2000009 bodily fluid specimen A specimen that is derived from bile. http://purl.obolibrary.org/obo/OBI_0002502 cerebrospinal fluid specimen http://purl.obolibrary.org/obo/OBI_2000009 bodily fluid specimen A specimen that is derived from cerbrospinal fluid. http://purl.obolibrary.org/obo/OBI_0002505 milk specimen http://purl.obolibrary.org/obo/OBI_2000009 bodily fluid specimen A specimen that is derived from milk. http://purl.obolibrary.org/obo/OBI_0002506 pericardial fluid specimen http://purl.obolibrary.org/obo/OBI_2000009 bodily fluid specimen A specimen that is derived from pericardial fluid. http://purl.obolibrary.org/obo/OBI_0002507 saliva specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from saliva. http://purl.obolibrary.org/obo/OBI_0002508 sputum specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from sputum. http://purl.obolibrary.org/obo/OBI_0002509 sweat specimen http://purl.obolibrary.org/obo/OBI_2000009 bodily fluid specimen A specimen that is derived from sweat. http://purl.obolibrary.org/obo/OBI_0002510 synovial fluid specimen http://purl.obolibrary.org/obo/OBI_2000009 bodily fluid specimen A specimen that is derived from synovial fluid. http://purl.obolibrary.org/obo/OBI_0002512 bone marrow specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from bone marrow. http://purl.obolibrary.org/obo/OBI_0002513 placenta specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from placenta. http://purl.obolibrary.org/obo/OBI_0002514 peritoneal fluid specimen http://purl.obolibrary.org/obo/OBI_2000009 bodily fluid specimen A specimen that is derived from peritoneal fluid. http://purl.obolibrary.org/obo/OBI_0002515 pleural fluid specimen http://purl.obolibrary.org/obo/OBI_2000009 bodily fluid specimen A specimen that is derived from pleural fluid. http://purl.obolibrary.org/obo/OBI_0002516 brain specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from brain. http://purl.obolibrary.org/obo/OBI_0002517 hair specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from hair. http://purl.obolibrary.org/obo/OBI_0002518 prostate gland specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from prostate gland. http://purl.obolibrary.org/obo/OBI_0002519 skeletal muscle tissue specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from skeletal muscle. http://purl.obolibrary.org/obo/OBI_0002520 heart specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from heart. http://purl.obolibrary.org/obo/OBI_0002522 adrenal gland specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from adrenal gland. http://purl.obolibrary.org/obo/OBI_0002524 urinary bladder specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from urinary bladder. http://purl.obolibrary.org/obo/OBI_0002525 tibial artery specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from tibial artery. http://purl.obolibrary.org/obo/OBI_0002527 pancreas specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from pancreas. http://purl.obolibrary.org/obo/OBI_0002528 stomach specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from stomach. http://purl.obolibrary.org/obo/OBI_0002529 pituitary gland specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from pituitary gland. http://purl.obolibrary.org/obo/OBI_0002530 adipose tissue specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from adipose tissue. http://purl.obolibrary.org/obo/OBI_0002532 esophagus mucosa specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from esophagus mucosa. http://purl.obolibrary.org/obo/OBI_0002533 colon specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from colon. http://purl.obolibrary.org/obo/OBI_0002534 lung specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from lung. http://purl.obolibrary.org/obo/OBI_0002537 thyroid gland specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from thyroid gland. http://purl.obolibrary.org/obo/OBI_0002539 tibial nerve specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from tibial nerve. http://purl.obolibrary.org/obo/OBI_0002540 coronary artery specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from coronary artery. http://purl.obolibrary.org/obo/OBI_0002541 spleen specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from spleen. http://purl.obolibrary.org/obo/OBI_0002542 aorta specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from aorta. http://purl.obolibrary.org/obo/OBI_0005246 injection function http://purl.obolibrary.org/obo/BFO_0000034 function The function of a device realized when administering a substance in vivo, applied particularly to the forcible insertion of a liquid or gas by means of a syringe, pump, etc. http://purl.obolibrary.org/obo/OBI_0100010 Epstein Barr virus transformed B cell http://purl.obolibrary.org/obo/OBI_0000047 processed material A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity http://purl.obolibrary.org/obo/OBI_0100014 chimera http://purl.obolibrary.org/obo/OBI_0100026 organism An organism which contains cells or tissues with a different genotype http://purl.obolibrary.org/obo/OBI_0100015 obsolete_anatomical entity http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class An anatomical entity is a material entity that is part of a multicellular organism, and which is large enough so that it forms an identifiable structure in the organism. Specifically, it excludes granular parts of the organism, such as atoms, molecules, cells, which can be removed from the organism without affecting it. It is defined as the union of 'multi-tissue structure', 'body substance' and 'portion of tissue' http://purl.obolibrary.org/obo/OBI_0100017 blood serum specimen http://purl.obolibrary.org/obo/OBI_0000953 processed specimen A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors. http://purl.obolibrary.org/obo/OBI_0100026 organism http://purl.obolibrary.org/obo/BFO_0000040 material entity A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. http://purl.obolibrary.org/obo/OBI_0100035 obsolete_immortal cell http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class a cell derived from a multicellular organism that has the potential to replicate indefinitely http://purl.obolibrary.org/obo/OBI_0100039 obsolete_fragment derived from protein http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class A material entity which is derived from a protein http://purl.obolibrary.org/obo/OBI_0100051 specimen http://purl.obolibrary.org/obo/BFO_0000040 material entity A material entity that has the specimen role. http://purl.obolibrary.org/obo/OBI_0100055 obsolete_cell line cell http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class A material entity that represents generations of a primary culture. http://purl.obolibrary.org/obo/OBI_0100064 screening library http://purl.obolibrary.org/obo/OBI_0000047 processed material a screening library is a collection of materials engineered to identify qualities of a subset of its members during a screening process? http://purl.obolibrary.org/obo/OBI_0100065 synthetic peptide http://purl.obolibrary.org/obo/CHEBI_16670 peptide a synthetic peptide is an material entity which is artificially engineered and results from the synthesis of a chain of amino acids which may also be found in natural protein and be identical in sequence to a protein fragment http://purl.obolibrary.org/obo/OBI_0100066 organ section http://purl.obolibrary.org/obo/OBI_0000047 processed material A processed material which derives from an organ and results from a process of dissection or histological sample preparation a portion(formerly an organ section is portion of an organ removed from the context of the organ) http://purl.obolibrary.org/obo/OBI_0100069 obsolete_polymer http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. http://purl.obolibrary.org/obo/OBI_0200002 logistic-log curve fitting http://purl.obolibrary.org/obo/OBI_0200072 curve fitting data transformation A logistic-log curve fitting is a curve fitting where a curve of the form y=d+((a-d)/(1+(x/c)^b)) is obtained, where a, b, c, and d are determined so to optimize its fit to the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n). http://purl.obolibrary.org/obo/OBI_0200003 logit-log curve fitting http://purl.obolibrary.org/obo/OBI_0200072 curve fitting data transformation A logit-log curve fitting is a curve fitting where first the limits y_0 an y_infty of y when x->0 and x->infinity, respectively, are estimated from the input data points (x_1, y_1), (x_2,y_2), ..., (x_n, y_n). Then a curve with equation log((y-y_0)/(y_infty-y))=a+b log(x) is obtained, where a and b are determined to optimize its fit to the input data points. http://purl.obolibrary.org/obo/OBI_0200004 log-log curve fitting http://purl.obolibrary.org/obo/OBI_0200072 curve fitting data transformation A log-log curve fitting is a curve fitting where first a logarithmic transformation is applied both to the x and the y coordinates of the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n), and then coefficients a and b are determined to optimize the fit of log(y)=a+b*log(x) to these input data points. http://purl.obolibrary.org/obo/OBI_0200005 feature extraction objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image. http://purl.obolibrary.org/obo/OBI_0200006 biexponential transformation http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating A biexponential transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation B(y)-x=0, where B denotes a b transformation. http://purl.obolibrary.org/obo/OBI_0200007 box-cox transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A box-cox transformation is a data transformation according to the methods of Box and Cox as described in the article Box, G. E. P. and Cox, D.R. (1964) An analysis of transformations. Journal of Royal Statistical Society, Series B, vol. 26, pp. 211-246. http://purl.obolibrary.org/obo/OBI_0200008 hyperlog transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A hyperlog transformation ia a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation EH(y)-x=0, where EH denotes an eh transformation. http://purl.obolibrary.org/obo/OBI_0200010 loess scale group transformation one-channel http://purl.obolibrary.org/obo/OBI_0200025 loess scale group transformation A loess scale group transformation one-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation one-channel, to render the M group variances similar. http://purl.obolibrary.org/obo/OBI_0200011 logical transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A logical transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation S(y)-x=0, where S denotes an s transformation. http://purl.obolibrary.org/obo/OBI_0200012 loess scale group transformation two-channel http://purl.obolibrary.org/obo/OBI_0200025 loess scale group transformation A loess scale group transformation two-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation two-channel, to render the M group variances similar. http://purl.obolibrary.org/obo/OBI_0200013 loess global transformation one-channel http://purl.obolibrary.org/obo/OBI_0200023 loess global transformation A loess global transformation one-channel is a loess global transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. http://purl.obolibrary.org/obo/OBI_0200014 split-scale transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation A split-scale transformation is a data transformation which is an application of a function f described as follows to a (one dimensional) real number input. f(x)=a*x+b if x=for x>t; where log denotes a logarithmic transformation and a, b, c, d, r, t are real constants, with a, c, d, r, t positive, chosen so that f is continuous with a continuous derivative at the transition point t. http://purl.obolibrary.org/obo/OBI_0200015 loess global transformation two-channel http://purl.obolibrary.org/obo/OBI_0200023 loess global transformation A loess global transformation two-channel is a loess global transformation in the special case where the input the result of an MA transformation applied to intensities from the two channels of a two-channel assay. http://purl.obolibrary.org/obo/OBI_0200016 sine transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A sine transformation is a data transformation which consists in applying the sine function to a (one dimensional) real number input. The sine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Sine.html. http://purl.obolibrary.org/obo/OBI_0200017 cosine transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A cosine transformation is a data transformation which consists in applying the cosine function to a (one dimensional) real number input. The cosine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Cosine.html. http://purl.obolibrary.org/obo/OBI_0200018 loess group transformation one-channel http://purl.obolibrary.org/obo/OBI_0200024 loess group transformation A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. http://purl.obolibrary.org/obo/OBI_0200019 loess group transformation two-channel http://purl.obolibrary.org/obo/OBI_0200024 loess group transformation A loess group transformation two-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from the two channels of a two-channel assay. http://purl.obolibrary.org/obo/OBI_0200020 homogeneous polynomial transformation http://purl.obolibrary.org/obo/OBI_0200093 polynomial transformation A homogeneous polynomial transformation is a polynomial transformation where all the term of the polynomial have the same degree. http://purl.obolibrary.org/obo/OBI_0200021 linlog transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A linlog transformation is a data transformation, described in PMID 16646782, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (9) of this paper, where values below an appropriately determined threshold (dependent on the row i) are transformed via a polynomial of degree 1, and values above this threshold are transformed via a logarithm. http://purl.obolibrary.org/obo/OBI_0200023 loess global transformation http://purl.obolibrary.org/obo/OBI_0200071 loess transformation A loess global transformation is a loess transformation where only one loess fitting is performed, utilizing one subset of (or possibly all of) the data points in the input so that there is only one resulting loess curve y=f(x) which is used for the transformation. http://purl.obolibrary.org/obo/OBI_0200024 loess group transformation http://purl.obolibrary.org/obo/OBI_0200071 loess transformation A loess group transformation is a loess transformation where the input is partitioned into groups and for each group a loess fitting is performed, utilizing a subset of (or possibly all of) the data points in that group. Thus, a collection of loess curves y=f_i(x) is generated, one per group. Each (x, y) in the input is transformed into (x, y-f_i(x)), where f_i(x) is the curve corresponding to the group to which that data point belongs. http://purl.obolibrary.org/obo/OBI_0200025 loess scale group transformation http://purl.obolibrary.org/obo/OBI_0200185 scaling data transformation A loess scale group transformation is a data transformation consisting in the application of a scale adjustment following a loess group transformation, to render the group variances for the second variable (y) similar. Has objective scaling. http://purl.obolibrary.org/obo/OBI_0200026 total intensity transformation single http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A total intensity transformation single is a data transformation that takes as input an n-dimensional (real) vector and multiplies each component of this vector by a coefficient, where the coefficient is obtained by taking the sum of the input components or of a subset of these, multiplied by a constant of choice. http://purl.obolibrary.org/obo/OBI_0200027 total intensity transformation paired http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A total intensity transformation paired is a data transformation that takes as input two n-dimensional (real) vectors and multiplies each component of the first vector by a coefficient, where the coefficient is obtained by taking the ratio of the sum of the second input components or of a subset of these by the sum of the first input components or of a subset of these (the same subset is used for the two vectors). http://purl.obolibrary.org/obo/OBI_0200028 quantile transformation http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating A quantile transformation is a data transformation that takes as input a collection of data sets, where each can be thought as an n-dimensional (real) vector, and which transforms each data set so that the resulting output data sets have equal quantiles. http://purl.obolibrary.org/obo/OBI_0200031 differential expression analysis objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions. http://purl.obolibrary.org/obo/OBI_0200032 K-fold cross validation method http://purl.obolibrary.org/obo/OBI_0000792 statistical model validation K-fold cross-validation randomly partitions the original sample into K subsamples. Of the K subsamples, a single subsample is retained as the validation data for testing the model, and the remaining K - 1 subsamples are used as training data. The cross-validation process is then repeated K times (the folds), with each of the K subsamples used exactly once as the validation data. The K results from the folds then can be averaged (or otherwise combined) to produce a single estimation. The advantage of this method over repeated random sub-sampling is that all observations are used for both training and validation, and each observation is used for validation exactly once. 10-fold cross-validation is commonly used http://purl.obolibrary.org/obo/OBI_0200033 leave one out cross validation method http://purl.obolibrary.org/obo/OBI_0000792 statistical model validation is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data http://purl.obolibrary.org/obo/OBI_0200035 boostrapping http://purl.obolibrary.org/obo/OBI_0000792 statistical model validation Bootstrapping is a statistical method for estimating the sampling distribution of a statistic by sampling with replacement from the original data, most often with the purpose of deriving robust estimates of standard errors and confidence intervals of a population parameter like a mean, median, proportion, odds ratio, correlation coefficient or regression coefficient http://purl.obolibrary.org/obo/OBI_0200036 Benjamini and Hochberg false discovery rate correction method http://purl.obolibrary.org/obo/OBI_0200163 false discovery rate correction method A data transformation process in which the Benjamini and Hochberg method sequential p-value procedure is applied with the aim of correcting false discovery rate http://purl.obolibrary.org/obo/OBI_0200037 pareto scaling http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A pareto scaling is a data transformation that divides all measurements of a variable by the square root of the standard deviation of that variable. http://purl.obolibrary.org/obo/OBI_0200040 modular decomposition http://purl.obolibrary.org/obo/OBI_0200080 network analysis Molecular decomposition is the partition of a network into distinct subgraphs for the purpose of identifying functional clusters. The network data is run through any of several existing algorithms designed to partition a network into distinct subgraphs for the purpose of isolating groups of functionally linked biological elements such as proteins. http://purl.obolibrary.org/obo/OBI_0200041 k-means clustering http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed). http://purl.obolibrary.org/obo/OBI_0200042 hierarchical clustering http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root). http://purl.obolibrary.org/obo/OBI_0200043 average linkage hierarchical clustering http://purl.obolibrary.org/obo/OBI_0200154 agglomerative hierarchical clustering An average linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the average distance between objects from the first cluster and objects from the second cluster. http://purl.obolibrary.org/obo/OBI_0200044 complete linkage hierarchical clustering http://purl.obolibrary.org/obo/OBI_0200154 agglomerative hierarchical clustering an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the maximum distance between objects from the first cluster and objects from the second cluster. http://purl.obolibrary.org/obo/OBI_0200045 single linkage hierarchical clustering http://purl.obolibrary.org/obo/OBI_0200154 agglomerative hierarchical clustering A single linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the minimum distance between objects from the first cluster and objects from the second cluster. http://purl.obolibrary.org/obo/OBI_0200049 Benjamini and Yekutieli false discovery rate correction method http://purl.obolibrary.org/obo/OBI_0200163 false discovery rate correction method A data transformation in which the Benjamini and Yekutieli method is applied with the aim of correcting false discovery rate http://purl.obolibrary.org/obo/OBI_0200052 probabilistic algorithm http://purl.obolibrary.org/obo/OBI_0200000 data transformation A probabilistic algorithm is one which involves an element of probability or randomness in the transformation of the data. http://purl.obolibrary.org/obo/OBI_0200053 expectation maximization http://purl.obolibrary.org/obo/OBI_0200052 probabilistic algorithm EM is a probabilistic algorithm used to estimate the maximum likelihood of parameters from existing data where the model involves unobserved latent variables. The input to this method is the data model for which the estimation is performed over and the output is an approximated probability function. http://purl.obolibrary.org/obo/OBI_0200054 global modularity calculation http://purl.obolibrary.org/obo/OBI_0200147 network graph quality calculation A network graph quality calculation in which an input data set of subgraph modules and their in-degree and out-degree qualities is used to calculate the average modularity of subgraphs within the network. http://purl.obolibrary.org/obo/OBI_0200055 dye swap merge http://purl.obolibrary.org/obo/OBI_0200057 replicate analysis A dye swap merge is a replicate analysis which takes as input data from paired two-channel microarray assays where the sample labeled with one dye in the first assay is labeled with the other dye in the second assay and vice versa. The output for each reporter is obtained by combining its (raw or possibly pre-processed) M values in the two assays, where the M value in an assay is defined as the difference of the log intensities in the two channels. This can be used as a normalization step, when appropriate assumptions are met. http://purl.obolibrary.org/obo/OBI_0200056 moving average http://purl.obolibrary.org/obo/OBI_0200170 averaging data transformation A moving average is a data transformation in which center calculations, usually mean calculations, are performed on values within a sliding window across the input data set. http://purl.obolibrary.org/obo/OBI_0200057 replicate analysis http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A replicate analysis is a data transformation in which data from replicates are combined, e.g. through descriptive statistics calculations, and the results might be utilized for a variety of purposes, like assessing reproducibility, identifying outliers, normalizing, etc. http://purl.obolibrary.org/obo/OBI_0200058 b cell epitope prediction http://purl.obolibrary.org/obo/OBI_0200187 sequence analysis data transformation A B cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a B Cell Epitope. http://purl.obolibrary.org/obo/OBI_0200059 mhc binding prediction http://purl.obolibrary.org/obo/OBI_0200187 sequence analysis data transformation An MHC binding prediction takes an input of a biomaterial sequence and through an analysis of this sequence, produces as output a prediction of the likelihood that the biomaterial will bind to an MHC molecule. http://purl.obolibrary.org/obo/OBI_0200060 t cell epitope prediction http://purl.obolibrary.org/obo/OBI_0200187 sequence analysis data transformation A T cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a T cell epitope. http://purl.obolibrary.org/obo/OBI_0200061 data imputation http://purl.obolibrary.org/obo/OBI_0200000 data transformation Imputation is a means of filling in missing data values from a predictive distribution of the missing values. The predictive distribution can be created either based on a formal statistical model (i,e, a multivariate normal distribution) or an algorithm. http://purl.obolibrary.org/obo/OBI_0200062 continuum mass spectrum http://purl.obolibrary.org/obo/OBI_0200085 mass spectrometry analysis A continuum mass spectrum is a data transformation that contains the full profile of the detected signals for a given ion. http://purl.obolibrary.org/obo/OBI_0200063 characteristic path length calculation http://purl.obolibrary.org/obo/OBI_0200085 mass spectrometry analysis Quantifying subgraph navigability based on shortest-path length averaged over all pairs of subgraph vertices http://purl.obolibrary.org/obo/OBI_0200066 Holm-Bonferroni family-wise error rate correction method http://purl.obolibrary.org/obo/OBI_0200073 family wise error rate correction method a data transformation that performs more than one hypothesis test simultaneously, a closed-test procedure, that controls the familywise error rate for all the k hypotheses at level α in the strong sense. Objective: multiple testing correction http://purl.obolibrary.org/obo/OBI_0200070 edge weighting http://purl.obolibrary.org/obo/OBI_0200080 network analysis Edge weighting is the substitution or transformation of edge length using numerical data. Data input include a symmetric adjacency matrix for a network and a second data set, for example a list of interactor pairs and a confidence score associated with the experimental detection of each pair's interaction. Each element in the adjacency matrix is transformed or replaced with the corresponding number in the second data set. Output data are a modified adjacency matrix reflecting the transformed state of the network. http://purl.obolibrary.org/obo/OBI_0200071 loess transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A loess transformation is a data transformation that takes as input a collection of real number pairs (x, y) and, after performing (one or more) loess fittings, utilizes the resulting curves to transform each (x, y) in the input into (x, y-f(x)) where f(x) is one of the fitted curves. http://purl.obolibrary.org/obo/OBI_0200072 curve fitting data transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation A curve fitting is a data transformation that has objective curve fitting and that consists of finding a curve which matches a series of data points and possibly other constraints. http://purl.obolibrary.org/obo/OBI_0200074 submatrix extraction http://purl.obolibrary.org/obo/OBI_0200050 dimensionality reduction A submatrix extraction is a projection whose input is a matrix and whose output is a matrix obtained by selecting certain rows and columns from the input. (Note that, if one represents the input matrix as a vector obtained by concatenating its rows, then extracting a submatrix is equivalent to projecting this vector into that composed by the entries belonging to the rows and columns of interest from the input matrix.) http://purl.obolibrary.org/obo/OBI_0200075 row submatrix extraction http://purl.obolibrary.org/obo/OBI_0200074 submatrix extraction A row submatrix extraction is a submatrix extraction where all the columns of the input matrix are retained and selection only occurs on the rows. http://purl.obolibrary.org/obo/OBI_0200076 column submatrix extraction http://purl.obolibrary.org/obo/OBI_0200074 submatrix extraction A column submatrix extraction is a submatrix extraction where all the rows of the input matrix are retained and selection only occurs on the columns. http://purl.obolibrary.org/obo/OBI_0200077 gating http://purl.obolibrary.org/obo/OBI_0200182 data vector reduction data transformation Gating is a property-based vector selection with the objective of partitioning a data vector set into vector subsets based on dimension values of individual vectors (events), in which vectors represent individual physical particles (often cells) of a sample and dimension values represent light intensity qualities as measured by flow cytometry. http://purl.obolibrary.org/obo/OBI_0200078 descriptive statistical calculation objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability. http://purl.obolibrary.org/obo/OBI_0200079 arithmetic mean calculation http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating An arithmetic mean calculation is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment. http://purl.obolibrary.org/obo/OBI_0200081 sequence analysis objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A sequence analysis objective is a data transformation objective which aims to analyse some ordered biological data for sequential patterns. http://purl.obolibrary.org/obo/OBI_0200085 mass spectrometry analysis http://purl.obolibrary.org/obo/OBI_0200000 data transformation A data transformation which has the objective of spectrum analysis. http://purl.obolibrary.org/obo/OBI_0200086 spread calculation data transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation A spread calculation is a data transformation that has objective spread calculation. http://purl.obolibrary.org/obo/OBI_0200088 Kaplan Meier http://purl.obolibrary.org/obo/OBI_0200194 survival analysis data transformation a nonparametric (actuarial) data transformation technique for estimating time-related events. It is a univariate analysis that estimates the probability of the proportion of subjects in remission at a particular time, starting from the initiation of active date (time zero), and takes into account those lost to follow-up or not yet in remission at end of study (censored) http://purl.obolibrary.org/obo/OBI_0200093 polynomial transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation A polynomial transformation is a data transformation that is obtained through a polynomial, where a polynomial is a mathematical expression involving a sum of powers in one or more variables multiplied by coefficients (e.g. see http://mathworld.wolfram.com/Polynomial.html). The number of variables and the degree are properties of a polynomial. The degree of a polynomial is the highest power of its terms, where the terms of a polynomial are the individual summands with the coefficients omitted. http://purl.obolibrary.org/obo/OBI_0200094 logarithmic transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A logarithmic transformation is a data transformation consisting in the application of the logarithm function with a given base a (where a>0 and a is not equal to 1) to a (one dimensional) positive real number input. The logarithm function with base a can be defined as the inverse of the exponential function with the same base. See e.g. http://en.wikipedia.org/wiki/Logarithm. http://purl.obolibrary.org/obo/OBI_0200095 exponential transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation An exponential transformation is a data transformation consisting in the application of the exponential function with a given base a (where a>0 and a is typically not equal to 1) to a (one dimensional) real number input. For alternative definitions and properties of this function see, e.g., http://en.wikipedia.org/wiki/Exponential_function and http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function. http://purl.obolibrary.org/obo/OBI_0200097 non-negative matrix factorization http://purl.obolibrary.org/obo/OBI_0200000 data transformation Non negative matrix factorization is a data transformation in which factorises a matrix and which forces that all elements must be equal to or greater than zero. http://purl.obolibrary.org/obo/OBI_0200099 discriminant function analysis http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating Discriminant function analysis is a form of discriminant analysis used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome. http://purl.obolibrary.org/obo/OBI_0200101 linear discriminant functional analysis http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating Linear discriminant functional analysis (LDFA) is a multivariate technique used in special applications where there are several intact groups (random assignment may be impossible) and they have been measured on several independent measures. Thus, you will want to describe how these groups differ on the basis of these measures. In this case, classification and prediction is the main objective. http://purl.obolibrary.org/obo/OBI_0200102 regression analysis method http://purl.obolibrary.org/obo/OBI_0200000 data transformation Regression analysis is a descriptive statistics technique that examines the relation of a dependent variable (response variable) to specified independent variables (explanatory variables). Regression analysis can be used as a descriptive method of data analysis (such as curve fitting) without relying on any assumptions about underlying processes generating the data. http://purl.obolibrary.org/obo/OBI_0200103 multiple linear regression analysis http://purl.obolibrary.org/obo/OBI_0200102 regression analysis method multiple linear regression is a regression method that models the relationship between a dependent variable Y, independent variables Xi, i = 1, ..., p, and a random term epsilon. The model can be written as Y = \beta_0 + \beta_1 X_1 + \beta_2 X_2 + \cdots +\beta_p X_p + \varepsilon where \beta_0 = 0 is the intercept ("constant" term), the \beta_i s are the respective parameters of independent variables, and p is the number of parameters to be estimated in the linear regression. http://purl.obolibrary.org/obo/OBI_0200104 principal component regression http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating The Principal Component Regression method is a regression analysis method that combines the Principal Component Analysis (PCA)spectral decomposition with an Inverse Least Squares (ILS) regression method to create a quantitative model for complex samples. Unlike quantitation methods based directly on Beer's Law which attempt to calculate the absorbtivity coefficients for the constituents of interest from a direct regression of the constituent concentrations onto the spectroscopic responses, the PCR method regresses the concentrations on the PCA scores. http://purl.obolibrary.org/obo/OBI_0200106 discriminant analysis http://purl.obolibrary.org/obo/OBI_0200000 data transformation Discriminant function analysis is used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome. http://purl.obolibrary.org/obo/OBI_0200108 eh transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation An eh transformation is a data transformation obtained by applying the function EH described in what follows to a (one dimensional) real number input. EH(x)=exp(x*d/r)+b*(d/r)*x-1, if x>=0, and EH(x)=-exp(-x*d/r)+b*(d/r)*x+1, otherwise. Here exp denotes an exponential transformation and b, d, r are positive real constants with the objective of normalization. http://purl.obolibrary.org/obo/OBI_0200109 b transformation http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating A b transformation is a data transformation obtained by applying the function B described in what follows to a (one dimensional) real number input. B(x)= a*exp(b*x)-c*exp(-d*x)+f, where exp denotes an exponential transformation and a, b, c, d, f are real constants with a, b, c, d positive with the objective of normalization. http://purl.obolibrary.org/obo/OBI_0200110 s transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation An s transformation is a data transformation obtained by applying the function S described in what follows to a (one dimensional) real number input. S(x)=T*exp(w-m)*(exp(x-w)-(p^2)*exp((w-x)/p)+p^2-1) if x>=w, S(x)=-S(w-x) otherwise; where exp denotes an exponential_transformations, 'p^' denotes the exponential transformation with base p; T, w, m, p are real constants with T, m, and p positive and w non-negative, and where w and p are related by w=2p*ln(p)(p+1) with the objective of normalization. http://purl.obolibrary.org/obo/OBI_0200113 similarity calculation http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating A similarity calculation is a data transformation that attaches to each pair of objects in the input a number that is meant to reflect how 'close' or 'similar' those objects are. http://purl.obolibrary.org/obo/OBI_0200114 euclidean distance calculation http://purl.obolibrary.org/obo/OBI_0200113 similarity calculation An euclidean distance calculation is a similarity calculation that attaches to each pair of real number vectors of the same dimension n the square root of the sum of the square differences between corresponding components. The smaller this number, the more similar the two vectors are considered. http://purl.obolibrary.org/obo/OBI_0200115 pearson correlation coefficient calculation http://purl.obolibrary.org/obo/OBI_0200113 similarity calculation A pearson correlation coefficient calculation is a similarity calculation which attaches to each pair of random variables X and Y the ratio of their covariance by the product of their standard deviations. Given a series of n measurements of X and Y written as x_i and y_i where i = 1, 2, ..., n, then their Pearson correlation coefficient refers to the "sample correlation coefficient" and is written as the sum over i of the ratios (x_i-xbar)*(y_i-ybar)/((n-1)*s_x*s_y) where xbar and ybar are the sample means of X and Y , s_x and s_y are the sample standard deviations of X and Y. The closer the pearson correlation coefficient is to 1, the more similar the inputs are considered. http://purl.obolibrary.org/obo/OBI_0200116 loess fitting http://purl.obolibrary.org/obo/OBI_0200072 curve fitting data transformation A loess fitting is a curve fitting obtained by localized regression. The latter refers to fitting a polynomial (straight line, quadratic, cubic, etc) to data values within a window covering a fraction of the total number of observations. As the window slides along the axis, a new polynomial is fit to the observations falling within the window. This continues until all points are fit with a local polynomial. The results are then smoothed together to form a curve. The smoothness of loess fits is controlled by a smoothing parameter (often denoted as alpha, usually between 1/4 and 1) and the degree of the polynomial that is fitted by the method (usually denoted by lambda). http://purl.obolibrary.org/obo/OBI_0200117 mode calculation http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating A mode calculation is a descriptive statistics calculation in which the mode is calculated which is the most common value in a data set. It is most often used as a measure of center for discrete data. http://purl.obolibrary.org/obo/OBI_0200118 quantile calculation http://purl.obolibrary.org/obo/OBI_0200184 descriptive statistical calculation data transformation A quantile calculation is a descriptive statistics calculation in which the kth quantile is the data value for which an approximate k fraction of the data is less than or equal to that value. See http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html for details. http://purl.obolibrary.org/obo/OBI_0200119 median calculation http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating A median calculation is a descriptive statistics calculation in which the midpoint of the data set (the 0.5 quantile) is calculated. First, the observations are sorted in increasing order. For an odd number of observations, the median is the middle value of the sorted data. For an even number of observations, the median is the average of the two middle values. http://purl.obolibrary.org/obo/OBI_0200120 variance calculation http://purl.obolibrary.org/obo/OBI_0200184 descriptive statistical calculation data transformation A variance calculation is a descriptive statistics calculation in which the variance is defined as the average squared distance of each observation in the data set to the mean of the data set. It is also known as the second central moment. http://purl.obolibrary.org/obo/OBI_0200121 standard deviation calculation http://purl.obolibrary.org/obo/OBI_0200184 descriptive statistical calculation data transformation A standard deviation calculation is a descriptive statistics calculation defined as the square root of the variance. Also thought of as the average distance of each value to the mean. http://purl.obolibrary.org/obo/OBI_0200122 interquartile-range calculation http://purl.obolibrary.org/obo/OBI_0200184 descriptive statistical calculation data transformation The interquartile range is a descriptive statistics calculation defined as the difference between the 0.75 quantile and the 0.25 quantile for a set of data. http://purl.obolibrary.org/obo/OBI_0200123 skewness calculation http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating A skewness calculation is a descriptive statistics calculation defined as a parameter that describes how much a distribution (or a data set) varies from a bell-shaped curve. See http://www.riskglossary.com/link/skewness.htm for details. It is also known as the third central moment http://purl.obolibrary.org/obo/OBI_0200124 kurtosis calculation http://purl.obolibrary.org/obo/OBI_0200184 descriptive statistical calculation data transformation A kurtosis calculation is a descriptive statistics calculation defined as a parameter that measures how large or small the tails of a distribution are relative to the mean. For details, see http://davidmlane.com/hyperstat/A53638.html http://purl.obolibrary.org/obo/OBI_0200126 network graph construction http://purl.obolibrary.org/obo/OBI_0200080 network analysis A network analysis in which an input data set describing objects and relationships between objects is transformed into an output representation of these objects as nodes and the relationships as edges of a network graph. http://purl.obolibrary.org/obo/OBI_0200127 weighted network graph construction http://purl.obolibrary.org/obo/OBI_0200126 network graph construction A network graph construction in which an input data set describing objects and quantitative relationships between objects is transformed into and output representation of these objects as nodes and the quantitative relationships as weighted edges of a network graph. http://purl.obolibrary.org/obo/OBI_0200128 directed network graph construction http://purl.obolibrary.org/obo/OBI_0200126 network graph construction A network graph construction in which an input data set describing objects and directional relationships between objects is transformed into and output representation of these objects as nodes and the directional relationships as directed edges of a network graph. http://purl.obolibrary.org/obo/OBI_0200129 node quality calculation http://purl.obolibrary.org/obo/OBI_0200080 network analysis A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the node objects in the network. http://purl.obolibrary.org/obo/OBI_0200130 node degree calculation http://purl.obolibrary.org/obo/OBI_0200129 node quality calculation A node quality calculation in which an input data set describing object nodes and relationship edges between object nodes is used to enumerate the number of unique relationships of an individual object node. http://purl.obolibrary.org/obo/OBI_0200131 quantitative node degree calculation http://purl.obolibrary.org/obo/OBI_0200129 node quality calculation A node quality calculation in which an input data set describing object nodes and quantitative relationship edges between object nodes is used to sum all of the quantitative relationships of an individual object node. http://purl.obolibrary.org/obo/OBI_0200132 node in-degree calculation http://purl.obolibrary.org/obo/OBI_0200129 node quality calculation A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing into an individual object node. http://purl.obolibrary.org/obo/OBI_0200133 node out-degree calculation http://purl.obolibrary.org/obo/OBI_0200129 node quality calculation A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing out of an individual object node. http://purl.obolibrary.org/obo/OBI_0200134 node shortest path identification http://purl.obolibrary.org/obo/OBI_0200129 node quality calculation A node quality calculation in which a path describing the shortest path needed to transverse through connected nodes and edges to arrive at a specific target node in the network. http://purl.obolibrary.org/obo/OBI_0200135 edge quality calculation http://purl.obolibrary.org/obo/OBI_0200080 network analysis A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the edge relationships in the network. http://purl.obolibrary.org/obo/OBI_0200136 edge betweenness calculation http://purl.obolibrary.org/obo/OBI_0200135 edge quality calculation An edge quality calculation in which the input is a data sets of shortest paths between all pairs of node in the network and the output is the sum of all shortest paths that traverse the specific edge. http://purl.obolibrary.org/obo/OBI_0200137 network subgraph quality calculation http://purl.obolibrary.org/obo/OBI_0200080 network analysis A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of a subgraph partition of the network. http://purl.obolibrary.org/obo/OBI_0200138 subgraph degree calculation http://purl.obolibrary.org/obo/OBI_0200137 network subgraph quality calculation A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships of an individual subgraph. http://purl.obolibrary.org/obo/OBI_0200139 quantitative subgraph degree calculation http://purl.obolibrary.org/obo/OBI_0200137 network subgraph quality calculation A network subgraph quality calculation in which an input data set describing subgraphs and quantitative relationship edges between subgraphs and other network objects is used to sum the quantitative relationships of an individual subgraph. http://purl.obolibrary.org/obo/OBI_0200140 mathematical feature http://purl.obolibrary.org/obo/OBI_0200000 data transformation feature is a (parent_class) that describes a characteristic, trait or quality of a data transformation http://purl.obolibrary.org/obo/OBI_0200143 subgraph in-degree calculation http://purl.obolibrary.org/obo/OBI_0200137 network subgraph quality calculation A network subgraph quality calculation in which an input data set describing subgraphs and directional relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing into an individual subgraph. http://purl.obolibrary.org/obo/OBI_0200144 subgraph out-degree calculation http://purl.obolibrary.org/obo/OBI_0200137 network subgraph quality calculation A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing out of an individual subgraph. http://purl.obolibrary.org/obo/OBI_0200145 intra subgraph connectivity calculation http://purl.obolibrary.org/obo/OBI_0200137 network subgraph quality calculation A network subgraph quality calculation in which an input data set describing internal nodes, edges and node degrees is used to determine the average node degree within the subgraph. http://purl.obolibrary.org/obo/OBI_0200146 subgraph modularity calculation http://purl.obolibrary.org/obo/OBI_0200137 network subgraph quality calculation A network subgraph quality calculation in which an input data set of subgraph in-degree and out-degree qualities is used to calculate the ratio of indegree to outdegree as a measure of modularity. http://purl.obolibrary.org/obo/OBI_0200147 network graph quality calculation http://purl.obolibrary.org/obo/OBI_0200080 network analysis A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of the network as a whole. http://purl.obolibrary.org/obo/OBI_0200150 MA transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation An MA transformation is a data transformation which takes as input a collection of data points (g_1, r_1), (g_2, r_2), ..., (g_n, r_n) with the r_i and g_i positive real numbers, and whose output is the collection of data points (A_1, M_1), (A_2, M_2), ..., (A_n, M_n) where, for each i, A_i=(log(g_i)+log(r_i))/2 and M_i=log(r_i)-log(g_i). Here log denotes a logarithmic transformation. http://purl.obolibrary.org/obo/OBI_0200151 exponential base http://purl.obolibrary.org/obo/OBI_0200140 mathematical feature The exponential base is a feature of an exponential function which is defined in http://en.wikipedia.org/wiki/Exponential_function. Its value can be any positive real number (typically different from 1). http://purl.obolibrary.org/obo/OBI_0200152 polynomial degree http://purl.obolibrary.org/obo/OBI_0200140 mathematical feature The polynomial degree is a feature of a polynomial function defined as the highest power of the polynomial's terms, where the terms of a polynomial are the individual summands with the coefficients omitted. http://purl.obolibrary.org/obo/OBI_0200153 number of variables http://purl.obolibrary.org/obo/OBI_0200140 mathematical feature The number of variables is a feature of any function (including polynomial functions) with domain contained in an n-dimensional vector space and is defined as n, the dimension of such space. http://purl.obolibrary.org/obo/OBI_0200156 data partitioning http://purl.obolibrary.org/obo/OBI_0200000 data transformation Data partitioning is a data transformation with the objective of partitioning or separating input data into output subsets. http://purl.obolibrary.org/obo/OBI_0200157 data vector reduction objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective Data vector reduction is a data transformation objective in which k m-dimensional input vectors are reduced to j m-dimensional output vectors, where j is smaller than k. http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification An objective specification to transformation input data into output data http://purl.obolibrary.org/obo/OBI_0200167 data normalization objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A normalization objective is a data transformation objective where the aim is to remove systematic sources of variation to put the data on equal footing in order to create a common base for comparisons. http://purl.obolibrary.org/obo/OBI_0200168 correction objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation A normalization data transformation is a data transformation that has objective normalization. http://purl.obolibrary.org/obo/OBI_0200170 averaging data transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation An averaging data transformation is a data transformation that has objective averaging. http://purl.obolibrary.org/obo/OBI_0200171 partitioning data transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation A partitioning data transformation is a data transformation that has objective partitioning. http://purl.obolibrary.org/obo/OBI_0200172 partitioning objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set. http://purl.obolibrary.org/obo/OBI_0200173 background correction objective http://purl.obolibrary.org/obo/OBI_0200168 correction objective A background correction objective is a data transformation objective where the aim is to remove irrelevant contributions from the measured signal, e.g. those due to instrument noise or sample preparation. http://purl.obolibrary.org/obo/OBI_0200174 curve fitting objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A curve fitting objective is a data transformation objective in which the aim is to find a curve which matches a series of data points and possibly other constraints. http://purl.obolibrary.org/obo/OBI_0200176 Fisher's exact test http://purl.obolibrary.org/obo/OBI_0000673 statistical hypothesis test Fisher's exact test is a data transformation used to determine if there are nonrandom associations between two Fisher's exact test is a statistical significance test used in the analysis of contingency tables where sample sizes are small where the significance of the deviation from a null hypothesis can be calculated exactly, rather than relying on an approximation that becomes exact in the limit as the sample size grows to infinity, as with many statistical tests. http://purl.obolibrary.org/obo/OBI_0200177 center calculation objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set. http://purl.obolibrary.org/obo/OBI_0200180 spread calculation objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective is a data transformation objective whereby the aim is to the calculate the spread of a dataset, spread is a descriptive statistic which describes the variability of values in a data set http://purl.obolibrary.org/obo/OBI_0200181 center calculation data transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation A center calculation data transformation is a data transformation that has objective of center calculation. http://purl.obolibrary.org/obo/OBI_0200182 data vector reduction data transformation http://purl.obolibrary.org/obo/OBI_0000707 decision tree building data transformation A data vector reduction is a data transformation that has objective data vector reduction and that consists of reducing the input vectors k to a smaller number of output vectors j, where jcells; output=>cell_lysate http://purl.obolibrary.org/obo/OBI_0600028 artificially induced reverse transcription http://purl.obolibrary.org/obo/OBI_0000094 material processing a protocol with the objective to transcribe single-stranded RNA into complementary DNA (cDNA) http://purl.obolibrary.org/obo/OBI_0600029 isolation of cell culture supernatant http://purl.obolibrary.org/obo/OBI_0600014 material component separation a protocol which results in the separation of supernatant material from a cell culture http://purl.obolibrary.org/obo/OBI_0600030 experimental disease induction http://purl.obolibrary.org/obo/OBI_0000094 material processing a protocol application to induce a specific disease in an organism http://purl.obolibrary.org/obo/OBI_0600032 artificially induced DNA repair http://purl.obolibrary.org/obo/OBI_0000094 material processing a protocol application to repair damaged DNA molecules http://purl.obolibrary.org/obo/OBI_0600033 cell permeabilization http://purl.obolibrary.org/obo/OBI_0000094 material processing A protocol application to permeabilize cell membranes, allowing molecules to more easily pass through the membrane than was possible prior to the protocol application http://purl.obolibrary.org/obo/OBI_0600034 precipitation http://purl.obolibrary.org/obo/OBI_0600014 material component separation a protocol application to cause a material to precipitate (becoming a solid) out of solution. Input is a solution, output is a solution plus a solid component (the precipitate) http://purl.obolibrary.org/obo/OBI_0600036 establishing cell culture http://purl.obolibrary.org/obo/OBI_0000094 material processing a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line). http://purl.obolibrary.org/obo/OBI_0600039 artificially induced methylation http://purl.obolibrary.org/obo/OBI_0000094 material processing A planned process of adding methyl groups to polymers http://purl.obolibrary.org/obo/OBI_0600041 concentrate http://purl.obolibrary.org/obo/OBI_0600014 material component separation a protocol application to create an output material with an increased density of a material of interest that is part of the input material by separating other parts of the input material http://purl.obolibrary.org/obo/OBI_0600042 recombinant plasmid cloning http://purl.obolibrary.org/obo/OBI_0600064 recombinant vector cloning the insertion of a particular DNA fragment into a plasmid in order to make copies of a biomaterial http://purl.obolibrary.org/obo/OBI_0600044 lavage http://purl.obolibrary.org/obo/OBI_0600014 material component separation A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid http://purl.obolibrary.org/obo/OBI_0600045 3D structure determination assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that determines the 3-dimensional configuration of an input material. http://purl.obolibrary.org/obo/OBI_0600046 preparative chromatography http://purl.obolibrary.org/obo/OBI_0600014 material component separation the use of a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials of differing affinity http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay the uses chemical or biochemical means to infer the sequence of a biomaterial http://purl.obolibrary.org/obo/OBI_0600048 vector mediated amplification http://purl.obolibrary.org/obo/OBI_0600064 recombinant vector cloning The process of creating a copy of some biological entity in cell culture http://purl.obolibrary.org/obo/OBI_0600049 DNA polymerase amplification http://purl.obolibrary.org/obo/OBI_0600058 enzymatic amplification DNA polymerase amplification is an enzymatic amplification which uses DNA polymerase enzyme to make copies of a DNA contained in biomaterial used as input http://purl.obolibrary.org/obo/OBI_0600050 specific enzymatic cleavage http://purl.obolibrary.org/obo/OBI_0000231 enzymatic cleavage an enzymatic cleavage that uses an enzyme with a strong affinity for specific cleavage sites in the input material http://purl.obolibrary.org/obo/OBI_0600051 gradient separation http://purl.obolibrary.org/obo/OBI_0600014 material component separation a protocol application that uses different concentrations of materials in a defined order to create a gradient to facilitate the separation of an input material into its components with specific qualities http://purl.obolibrary.org/obo/OBI_0600052 dialysis http://purl.obolibrary.org/obo/OBI_0600014 material component separation a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition http://purl.obolibrary.org/obo/OBI_0600053 electrophoresis http://purl.obolibrary.org/obo/OBI_0600014 material component separation a protocol application that uses an electrical potential to move material through a defined matrix in order to separate it by its resistance to movement and its charge http://purl.obolibrary.org/obo/OBI_0600054 selection by survival http://purl.obolibrary.org/obo/OBI_0000094 material processing the use of environmental conditions to select for the organism or cells that have a certain trait http://purl.obolibrary.org/obo/OBI_0600056 protease cleavage http://purl.obolibrary.org/obo/OBI_0000231 enzymatic cleavage protease cleavage is an enzymatic cleavage which relies on enzyme with protease activity to act on proteins and produce polypeptides (protein fragments). http://purl.obolibrary.org/obo/OBI_0600057 enzymatic DNA replication http://purl.obolibrary.org/obo/OBI_0600058 enzymatic amplification the use of enzymes to duplicate DNA molecule any process used to make additional copies of a biomaterial http://purl.obolibrary.org/obo/OBI_0600058 enzymatic amplification http://purl.obolibrary.org/obo/OBI_0000094 material processing the use of enzymes to increase the number of molecules of a biomaterial http://purl.obolibrary.org/obo/OBI_0600059 DNA transduction http://purl.obolibrary.org/obo/OBI_0600043 genetic transformation a genetic transformation which relies on the use of lysogenic infection to transfer DNA sequences into an organism http://purl.obolibrary.org/obo/OBI_0600060 DNA transfection http://purl.obolibrary.org/obo/OBI_0001152 transfection a transfection which relies on the use of physical, electrical and chemical phenomena to introduce DNA into a cell http://purl.obolibrary.org/obo/OBI_0600063 vector mediated expression http://purl.obolibrary.org/obo/OBI_0600064 recombinant vector cloning vector mediated expression sis the generation of copies of biomaterial by in a cell_culture modified for this purpose by insertion of an expression vector http://purl.obolibrary.org/obo/OBI_0600065 obsolete_defined processes http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class Place holder class, see editor note http://purl.obolibrary.org/obo/OBI_0600067 specific labeling http://purl.obolibrary.org/obo/OBI_0600038 addition of molecular label a labeling in which the labeling reagent used has a specificity to bind only certain components of the input material http://purl.obolibrary.org/obo/OBI_0666666 RNA extraction http://purl.obolibrary.org/obo/OBI_0666667 nucleic acid extraction A RNA extraction is a nucleic acid extraction where the desired output material is RNA http://purl.obolibrary.org/obo/OBI_0666667 nucleic acid extraction http://purl.obolibrary.org/obo/OBI_0302884 extraction a material separation to recover the nucleic acid fraction of an input material http://purl.obolibrary.org/obo/OBI_1000023 cell culture supernatant http://purl.obolibrary.org/obo/OBI_0000047 processed material Supernatant of a cell culture is a material entity which contains media, supplements, and secreted products of the cells and becomes the environment of cultivated cell. http://purl.obolibrary.org/obo/OBI_1000024 cell pellet http://purl.obolibrary.org/obo/OBI_0000047 processed material A material entity which results from the aggregation of cells produced by the application of centrifugal force to a liquid containing cells in suspension http://purl.obolibrary.org/obo/OBI_1000042 peptide construct http://purl.obolibrary.org/obo/OBI_0000047 processed material a material entity synthesized to contain a number of peptides conjugated together in a non-linear fashion http://purl.obolibrary.org/obo/OBI_1000048 transgenic organism http://purl.obolibrary.org/obo/OBI_0302859 genetically modified organism a transgenic organism is material entity which derives from an organism which has been modified to express a gene not normally part of it http://purl.obolibrary.org/obo/OBI_1110001 epitope http://purl.obolibrary.org/obo/BFO_0000040 material entity a material entity bearing the epitope role http://purl.obolibrary.org/obo/OBI_1110002 obsolete_occurrence of disease http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class An occurrence of disease is a process involving pathologic changes within an organism http://purl.obolibrary.org/obo/OBI_1110003 host exposure to infectious agent http://purl.obolibrary.org/obo/GO_0008150 biological_process a process in which an infectious agent comes into physical contact with a host organism. http://purl.obolibrary.org/obo/OBI_1110007 administration in vivo with infectious agent http://purl.obolibrary.org/obo/OBI_0600007 administering substance in vivo is an administration of an infectious agent to a host organism http://purl.obolibrary.org/obo/OBI_1110008 occurrence of infectious disease http://purl.obolibrary.org/obo/OGMS_0000063 disease course Is an occurrence of a disease caused by an infection http://purl.obolibrary.org/obo/OBI_1110011 allergic reaction http://purl.obolibrary.org/obo/OBI_1110122 pathologic process an allergic reaction is an pathologic immune response by an organism to a non-self entity that is normally harmless(the allergen) http://purl.obolibrary.org/obo/OBI_1110012 occurrence of allergy http://purl.obolibrary.org/obo/OGMS_0000063 disease course The process of an allergic disease occurring in an organism. http://purl.obolibrary.org/obo/OBI_1110013 ELISPOT assay measuring epitope specific interleukin-2 production by T cells http://purl.obolibrary.org/obo/OBI_0001445 biological activity assay measuring epitope specific interleukin-2 production by T cells An assay of epitope specific interleukin-2 production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_1110014 epitope binding by adaptive immune receptor http://purl.obolibrary.org/obo/GO_0008150 biological_process is the process in which an adaptive immune receptor binds to a material entity (realizing its disposition). The binding affinity is significant enough to trigger an immune response. Specifically, transient non-specific binding of adaptive immune receptors occurring during immune surveillance is not considered significant binding. http://purl.obolibrary.org/obo/OBI_1110015 Immunization in vivo http://purl.obolibrary.org/obo/OBI_1110094 immunization Process of administering an object playing the role of immunogen to a living organism http://purl.obolibrary.org/obo/OBI_1110016 adaptive immune effector function http://purl.obolibrary.org/obo/BFO_0000034 function A function realized as an immune response, which inheres in a T cell, B cell or antibody which derives from or is produced by a cell with prior antigen experience. http://purl.obolibrary.org/obo/OBI_1110017 living with infected household contact http://purl.obolibrary.org/obo/OBI_1110111 environmental proximity to infectious agent a process in which a a human being lives in the same household as another human being that is known to be infected with an infectious agent http://purl.obolibrary.org/obo/OBI_1110018 living in endemic area http://purl.obolibrary.org/obo/OBI_1110111 environmental proximity to infectious agent a process in which a potential host organism lives in a geographic area in which an infectious agent is present to such a degree of frequency that contact is likely http://purl.obolibrary.org/obo/OBI_1110019 pathogen release in laboratory accident http://purl.obolibrary.org/obo/OBI_1110111 environmental proximity to infectious agent a process in which a an infectious agent maintained in a laboratory setting is not contained as planned, leading to potential exposure of human beings to the agent http://purl.obolibrary.org/obo/OBI_1110020 Immunization in vitro http://purl.obolibrary.org/obo/OBI_0000094 material processing Process of administering an object playing the role of immunogen to a cell culture http://purl.obolibrary.org/obo/OBI_1110021 infection process http://purl.obolibrary.org/obo/OBI_1110122 pathologic process the detrimental process in which an infectious agent colonizes or replicates in a host environment http://purl.obolibrary.org/obo/OBI_1110022 adaptive immune receptor http://purl.obolibrary.org/obo/GO_0032991 protein-containing complex is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes. http://purl.obolibrary.org/obo/OBI_1110023 immunogen http://purl.obolibrary.org/obo/BFO_0000040 material entity a material entity bearing the immunogen role http://purl.obolibrary.org/obo/OBI_1110024 environmental exposure to infectious agent http://purl.obolibrary.org/obo/GO_0008150 biological_process Is a process in which an infectious agent is in direct contact with a potential host organism in its habitat. This is preceded by proximity to the infectious agent http://purl.obolibrary.org/obo/OBI_1110026 host of immune response http://purl.obolibrary.org/obo/OBI_0100026 organism An organism in which an immune response process occurs. http://purl.obolibrary.org/obo/OBI_1110028 293-T cell line http://purl.obolibrary.org/obo/CLO_0009828 immortal cell line A cell line derived from human embryonic kidney cells. This cell line contains the SV40 Large T-antigen, allowing episomal replication of transfected plasmids containing the SV40 origin of replication. http://purl.obolibrary.org/obo/OBI_1110029 C1R cell line http://purl.obolibrary.org/obo/CLO_0009828 immortal cell line A cell line derived from human B cells. This cell line was created by EBV transformation (B-lymphoblastoid cell-line (BLCL)). http://purl.obolibrary.org/obo/OBI_1110030 experimental infection of cell culture http://purl.obolibrary.org/obo/OBI_0600000 adding substance to cell culture is the administration of an infectious agent to a cell culture with the objective to have the agent colonize and replicate in culture http://purl.obolibrary.org/obo/OBI_1110031 EL-4 cell line http://purl.obolibrary.org/obo/CLO_0009828 immortal cell line A cell line derived from mouse (C57BL/6N) lymphoma cells. http://purl.obolibrary.org/obo/OBI_1110032 HeLa cell line http://purl.obolibrary.org/obo/CLO_0009828 immortal cell line A cell line derived from human cervical cancer cells. http://purl.obolibrary.org/obo/OBI_1110033 JAWS II cell line http://purl.obolibrary.org/obo/CLO_0009828 immortal cell line A cell line derived from mouse dendritic cells. http://purl.obolibrary.org/obo/OBI_1110034 antigen http://purl.obolibrary.org/obo/BFO_0000040 material entity is a material entity that has the antigen role http://purl.obolibrary.org/obo/OBI_1110035 Jurkat cell line http://purl.obolibrary.org/obo/CLO_0009828 immortal cell line A cell line derived from human T cells. http://purl.obolibrary.org/obo/OBI_1110036 JY cell line http://purl.obolibrary.org/obo/CLO_0009828 immortal cell line The JY cell line is an Epstein-Barr virus (EBV)-immortalised b cell lymphoblastoid line.(wikipedia) http://purl.obolibrary.org/obo/OBI_1110037 assay measuring binding of a T cell epitope:MHC:TCR complex http://purl.obolibrary.org/obo/OBI_1110128 immune epitope assay An immune epitope assay that detects T cell epitope recognition. http://purl.obolibrary.org/obo/OBI_1110038 RMA cell line http://purl.obolibrary.org/obo/CLO_0009828 immortal cell line A cell line derived from a mouse lymphoma, specifically a Rauscher virus-induced tumor.This cell ine is antigen processing-defective and expresses a very low level of MHC molecules on its surface. http://purl.obolibrary.org/obo/OBI_1110039 T2 cell line http://purl.obolibrary.org/obo/CLO_0009828 immortal cell line A human T-B lymphoblastoid hybrid cell line http://purl.obolibrary.org/obo/OBI_1110040 infectious disease http://purl.obolibrary.org/obo/OGMS_0000031 disease is a disease caused by an infectious agent http://purl.obolibrary.org/obo/OBI_1110041 lymph node cell specimen http://purl.obolibrary.org/obo/OBI_0001468 cell specimen A cell specimen comprised of a mixed population of cells obtained by processing whole lymph node into individual cells, typically performed using a sieve. This population includes T cells, B cells, macrophages, and other cell types. http://purl.obolibrary.org/obo/OBI_1110046 organ harvesting http://purl.obolibrary.org/obo/OBI_0600014 material component separation The process of removing an organ from its source organism http://purl.obolibrary.org/obo/OBI_1110049 allergy http://purl.obolibrary.org/obo/OGMS_0000031 disease is a disease in which an abnormally strong inflammatory immune response is triggered against non-self entities, and the immune response has no protective effect http://purl.obolibrary.org/obo/OBI_1110053 cancer http://purl.obolibrary.org/obo/OGMS_0000031 disease A disease characterized by abnormal and uncontrolled cell division http://purl.obolibrary.org/obo/OBI_1110054 autoimmune disease http://purl.obolibrary.org/obo/OGMS_0000031 disease Is a disease characterized by an immune response of an organism against parts of itself http://purl.obolibrary.org/obo/OBI_1110055 obsolete_disease http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class placeholder to be imported from disease ontology http://purl.obolibrary.org/obo/OBI_1110056 epitope specific IL-2 release by T cells http://purl.obolibrary.org/obo/GO_0032623 interleukin-2 production A biological process where T cells produce IL-2 resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_1110057 MHC:epitope complex binding to TCR http://purl.obolibrary.org/obo/OBI_1110014 epitope binding by adaptive immune receptor a process of an MHC molecule binding to an entity playing the role of epitope to create an MHC:epitope complex which is then bound by a TCR molecule. http://purl.obolibrary.org/obo/OBI_1110059 ELISPOT assay measuring epitope specific interferon-gamma production by T cells http://purl.obolibrary.org/obo/OBI_0001414 biological activity assay measuring epitope specific interferon-gamma production by T cells An assay of epitope specific interferon-gamma production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_1110061 exposure resulting in immune reactivity http://purl.obolibrary.org/obo/GO_0008150 biological_process a process in which an organism (host) is exposed to some material entity, which results in an immune reactivity http://purl.obolibrary.org/obo/OBI_1110082 immunogen role http://purl.obolibrary.org/obo/BFO_0000023 role any entity capable of eliciting an immune response when introduced to components of the immune system http://purl.obolibrary.org/obo/OBI_1110083 host of immune response role http://purl.obolibrary.org/obo/BFO_0000023 role is a role borne by an organism. It is realized by the organism during an immunization or an immune response taking place inside or on the surface of the organism, and in which the responding or stimulated immune system is part of the host. http://purl.obolibrary.org/obo/OBI_1110084 effector T cell function http://purl.obolibrary.org/obo/OBI_1110016 adaptive immune effector function The function inhering in a T cell that is realized in an immune response that results from the T cell receptor binding to the MHC:epitope complex. http://purl.obolibrary.org/obo/OBI_1110086 restricting MHC role http://purl.obolibrary.org/obo/BFO_0000023 role The role played by an MHC molecule by binding a material entity playing the role of epitope when that epitope/MHC molecule pair are recognized (bound) by a TCR molecule on the surface of a cell playing the role of effector cell. http://purl.obolibrary.org/obo/OBI_1110091 immune epitope carrier role http://purl.obolibrary.org/obo/BFO_0000023 role A role inhering in a material entity that is covalently bound to an epitope in order to increase the epitopes immunogenicity. http://purl.obolibrary.org/obo/OBI_1110093 disposition to infect an organism http://purl.obolibrary.org/obo/BFO_0000016 disposition Is a role borne by an agent, and realized when in contact with or inside another organism in which it is capable of replicating and causing disease http://purl.obolibrary.org/obo/OBI_1110094 immunization http://purl.obolibrary.org/obo/GO_0008150 biological_process The process of an epitope that is part of or derived from an immunogen coming into contact with adaptive immune cells resulting in these cells acquiring immune effector functions specific for the epitope. http://purl.obolibrary.org/obo/OBI_1110095 blood harvesting http://purl.obolibrary.org/obo/OBI_0600014 material component separation A material separation where blood is taken from an organism. http://purl.obolibrary.org/obo/OBI_1110099 L cell line http://purl.obolibrary.org/obo/CLO_0009828 immortal cell line A cell line derived from mouse fibroblasts. http://purl.obolibrary.org/obo/OBI_1110108 material to be added http://purl.obolibrary.org/obo/BFO_0000040 material entity a material that is added to another one in a material combination process http://purl.obolibrary.org/obo/OBI_1110109 target of material addition http://purl.obolibrary.org/obo/BFO_0000040 material entity A material entity into which another is being added in a material combinatino process http://purl.obolibrary.org/obo/OBI_1110111 environmental proximity to infectious agent http://purl.obolibrary.org/obo/GO_0008150 biological_process Is a process in which an infectious agent comes close enough to a potential host organism in its habitat that a contact can result http://purl.obolibrary.org/obo/OBI_1110114 contact to pathogen carrying biological vector http://purl.obolibrary.org/obo/OBI_1110111 environmental proximity to infectious agent a process in which a vector carrying an infectious agent comes close enough to a potential host organism that a contact can result http://purl.obolibrary.org/obo/OBI_1110116 splenocyte specimen http://purl.obolibrary.org/obo/OBI_0001468 cell specimen A cell specimen comprised of a mixed cell population obtained by processing whole spleen into individual cells, typically performed using a sieve or blender. This population includes T cells, B cells, macrophages, and other cell types. http://purl.obolibrary.org/obo/OBI_1110118 P815 cell line http://purl.obolibrary.org/obo/CLO_0009828 immortal cell line A cell line derived from mouse mastocytoma. http://purl.obolibrary.org/obo/OBI_1110120 assay antigen role http://purl.obolibrary.org/obo/BFO_0000023 role Any molecule recognized by the adaptive immune receptors? Recognized means bound with a certain affinity? From GO ag binding:Interacting selectively with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. see OBI_1110120 below http://purl.obolibrary.org/obo/OBI_1110122 pathologic process http://purl.obolibrary.org/obo/GO_0008150 biological_process abnormal, harmful processes caused by or associated with a disease http://purl.obolibrary.org/obo/OBI_1110124 assay measuring qualitiative binding of a T cell epitope:MHC:TCR complex http://purl.obolibrary.org/obo/OBI_1110037 assay measuring binding of a T cell epitope:MHC:TCR complex A T cell epitope recognition assay that qualitatively detects MHC:epitope complex binding to TCR. http://purl.obolibrary.org/obo/OBI_1110125 assay measuring MHC ligand processing and presentation http://purl.obolibrary.org/obo/OBI_0002075 MHC ligand assay A MHC ligand assay that determines what ligands are processed and loaded onto MHC molecules by eluting ligands and identifying them. http://purl.obolibrary.org/obo/OBI_1110126 assay measuring binding of a MHC:ligand complex http://purl.obolibrary.org/obo/OBI_0002075 MHC ligand assay A MHC ligand assay that detects the binding of a ligand to an MHC molecule. http://purl.obolibrary.org/obo/OBI_1110127 assay measuring binding of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_1110128 immune epitope assay An immune epitope assay that detects B cell epitope recognition. http://purl.obolibrary.org/obo/OBI_1110128 immune epitope assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that detects the binding of an epitope to an adaptive immune receptor or a immune response process resulting from such a binding event http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells http://purl.obolibrary.org/obo/OBI_0002055 assay measuring T cell epitope specific biological activity A T cell epitope dependent biological activity assay that detects cytokine production. http://purl.obolibrary.org/obo/OBI_1110130 biological activity assay measuring epitope specific T cell killing http://purl.obolibrary.org/obo/OBI_0002055 assay measuring T cell epitope specific biological activity A T cell epitope dependent biological activity assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC. http://purl.obolibrary.org/obo/OBI_1110131 biological activity assay measuring epitope specific proliferation of T cells http://purl.obolibrary.org/obo/OBI_0002055 assay measuring T cell epitope specific biological activity A T cell epitope dependent biological activity assay that detects T cell proliferation. http://purl.obolibrary.org/obo/OBI_1110150 51 chromium assay measuring epitope specific T cell killing http://purl.obolibrary.org/obo/OBI_0002062 in vitro assay measuring epitope specific T cell killing A T cell epitope specific killing assay performed in vitro that uses a chromium release assay. http://purl.obolibrary.org/obo/OBI_1110151 ELISA measuring epitope specific interferon-gamma production by T cells http://purl.obolibrary.org/obo/OBI_0001414 biological activity assay measuring epitope specific interferon-gamma production by T cells An assay of epitope specific interferon-gamma production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_1110152 ELISA measuring epitope specific interleukin-2 production by T cells http://purl.obolibrary.org/obo/OBI_0001445 biological activity assay measuring epitope specific interleukin-2 production by T cells An assay of epitope specific interleukin-2 production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_1110153 ELISA measuring epitope specific interleukin-4 production by T cells http://purl.obolibrary.org/obo/OBI_0001450 biological activity assay measuring epitope specific interleukin-4 production by T cells An assay of epitope specific interleukin-4 production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_1110154 ELISA measuring epitope specific interleukin-5 production by T cells http://purl.obolibrary.org/obo/OBI_0001230 biological activity assay measuring epitope specific interleukin-5 production by T cells An assay of epitope specific interleukin-5 production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_1110155 ELISA measuring epitope specific tumor necrosis factor production by T cells http://purl.obolibrary.org/obo/OBI_0001416 biological activity assay measuring epitope specific tumor necrosis factor production by T cells A T cell epitope specific tumor necrosis factor production assay that uses an ELISA. http://purl.obolibrary.org/obo/OBI_1110156 ELISA measuring epitope specific interleukin-10 production by T cells http://purl.obolibrary.org/obo/OBI_0001209 biological activity assay measuring epitope specific interleukin-10 production by T cells An assay of epitope specific interleukin-10 production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_1110157 ELISA measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells http://purl.obolibrary.org/obo/OBI_0001233 biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_1110158 ELISA measuring epitope specific interleukin-6 production by T cells http://purl.obolibrary.org/obo/OBI_0001451 biological activity assay measuring epitope specific interleukin-6 production by T cells An assay of epitope specific interleukin-6 production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_1110159 ELISA measuring epitope specific interleukin-13 production by T cells http://purl.obolibrary.org/obo/OBI_0001251 biological activity assay measuring epitope specific interleukin-13 production by T cells An assay of epitope specific interleukin-13 production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_1110160 ELISA measuring epitope specific interleukin-12 production by T cells http://purl.obolibrary.org/obo/OBI_0001391 biological activity assay measuring epitope specific interleukin-12 production by T cells An assay of epitope specific interleukin-12 production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_1110161 ELISA measuring epitope specific interleukin-1 beta production by T cells http://purl.obolibrary.org/obo/OBI_0001449 biological activity assay measuring epitope specific interleukin-1 beta production by T cells An assay of epitope specific interleukin-1 beta production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_1110162 ELISA measuring epitope specific interleukin-17 production by T cells http://purl.obolibrary.org/obo/OBI_0001295 biological activity assay measuring epitope specific interleukin-17 production by T cells An assay of epitope specific interleukin-17 production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_1110163 ELISA measuring epitope specific interleukin-18 production by T cells http://purl.obolibrary.org/obo/OBI_0001380 biological activity assay measuring epitope specific interleukin-18 production by T cells An assay of epitope specific interleukin-18 production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_1110167 ELISPOT assay measuring epitope specific interleukin-4 production by T cells http://purl.obolibrary.org/obo/OBI_0001450 biological activity assay measuring epitope specific interleukin-4 production by T cells An assay of epitope specific interleukin-4 production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_1110168 ELISPOT assay measuring epitope specific tumor necrosis factor production by T cells http://purl.obolibrary.org/obo/OBI_0001416 biological activity assay measuring epitope specific tumor necrosis factor production by T cells A T cell epitope specific tumor necrosis factor production assay that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_1110170 ELISPOT assay measuring epitope specific interleukin-10 production by T cells http://purl.obolibrary.org/obo/OBI_0001209 biological activity assay measuring epitope specific interleukin-10 production by T cells An assay of epitope specific interleukin-10 production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_1110171 ELISPOT assay measuring epitope specific interleukin-13 production by T cells http://purl.obolibrary.org/obo/OBI_0001251 biological activity assay measuring epitope specific interleukin-13 production by T cells An assay of epitope specific interleukin-13 production by T cells that uses an ELISPOT assay. http://purl.obolibrary.org/obo/OBI_1110172 intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells http://purl.obolibrary.org/obo/OBI_0001414 biological activity assay measuring epitope specific interferon-gamma production by T cells An assay of epitope specific interferon-gamma production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_1110173 intracellular cytokine staining assay measuring epitope specific interleukin-2 production by T cells http://purl.obolibrary.org/obo/OBI_0001445 biological activity assay measuring epitope specific interleukin-2 production by T cells An assay of epitope specific interleukin-2 production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_1110174 intracellular cytokine staining assay measuring epitope specific tumor necrosis factor production by T cells http://purl.obolibrary.org/obo/OBI_0001416 biological activity assay measuring epitope specific tumor necrosis factor production by T cells A T cell epitope specific tumor necrosis factor production assay that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_1110175 intracellular cytokine staining assay measuring epitope specific interleukin-4 production by T cells http://purl.obolibrary.org/obo/OBI_0001450 biological activity assay measuring epitope specific interleukin-4 production by T cells An assay of epitope specific interleukin-4 production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_1110177 intracellular cytokine staining assay measuring epitope specific interleukin-10 production by T cells http://purl.obolibrary.org/obo/OBI_0001209 biological activity assay measuring epitope specific interleukin-10 production by T cells An assay of epitope specific interleukin-10 production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_1110178 intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells http://purl.obolibrary.org/obo/OBI_0001295 biological activity assay measuring epitope specific interleukin-17 production by T cells An assay of epitope specific interleukin-17 production by T cells that uses an intracellular cytokine staining assay. http://purl.obolibrary.org/obo/OBI_1110179 MHC tetramer/multimer assay measuring binding of a T cell epitope:MHC:TCR complex http://purl.obolibrary.org/obo/OBI_0001317 flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex A T cell epitope qualitative binding assay that uses an MHC multimer staining assay. http://purl.obolibrary.org/obo/OBI_1110180 3H-thymidine assay measuring epitope specific proliferation of T cells http://purl.obolibrary.org/obo/OBI_0002071 in vitro assay measuring epitope specific proliferation of T cells A T cell epitope specific proliferation assay performed on cells in vitro that uses a tritiated thymidine incorporation assay. http://purl.obolibrary.org/obo/OBI_1110181 BrdU assay measuring epitope specific proliferation of T cells http://purl.obolibrary.org/obo/OBI_0002071 in vitro assay measuring epitope specific proliferation of T cells A T cell epitope specific proliferation assay performed on cells in vitro that uses a BrdU incorporation assay. http://purl.obolibrary.org/obo/OBI_1110182 epitope specific T cell proliferation http://purl.obolibrary.org/obo/GO_0042098 T cell proliferation A biological process where T cells proliferate resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_1110184 epitope specific GM-CSF release by T cells http://purl.obolibrary.org/obo/GO_0032604 granulocyte macrophage colony-stimulating factor production A biological process where T cells produce GM-CSF resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_1110185 epitope specific IFN-g release by T cells http://purl.obolibrary.org/obo/GO_0032609 interferon-gamma production A biological process where T cells produce IFNg resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_1110187 epitope specific IL-10 release by T cells http://purl.obolibrary.org/obo/GO_0032613 interleukin-10 production A biological process where T cells produce IL-10 resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_1110190 epitope specific IL-12 release by T cells http://purl.obolibrary.org/obo/GO_0032615 interleukin-12 production A biological process where T cells produce IL-12 resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_1110191 epitope specific IL-13 release by T cells http://purl.obolibrary.org/obo/GO_0032616 interleukin-13 production A biological process where T cells produce IL-13 resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_1110193 epitope specific IL-17 release by T cells http://purl.obolibrary.org/obo/GO_0032620 interleukin-17 production A biological process where T cells produce IL-17 resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_1110195 epitope specific IL-18 release by T cells http://purl.obolibrary.org/obo/GO_0032621 interleukin-18 production A biological process where T cells produce IL-18 resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_1110196 epitope specific IL-1b release by T cells http://purl.obolibrary.org/obo/GO_0032611 interleukin-1 beta production A biological process where T cells produce IL-1b resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_1110199 epitope specific IL-4 release by T cells http://purl.obolibrary.org/obo/GO_0032633 interleukin-4 production A biological process where T cells produce IL-4 resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_1110201 allergen http://purl.obolibrary.org/obo/BFO_0000040 material entity A material entity bearing the disposition to cause an allergic reaction http://purl.obolibrary.org/obo/OBI_1110202 epitope specific IL-5 release by T cells http://purl.obolibrary.org/obo/GO_0032634 interleukin-5 production A biological process where T cells produce IL-5 resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_1110203 epitope specific IL-6 release by T cells http://purl.obolibrary.org/obo/GO_0032635 interleukin-6 production A biological process where T cells produce IL-6 resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_1110204 epitope specific killing by T cells http://purl.obolibrary.org/obo/GO_0001913 T cell mediated cytotoxicity A biological process where T cells lyse antigen presenting cells resulting from the recognition of a T cell epitope on MHC molecules of the antigen presenting cell. http://purl.obolibrary.org/obo/OBI_1110206 epitope specific TNF release by T cells http://purl.obolibrary.org/obo/GO_0032640 tumor necrosis factor production A biological process where T cells produce TNF resulting from the recognition of a T cell epitope. http://purl.obolibrary.org/obo/OBI_1110300 direct submission to IEDB http://purl.obolibrary.org/obo/IAO_0000088 report A report about experiments in an investigation that characterize immune epitopes, and was submitted directly by the authors to the Immune Epitope Database (IEDB) http://purl.obolibrary.org/obo/OBI_9999994 chromium release assay http://purl.obolibrary.org/obo/OBI_0000903 in vitro cell killing assay An in vitro cell killing assay in which radioactive chromium is absorbed by cells and released into supernatant when the cells die. The amount of radioactivity measured in the supernatant is a proxy for the number of cells that have died. http://purl.obolibrary.org/obo/OGMS_0000015 clinical history http://purl.obolibrary.org/obo/IAO_0000030 information content entity A series of statements representing health-relevant qualities of a patient and of a patient's family. http://purl.obolibrary.org/obo/OGMS_0000023 phenotype http://purl.obolibrary.org/obo/BFO_0000019 quality A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. http://purl.obolibrary.org/obo/OGMS_0000031 disease http://purl.obolibrary.org/obo/BFO_0000016 disposition A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. http://purl.obolibrary.org/obo/OGMS_0000063 disease course http://purl.obolibrary.org/obo/GO_0008150 biological_process The totality of all processes through which a given disease instance is realized. http://purl.obolibrary.org/obo/OGMS_0000090 treatment http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate the signs and symptoms of a disorder or pathological process http://purl.obolibrary.org/obo/PATO_0000011 age http://purl.obolibrary.org/obo/PATO_0000165 time A time quality inhering in a bearer by virtue of how long the bearer has existed. http://purl.obolibrary.org/obo/PATO_0000018 fluorescence http://purl.obolibrary.org/obo/PATO_0001296 luminous flux A luminous flux quality inhering in a bearer by virtue of the bearer's emitting longer wavelength light following the absorption of shorter wavelength radiation; fluorescence is common with aromatic compounds with several rings joined together. http://purl.obolibrary.org/obo/PATO_0000047 biological sex http://purl.obolibrary.org/obo/PATO_0001995 organismal quality An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. http://purl.obolibrary.org/obo/PATO_0000122 length http://purl.obolibrary.org/obo/PATO_0000051 morphology A 1-D extent quality which is equal to the distance between two points. http://purl.obolibrary.org/obo/PATO_0000125 mass http://purl.obolibrary.org/obo/PATO_0001018 physical quality A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. http://purl.obolibrary.org/obo/PATO_0000146 temperature http://purl.obolibrary.org/obo/PATO_0001018 physical quality A physical quality of the thermal energy of a system. http://purl.obolibrary.org/obo/PATO_0000186 behavioral quality http://purl.obolibrary.org/obo/PATO_0001995 organismal quality An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation. http://purl.obolibrary.org/obo/PATO_0000383 female http://purl.obolibrary.org/obo/PATO_0001894 phenotypic sex A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. http://purl.obolibrary.org/obo/PATO_0000384 male http://purl.obolibrary.org/obo/PATO_0001894 phenotypic sex A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. http://purl.obolibrary.org/obo/PATO_0000918 volume http://purl.obolibrary.org/obo/PATO_0001710 3-D extent A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies. http://purl.obolibrary.org/obo/PATO_0001025 pressure http://purl.obolibrary.org/obo/PATO_0001018 physical quality A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts. http://purl.obolibrary.org/obo/PATO_0001161 diluted http://purl.obolibrary.org/obo/PATO_0000033 concentration of A concentration which relatively low. http://purl.obolibrary.org/obo/PATO_0001167 damaged http://purl.obolibrary.org/obo/PATO_0001020 damage A structural quality inhering in a bearer by virtue of the bearer being harmed or injured or spoiled, such that its functionality is impaired. http://purl.obolibrary.org/obo/PATO_0001193 lateral to http://purl.obolibrary.org/obo/PATO_0000140 position A spatial quality inhering in a bearer by virtue of the bearer's being located toward the side relative to another entity. http://purl.obolibrary.org/obo/PATO_0001196 ventral to http://purl.obolibrary.org/obo/PATO_0000140 position A spatial quality inhering in a bearer by virtue of the bearer's being located toward the abdomen of an organism relative to another entity. http://purl.obolibrary.org/obo/PATO_0001233 dorsal to http://purl.obolibrary.org/obo/PATO_0000140 position A spatial quality inhering in a bearer by virtue of the bearer's being located toward the back or upper surface of an organism relative to another entity. http://purl.obolibrary.org/obo/PATO_0001338 mixed sex http://purl.obolibrary.org/obo/PATO_0002003 population quality A biological sex quality inhering in a population of multiple sexes. http://purl.obolibrary.org/obo/PATO_0001339 biomaterial purity http://purl.obolibrary.org/obo/PATO_0000025 composition A composition quality inhering in an bearer by virtue of the bearer's homogeneity of a biomaterial. http://purl.obolibrary.org/obo/PATO_0001340 hermaphrodite http://purl.obolibrary.org/obo/PATO_0001894 phenotypic sex A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual. http://purl.obolibrary.org/obo/PATO_0001341 a mating type (yeast) http://purl.obolibrary.org/obo/PATO_0001342 Saccharomyces cerevisiae mating type A S. cerevisiae mating type cells that secrete a pheromone that in alpha haploids stimulates processes that lead to mating. http://purl.obolibrary.org/obo/PATO_0001344 alpha mating type (yeast) http://purl.obolibrary.org/obo/PATO_0001342 Saccharomyces cerevisiae mating type A S. cerevisiae mating type cells that secrete a pheromone that stimulates a haploids. http://purl.obolibrary.org/obo/PATO_0001345 h minus http://purl.obolibrary.org/obo/PATO_0001343 Schizosaccharomyces pombe mating type A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 locus. http://purl.obolibrary.org/obo/PATO_0001346 h plus http://purl.obolibrary.org/obo/PATO_0001343 Schizosaccharomyces pombe mating type A S. pombe mating type determined by the mat1-Pc and mat1-Pi on the mat1 locus. http://purl.obolibrary.org/obo/PATO_0001347 F mating type http://purl.obolibrary.org/obo/PATO_0001335 bacterial mating type A bacterial mating type indicating the presence of F plasmid in a bacterial cell. http://purl.obolibrary.org/obo/PATO_0001348 F minus mating type http://purl.obolibrary.org/obo/PATO_0001335 bacterial mating type A bacterial mating type indicating the absence of F plasmid in a bacterial cell. http://purl.obolibrary.org/obo/PATO_0001374 ploidy http://purl.obolibrary.org/obo/PATO_0001396 cellular quality A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism. http://purl.obolibrary.org/obo/PATO_0001375 haploid http://purl.obolibrary.org/obo/PATO_0001393 euploid A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes. http://purl.obolibrary.org/obo/PATO_0001377 polyploid http://purl.obolibrary.org/obo/PATO_0001393 euploid A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes. http://purl.obolibrary.org/obo/PATO_0001385 aneuploid http://purl.obolibrary.org/obo/PATO_0001374 ploidy A ploidy quality inhering in a bearer by virtue of the bearer's containing a non-integral multiple of the monoploid number, due to extra or missing chromosomes. http://purl.obolibrary.org/obo/PATO_0001394 diploid http://purl.obolibrary.org/obo/PATO_0001393 euploid A ploidy quality inhering in a bearer by virtue of the bearer's having two copies (homologs) of each chromosome, usually one from the mother and one from the father. http://purl.obolibrary.org/obo/PATO_0001396 cellular quality http://purl.obolibrary.org/obo/PATO_0001241 physical object quality A monadic quality of continuant that exists at the cellular level of organisation. http://purl.obolibrary.org/obo/PATO_0001421 alive http://purl.obolibrary.org/obo/PATO_0000169 viability A viability quality inhering in a bearer by virtue of the bearer's condition before death. http://purl.obolibrary.org/obo/PATO_0001422 dead http://purl.obolibrary.org/obo/PATO_0000169 viability A viability quality inhering in a bearer by virtue of the cessation of the bearer's life. http://purl.obolibrary.org/obo/PATO_0001546 quality of a solid http://purl.obolibrary.org/obo/PATO_0002198 quality of a substance A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable. http://purl.obolibrary.org/obo/PATO_0001547 quality of a gas http://purl.obolibrary.org/obo/PATO_0002198 quality of a substance A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape. http://purl.obolibrary.org/obo/PATO_0001548 quality of a liquid http://purl.obolibrary.org/obo/PATO_0002198 quality of a substance A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape. http://purl.obolibrary.org/obo/PATO_0001741 radioactive http://purl.obolibrary.org/obo/PATO_0001740 activity (of a radionuclide) A radiation quality inhering in bearer by virtue of the bearer's exhibiting or being caused by radioactivity. http://purl.obolibrary.org/obo/PATO_0001792 left side of http://purl.obolibrary.org/obo/PATO_0000140 position A spatial quality inhering in a bearer by virtue of the bearer's being located on left side of from the a another entity. http://purl.obolibrary.org/obo/PATO_0001793 right side of http://purl.obolibrary.org/obo/PATO_0000140 position A spatial quality inhering in a bearer by virtue of the bearer's being located on right side of a another entity. http://purl.obolibrary.org/obo/PATO_0001985 frozen http://purl.obolibrary.org/obo/PATO_0000146 temperature A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point. http://purl.obolibrary.org/obo/PATO_0001995 organismal quality http://purl.obolibrary.org/obo/PATO_0001241 physical object quality A quality that inheres in an entire organism or part of an organism. http://purl.obolibrary.org/obo/PATO_0002201 handedness http://purl.obolibrary.org/obo/PATO_0000186 behavioral quality A behavioral quality inhering ina bearer by virtue of the bearer's unequal distribution of fine motor skill between its left and right hands or feet. http://purl.obolibrary.org/obo/PATO_0002202 left handedness http://purl.obolibrary.org/obo/PATO_0002201 handedness Handedness where the organism preferentially uses the left hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. http://purl.obolibrary.org/obo/PATO_0002203 right handedness http://purl.obolibrary.org/obo/PATO_0002201 handedness Handedness where the organism preferentially uses the right hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. http://purl.obolibrary.org/obo/PATO_0002204 ambidextrous handedness http://purl.obolibrary.org/obo/PATO_0002201 handedness Handedness where the organism exhibits no overall dominance in the use of right or left hand or foot in the performance of tasks that require one hand or foot or a dominant hand or foot. http://purl.obolibrary.org/obo/PATO_0002243 fluid flow rate http://purl.obolibrary.org/obo/PATO_0001574 flow rate A physical quality inhering in a fluid (liquid or gas) by virtue of the amount of fluid which passes through a given surface per unit time. http://purl.obolibrary.org/obo/PR_000000001 protein http://purl.obolibrary.org/obo/CHEBI_16670 peptide An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. http://purl.obolibrary.org/obo/PR_000001004 CD4 molecule http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence. http://purl.obolibrary.org/obo/PR_000001018 CD3 subunit with immunoglobulin domain http://purl.obolibrary.org/obo/PR_000000001 protein A protein with a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response. http://purl.obolibrary.org/obo/PR_000003252 antithrombin-III http://purl.obolibrary.org/obo/PR_000000001 protein A serpin that is a translation product of the human SERPINC1 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000003745 double-stranded RNA-specific adenosine deaminase http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human ADAR gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000006592 deoxyribonuclease-1 http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human DNASE1 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000007928 glial cell line-derived neurotrophic factor http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human GDNF gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000014060 ribonuclease T2 http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human RNASET2 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000025402 T cell receptor co-receptor CD8 http://purl.obolibrary.org/obo/PR_000000001 protein A protein complex that is a membrane-bound heterodimeric co-receptor for MHC class-I antigen/T-cell receptor interaction. http://purl.obolibrary.org/obo/PR_000025467 guanyl-specific ribonuclease T1 http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the Aspergillus oryzae RIB40 rntA gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000025471 nuclease S1 http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the Aspergillus oryzae RIB40 nucS gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000025475 ribonuclease U2 http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the Ustilago sphaerogena RNU2 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000025477 ribonuclease V1 (cobra) http://purl.obolibrary.org/obo/PR_000000001 protein A protein with ribonuclease activity that is a constituent of cobra venom. http://purl.obolibrary.org/obo/PR_000025478 ribonuclease CL3 (chicken) http://purl.obolibrary.org/obo/PR_000000001 protein A protein with ribonuclease activity that is purified from chicken liver. http://purl.obolibrary.org/obo/SO_0000148 supercontig http://purl.obolibrary.org/obo/SO_0000353 sequence_assembly One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's. http://purl.obolibrary.org/obo/SO_0000149 contig http://purl.obolibrary.org/obo/SO_0000353 sequence_assembly A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. http://purl.obolibrary.org/obo/SO_0000276 miRNA http://purl.obolibrary.org/obo/SO_0000001 region Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors. http://purl.obolibrary.org/obo/SO_0000353 sequence_assembly http://purl.obolibrary.org/obo/SO_0001248 assembly A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. http://purl.obolibrary.org/obo/SO_0000988 circular http://purl.obolibrary.org/obo/PATO_0001241 physical object quality A quality of a nucleotide polymer that has no terminal nucleotide residues. http://purl.obolibrary.org/obo/SO_0001248 assembly http://purl.obolibrary.org/obo/SO_0001410 experimental_feature A region of the genome of known length that is composed by ordering and aligning two or more different regions. http://purl.obolibrary.org/obo/UO_0000001 length unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label A unit which is a standard measure of the distance between two points. http://purl.obolibrary.org/obo/UO_0000002 mass unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label A unit which is a standard measure of the amount of matter/energy of a physical object. http://purl.obolibrary.org/obo/UO_0000003 time unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label A unit which is a standard measure of the dimension in which events occur in sequence. http://purl.obolibrary.org/obo/VO_0000001 vaccine http://purl.obolibrary.org/obo/BFO_0000040 material entity A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine. http://purl.obolibrary.org/obo/VO_0000002 vaccination http://purl.obolibrary.org/obo/OBI_0600007 administering substance in vivo a process of administering substance in vivo that involves in adding a vaccine into a host (e.g., human) in vivo with the intent to invoke a protective or therapeutic adaptive immune response. http://purl.obolibrary.org/obo/APOLLO_SV_00000032 count http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement datum that is the output of counting. http://purl.obolibrary.org/obo/IAO_0020000 identifier http://purl.obolibrary.org/obo/IAO_0000030 information content entity An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. http://purl.obolibrary.org/obo/OMIABIS_0000050 fixed tissue specimen http://purl.obolibrary.org/obo/OBI_0000953 processed specimen A processed specimen that is the output of a fixation process. http://purl.obolibrary.org/obo/OMIABIS_0000052 fixed tissue slide specimen http://purl.obolibrary.org/obo/OMIABIS_0000050 fixed tissue specimen A fixed tissue specimen that is placed in a slide. http://purl.obolibrary.org/obo/CHEBI_17709 5'-adenylyl sulfate http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity An adenosine 5'-phosphate having a sulfo group attached to one the phosphate OH groups. http://purl.obolibrary.org/obo/CHEBI_15956 biotin http://purl.obolibrary.org/obo/OBI_0002744 molecular label An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins. http://purl.obolibrary.org/obo/CHEBI_16991 deoxyribonucleic acid http://purl.obolibrary.org/obo/CHEBI_33696 nucleic acid High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. http://purl.obolibrary.org/obo/CHEBI_17234 glucose http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity An aldohexose used as a source of energy and metabolic intermediate. http://purl.obolibrary.org/obo/CHEBI_33696 nucleic acid http://purl.obolibrary.org/obo/CHEBI_33839 macromolecule A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. http://purl.obolibrary.org/obo/CHEBI_33709 amino acid http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity A carboxylic acid containing one or more amino groups. http://purl.obolibrary.org/obo/CHEBI_29237 deuterium atom http://purl.obolibrary.org/obo/CHEBI_33250 atom The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek deltaepsilonupsilontauepsilonrhoomicronnu, second). http://purl.obolibrary.org/obo/CHEBI_59052 1,1-dihydroxy-3-ethoxy-2-butanone http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity A butanone derivative having two hydroxy substituents at the 1-position and an ethoxy substituent at the 3-position. http://purl.obolibrary.org/obo/CHEBI_59053 N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two N-substituents. http://purl.obolibrary.org/obo/CHEBI_59054 N-methylisatoic anhydride http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity A 3,1-benzoxazin-1,4-dione having an N-methyl substituent. http://purl.obolibrary.org/obo/CHEBI_59055 (S)-1-(4-bromoacetamidobenzyl)EDTA http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (S)-configuration. http://purl.obolibrary.org/obo/CHEBI_59056 EDTA methidiumpropylamide http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity A combined intercalating and chelating reagent. The iron chelate, prepared by adding Fe(NH4)2(SO4)2, effects random oxidative cleavage of DNA in the presence of O2 and a reducing agent. This activity is useful as a footprinting probe. http://purl.obolibrary.org/obo/CHEBI_59424 bromophenol blue http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye. http://purl.obolibrary.org/obo/CL_0000000 cell http://purl.obolibrary.org/obo/BFO_0000040 material entity A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. http://purl.obolibrary.org/obo/CL_0000001 primary cultured cell http://purl.obolibrary.org/obo/CL_0000010 cultured cell A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged. http://purl.obolibrary.org/obo/CL_0000003 native cell http://purl.obolibrary.org/obo/CL_0000000 cell A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). http://purl.obolibrary.org/obo/CL_0000010 cultured cell http://purl.obolibrary.org/obo/CL_0000578 experimentally modified cell in vitro A cell in vitro that is or has been maintained or propagated as part of a cell culture. http://purl.obolibrary.org/obo/CL_0000057 fibroblast http://purl.obolibrary.org/obo/CL_0000000 cell A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. http://purl.obolibrary.org/obo/CL_0000066 epithelial cell http://purl.obolibrary.org/obo/CL_0000000 cell A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina. http://purl.obolibrary.org/obo/CL_0000084 T cell http://purl.obolibrary.org/obo/CL_0000542 lymphocyte A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex. http://purl.obolibrary.org/obo/CL_0000097 mast cell http://purl.obolibrary.org/obo/CL_0000000 cell A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development. http://purl.obolibrary.org/obo/CL_0000182 hepatocyte http://purl.obolibrary.org/obo/CL_0000066 epithelial cell The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated. http://purl.obolibrary.org/obo/CL_0000232 erythrocyte http://purl.obolibrary.org/obo/CL_0000000 cell A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen. http://purl.obolibrary.org/obo/CL_0000235 macrophage http://purl.obolibrary.org/obo/CL_0000000 cell A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. http://purl.obolibrary.org/obo/CL_0000236 B cell http://purl.obolibrary.org/obo/CL_0000542 lymphocyte A lymphocyte of B lineage that is capable of B cell mediated immunity. http://purl.obolibrary.org/obo/CL_0000451 dendritic cell http://purl.obolibrary.org/obo/CL_0000000 cell A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative). http://purl.obolibrary.org/obo/CL_0000540 neuron http://purl.obolibrary.org/obo/CL_0000000 cell The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. http://purl.obolibrary.org/obo/CL_0000542 lymphocyte http://purl.obolibrary.org/obo/CL_0000842 mononuclear cell A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. http://purl.obolibrary.org/obo/CL_0000558 reticulocyte http://purl.obolibrary.org/obo/CL_0000000 cell An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds. http://purl.obolibrary.org/obo/CL_0000578 experimentally modified cell in vitro http://purl.obolibrary.org/obo/CL_0000000 cell A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. http://purl.obolibrary.org/obo/CL_0000624 CD4-positive, alpha-beta T cell http://purl.obolibrary.org/obo/CL_0000789 alpha-beta T cell A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor. http://purl.obolibrary.org/obo/CL_0000625 CD8-positive, alpha-beta T cell http://purl.obolibrary.org/obo/CL_0000789 alpha-beta T cell A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor. http://purl.obolibrary.org/obo/CL_0000738 leukocyte http://purl.obolibrary.org/obo/CL_0000000 cell An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. http://purl.obolibrary.org/obo/CL_0000767 basophil http://purl.obolibrary.org/obo/CL_0000000 cell Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive. http://purl.obolibrary.org/obo/CL_0000786 plasma cell http://purl.obolibrary.org/obo/CL_0000236 B cell A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin. http://purl.obolibrary.org/obo/CL_0000789 alpha-beta T cell http://purl.obolibrary.org/obo/CL_0000084 T cell A T cell that expresses an alpha-beta T cell receptor complex. http://purl.obolibrary.org/obo/CL_0000794 CD8-positive, alpha-beta cytotoxic T cell http://purl.obolibrary.org/obo/CL_0000625 CD8-positive, alpha-beta T cell A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive. http://purl.obolibrary.org/obo/CL_0000814 mature NK T cell http://purl.obolibrary.org/obo/CL_0000789 alpha-beta T cell A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response. http://purl.obolibrary.org/obo/CL_0000842 mononuclear cell http://purl.obolibrary.org/obo/CL_0000000 cell A leukocyte with a single non-segmented nucleus in the mature form. http://purl.obolibrary.org/obo/UBERON_0000007 pituitary gland http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN]. http://purl.obolibrary.org/obo/UBERON_0000029 lymph node http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph. http://purl.obolibrary.org/obo/UBERON_0000165 mouth http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). http://purl.obolibrary.org/obo/UBERON_0000178 blood http://purl.obolibrary.org/obo/UBERON_0006314 bodily fluid A fluid that is composed of blood plasma and erythrocytes. http://purl.obolibrary.org/obo/UBERON_0000945 stomach http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. http://purl.obolibrary.org/obo/UBERON_0000948 heart http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. http://purl.obolibrary.org/obo/UBERON_0000955 brain http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. http://purl.obolibrary.org/obo/UBERON_0000970 eye http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity An organ that detects light. http://purl.obolibrary.org/obo/UBERON_0000992 ovary http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity the gonad of a female organism which contains germ cells http://purl.obolibrary.org/obo/UBERON_0000995 uterus http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth http://purl.obolibrary.org/obo/UBERON_0000996 vagina http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]. http://purl.obolibrary.org/obo/UBERON_0001004 respiratory system http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity Functional system which consists of structures involved in respiration. http://purl.obolibrary.org/obo/UBERON_0001052 rectum http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity the terminal portion of the intestinal tube, terminating with the anus http://purl.obolibrary.org/obo/UBERON_0001134 skeletal muscle tissue http://purl.obolibrary.org/obo/UBERON_0000479 tissue Muscle tissue that consists primarily of skeletal muscle fibers. http://purl.obolibrary.org/obo/UBERON_0001155 colon http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity Last portion of the large intestine before it becomes the rectum. http://purl.obolibrary.org/obo/UBERON_0001159 sigmoid colon http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity. http://purl.obolibrary.org/obo/UBERON_0001255 urinary bladder http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]. http://purl.obolibrary.org/obo/UBERON_0001323 tibial nerve http://purl.obolibrary.org/obo/UBERON_0000477 anatomical cluster The tibial nerve is a branch of the sciatic nerve. The tibial nerve passes through the popliteal fossa to pass below the arch of soleus. In the popliteal fossa the nerve gives off branches to gastrocnemius, popliteus, soleus and plantaris muscles, an articular branch to the knee joint, and a cutaneous branch that will become the sural nerve. The sural nerve is joined by fibres from the common peroneal nerve and runs down the calf to supply the lateral side of the foot. Below the soleus muscle the nerve lies close to the tibia and supplies the tibialis posterior, the flexor digitorum longus and the flexor hallucis longus. The nerve passes into the foot running posterior to the medial malleolus. Here it is bound down by the flexor retinaculum in company with the posterior tibial artery. [WP,unvetted]. http://purl.obolibrary.org/obo/UBERON_0001558 lower respiratory tract http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified] http://purl.obolibrary.org/obo/UBERON_0001723 tongue http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity A muscular organ in the floor of the mouth. http://purl.obolibrary.org/obo/UBERON_0002046 thyroid gland http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO]. http://purl.obolibrary.org/obo/UBERON_0002048 lung http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity Respiration organ that develops as an outpocketing of the esophagus. http://purl.obolibrary.org/obo/UBERON_0002106 spleen http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity the organ that functions to filter blood and to store red corpuscles and platelets http://purl.obolibrary.org/obo/UBERON_0002107 liver http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. http://purl.obolibrary.org/obo/UBERON_0002116 ileum http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity the portion of the small intestine that extends from the jejunum to the colon http://purl.obolibrary.org/obo/UBERON_0002358 peritoneum http://purl.obolibrary.org/obo/UBERON_0000481 multi-tissue structure A serous membrane that lines the peritoneal cavity[VHOG,modified]. http://purl.obolibrary.org/obo/UBERON_0002367 prostate gland http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid. http://purl.obolibrary.org/obo/UBERON_0003126 trachea http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. http://purl.obolibrary.org/obo/OBI_0002460 defined population inclusion criterion http://purl.obolibrary.org/obo/OBI_0500027 inclusion criterion An inclusion criterion that is based on fitting within the defined characteristics of a population based study design. http://purl.obolibrary.org/obo/OBI_0002573 polyA depleted RNA extract http://purl.obolibrary.org/obo/OBI_0000880 RNA extract A RNA extract that is the output of an extraction process in which RNA molecules lacking poly A tails at thier 3' ends are purified. http://purl.obolibrary.org/obo/OBI_0002574 RNA extraction with polyA depletion http://purl.obolibrary.org/obo/OBI_0666666 RNA extraction A RNA extraction process in which only RNAs lacking a polyA tail are retained http://purl.obolibrary.org/obo/CHEBI_16670 peptide http://purl.obolibrary.org/obo/CHEBI_33839 macromolecule Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. http://purl.obolibrary.org/obo/CHEBI_25078 luciferin http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase. http://purl.obolibrary.org/obo/CHEBI_33697 ribonucleic acid http://purl.obolibrary.org/obo/CHEBI_33696 nucleic acid High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. http://purl.obolibrary.org/obo/CHEBI_61073 oxygen radical http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity An inorganic radical in which a free electron resides on one or more oxygen atoms of an oxygen species. http://purl.obolibrary.org/obo/CHEBI_31642 gadodiamide hydrate http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity The hydrate of gadodiamide. http://purl.obolibrary.org/obo/CHEBI_31643 gadoteridol http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity A non-ionic gadolinium chelate having a macrocyclic tetraamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). http://purl.obolibrary.org/obo/CHEBI_31991 phenol red http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 4-hydroxyphenyl groups. A pH indicator changing colour from yellow below pH 6.8 to bright pink above pH 8.2, it is commonly used as an indicator in cell cultures and in home swimming pool test kits. It is also used in the (now infrequently performed) phenolsulfonphthalein (PSP) test for estimation of overall blood flow through the kidney. http://purl.obolibrary.org/obo/CHEBI_32142 sodium citrate dihydrate http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity The dihydrate of trisodium citrate. http://purl.obolibrary.org/obo/CHEBI_37333 gadodiamide http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity A non-ionic gadolinium chelate having a macrocyclic triamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). http://purl.obolibrary.org/obo/CHEBI_33359 rhodium atom http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity A cobalt group element atom of atomic number 45. http://purl.obolibrary.org/obo/CHEBI_472552 5-bromo-2'-deoxyuridine http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase. http://purl.obolibrary.org/obo/CHEBI_59051 diethyl pyrocarbonate http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity The diethyl ester of dicarbonic acid. http://purl.obolibrary.org/obo/CHEBI_52673 Alexa Fluor 555 http://purl.obolibrary.org/obo/OBI_0002744 molecular label A fluorescent dye of absorption wavelength 555 nm and emission wavelength 565 nm, derived from a 3,6-diaminoxanthene-4,5-disulfate. http://purl.obolibrary.org/obo/GO_0005216 ion channel activity http://purl.obolibrary.org/obo/GO_0009987 cellular process Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size). http://purl.obolibrary.org/obo/GO_0005575 cellular_component http://purl.obolibrary.org/obo/BFO_0000040 material entity A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). http://purl.obolibrary.org/obo/GO_0006006 glucose metabolic process http://purl.obolibrary.org/obo/GO_0008150 biological_process The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides. http://purl.obolibrary.org/obo/GO_0006306 DNA methylation http://purl.obolibrary.org/obo/GO_0008150 biological_process The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. http://purl.obolibrary.org/obo/GO_0006338 chromatin remodeling http://purl.obolibrary.org/obo/GO_0009987 cellular process Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation. http://purl.obolibrary.org/obo/GO_0007596 blood coagulation http://purl.obolibrary.org/obo/GO_0008150 biological_process The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers. http://purl.obolibrary.org/obo/GO_0009566 fertilization http://purl.obolibrary.org/obo/GO_0008150 biological_process The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). http://purl.obolibrary.org/obo/GO_0016788 hydrolase activity, acting on ester bonds http://purl.obolibrary.org/obo/GO_0003824 catalytic activity Catalysis of the hydrolysis of any ester bond. http://purl.obolibrary.org/obo/GO_0033036 macromolecule localization http://purl.obolibrary.org/obo/GO_0008150 biological_process Any process in which a macromolecule is transported to, or maintained in, a specific location. http://purl.obolibrary.org/obo/GO_0040029 regulation of gene expression, epigenetic http://purl.obolibrary.org/obo/GO_0040030 regulation of molecular function, epigenetic Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence. http://purl.obolibrary.org/obo/GO_0050896 response to stimulus http://purl.obolibrary.org/obo/GO_0008150 biological_process Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. http://purl.obolibrary.org/obo/UBERON_0000105 life cycle stage http://purl.obolibrary.org/obo/GO_0008150 biological_process A spatiotemporal region encompassing some part of the life cycle of an organism. http://purl.obolibrary.org/obo/UBERON_0000173 amniotic fluid http://purl.obolibrary.org/obo/UBERON_0000463 organism substance Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid. http://purl.obolibrary.org/obo/UBERON_0000316 cervical mucus http://purl.obolibrary.org/obo/UBERON_0006314 bodily fluid A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation[WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus. http://purl.obolibrary.org/obo/UBERON_0000341 throat http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity In anatomy, the throat is the anterior part of the neck, in front of the vertebral column. It consists of the pharynx and larynx. An important feature of the throat is the epiglottis, a flap which separates the esophagus from the trachea and prevents inhalation of food or drink. The throat contains various blood vessels, various pharyngeal muscles, the trachea (windpipe) and the esophagus. The hyoid bone and the clavicle are the only bones located in the throat of mammals. It is sometimes considered a synonym for fauces. [WP,unvetted]. http://purl.obolibrary.org/obo/UBERON_0000362 renal medulla http://purl.obolibrary.org/obo/UBERON_0000481 multi-tissue structure the inner portion of the kidney consisting of the renal pyramids http://purl.obolibrary.org/obo/UBERON_0000463 organism substance http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity http://purl.obolibrary.org/obo/BFO_0000040 material entity Anatomical entity that has mass. http://purl.obolibrary.org/obo/UBERON_0000477 anatomical cluster http://purl.obolibrary.org/obo/BFO_0000040 material entity Anatomical group that has its parts adjacent to one another. http://purl.obolibrary.org/obo/UBERON_0000479 tissue http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. http://purl.obolibrary.org/obo/UBERON_0000481 multi-tissue structure http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. http://purl.obolibrary.org/obo/UBERON_0000483 epithelium http://purl.obolibrary.org/obo/UBERON_0000479 tissue Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. http://purl.obolibrary.org/obo/UBERON_0000956 cerebral cortex http://purl.obolibrary.org/obo/UBERON_0000477 anatomical cluster The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex. http://purl.obolibrary.org/obo/UBERON_0001013 adipose tissue http://purl.obolibrary.org/obo/UBERON_0000479 tissue Portion of connective tissue composed of adipocytes enmeshed in areolar tissue http://purl.obolibrary.org/obo/UBERON_0001087 pleural fluid http://purl.obolibrary.org/obo/UBERON_0006314 bodily fluid Transudate contained in the pleural cavity. http://purl.obolibrary.org/obo/UBERON_0001088 urine http://purl.obolibrary.org/obo/UBERON_0000463 organism substance Excretion that is the output of a kidney http://purl.obolibrary.org/obo/UBERON_0001089 sweat http://purl.obolibrary.org/obo/UBERON_0006314 bodily fluid Secretion produced by a sweat gland. http://purl.obolibrary.org/obo/UBERON_0001090 synovial fluid http://purl.obolibrary.org/obo/UBERON_0006314 bodily fluid Joint fluid is a transudate of plasma that is actively secreted by synovial cells. http://purl.obolibrary.org/obo/UBERON_0001225 cortex of kidney http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity Outer cortical portion of the kidney, between the renal capsule and the renal medulla. http://purl.obolibrary.org/obo/UBERON_0001268 peritoneal fluid http://purl.obolibrary.org/obo/UBERON_0006314 bodily fluid Transudate contained in the peritoneal cavity. http://purl.obolibrary.org/obo/UBERON_0001359 cerebrospinal fluid http://purl.obolibrary.org/obo/UBERON_0006314 bodily fluid A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord. http://purl.obolibrary.org/obo/UBERON_0001567 cheek http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity A fleshy subdivision of one side of the face bounded by an eye, ear and the nose. http://purl.obolibrary.org/obo/UBERON_0001830 minor salivary gland http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity One of the smaller, largely mucus-secreting, exocrine glands of the oral cavity, consisting of the labial, buccal, molar, lingual, and palatine glands[MP]. http://purl.obolibrary.org/obo/UBERON_0001836 saliva http://purl.obolibrary.org/obo/UBERON_0000463 organism substance A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. http://purl.obolibrary.org/obo/UBERON_0001873 caudate nucleus http://purl.obolibrary.org/obo/UBERON_0000477 anatomical cluster Subcortical nucleus of telecephalic origin consisting of an elongated gray mass lying lateral to and bordering the lateral ventricle. It is divided into a head, body and tail in some species. http://purl.obolibrary.org/obo/UBERON_0001874 putamen http://purl.obolibrary.org/obo/UBERON_0000477 anatomical cluster Subcortical nucleus of telencephalic , which together with the caudate nucleus, forms the striatum. The putamen lies lateral to the internal capsule and medial to the external medullary lamina, and is separated from the caudate nucleus by the fibers of the internal capsule for most of its length, except at its anterior portion. http://purl.obolibrary.org/obo/UBERON_0001913 milk http://purl.obolibrary.org/obo/UBERON_0006314 bodily fluid An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. http://purl.obolibrary.org/obo/UBERON_0001968 semen http://purl.obolibrary.org/obo/UBERON_0000463 organism substance Organism substance that is composed of sperm cells suspended in seminal fluid. http://purl.obolibrary.org/obo/UBERON_0001970 bile http://purl.obolibrary.org/obo/UBERON_0006314 bodily fluid vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium. http://purl.obolibrary.org/obo/UBERON_0001988 feces http://purl.obolibrary.org/obo/UBERON_0000463 organism substance Portion of semisolid bodily waste discharged through the anus[MW,modified] http://purl.obolibrary.org/obo/UBERON_0002032 areola http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity Subdivision of breast which consists of skin, connective tissue and smooth muscle bundle and modified sebaceous glands and which surrounds the nipple. http://purl.obolibrary.org/obo/UBERON_0002072 hypodermis http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. http://purl.obolibrary.org/obo/UBERON_0002097 skin of body http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity The organ covering the body that consists of the dermis and epidermis. http://purl.obolibrary.org/obo/UBERON_0002199 integument http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity The dermis, epidermis and hypodermis. http://purl.obolibrary.org/obo/UBERON_0002409 pericardial fluid http://purl.obolibrary.org/obo/UBERON_0006314 bodily fluid Transudate contained in the pericardial cavity.[FMA] http://purl.obolibrary.org/obo/UBERON_0002415 tail http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail http://purl.obolibrary.org/obo/UBERON_0002469 esophagus mucosa http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity A mucosa that is part of a esophagus [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0002812 left cerebral hemisphere http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity A cerebral hemisphere that is in the left side of a brain. http://purl.obolibrary.org/obo/UBERON_0002813 right cerebral hemisphere http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity A cerebral hemisphere that is in the right side of a brain. http://purl.obolibrary.org/obo/UBERON_0003688 omentum http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity A fold of peritoneum originating at the stomach and supporting the viscera. http://purl.obolibrary.org/obo/UBERON_0004648 esophagus muscularis mucosa http://purl.obolibrary.org/obo/UBERON_0000479 tissue A muscularis mucosa that is part of a esophagus. http://purl.obolibrary.org/obo/UBERON_0005022 mucosa of nasopharynx http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity A mucosa that is part of a nasopharynx [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0005023 mucosa of oropharynx http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity A mucosa that is part of a oropharynx [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0005921 middle nasal concha http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity The medial surface of the labyrinth of ethmoid consists of a thin lamella, which descends from the under surface of the cribriform plate, and ends below in a free, convoluted margin, the middle nasal concha. It is rough, and marked above by numerous grooves, directed nearly vertically downward from the cribriform plate; they lodge branches of the olfactory nerves, which are distributed to the mucous membrane covering the superior nasal concha. http://purl.obolibrary.org/obo/UBERON_0006314 bodily fluid http://purl.obolibrary.org/obo/UBERON_0000463 organism substance Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. http://purl.obolibrary.org/obo/UBERON_0006538 respiratory system fluid/secretion http://purl.obolibrary.org/obo/UBERON_0000463 organism substance A portion of organism substance that secreted_by a respiratory system. http://purl.obolibrary.org/obo/UBERON_0006618 atrium auricular region http://purl.obolibrary.org/obo/UBERON_0000481 multi-tissue structure A small conical pouch projections located on the upper anterior portion of each atrium of the heart. http://purl.obolibrary.org/obo/UBERON_0007106 chorionic villus http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity One of the minute vascular projections of the fetal chorion that combines with maternal uterine tissue to form the placenta. http://purl.obolibrary.org/obo/UBERON_0007109 meconium http://purl.obolibrary.org/obo/UBERON_0001988 feces A dark greenish mass that accumulates in the bowel during fetal life and is discharged shortly after birth. http://purl.obolibrary.org/obo/UBERON_0007311 sputum http://purl.obolibrary.org/obo/UBERON_0006538 respiratory system fluid/secretion Matter ejected from the lungs, bronchi, and trachea, through the mouth. http://purl.obolibrary.org/obo/UBERON_0007610 tibial artery http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity The anterior and posterior arteries created at the bifurcation of the popliteal artery. The anterior tibial artery begins at the lower border of the popliteus muscle and lies along the tibia at the distal part of the leg to surface superficially anterior to the ankle joint. Its branches are distributed throughout the leg, ankle, and pes. The posterior tibial artery begins at the lower border of the popliteus muscle, lies behind the tibia in the lower part of its course, and is found situated between the medial malleolus and the medial process of the calcaneal tuberosity. Its branches are distributed throughout the leg and foot. http://purl.obolibrary.org/obo/UBERON_0010414 omental fat pad http://purl.obolibrary.org/obo/UBERON_0001013 adipose tissue encapsulated adipose tissue associated with the fold of peritoneal tissue that extends from the stomach to the posterior abdominal wall after associating with the transverse colon http://purl.obolibrary.org/obo/UBERON_0012168 umbilical cord blood http://purl.obolibrary.org/obo/UBERON_0000178 blood blood that remains in the placenta and in the attached umbilical cord after childbirth[WP]. http://purl.obolibrary.org/obo/UBERON_0013755 arterial blood http://purl.obolibrary.org/obo/UBERON_0000178 blood A blood that is part of a artery. http://purl.obolibrary.org/obo/UBERON_0013756 venous blood http://purl.obolibrary.org/obo/UBERON_0000178 blood A blood that is part of a vein. http://purl.obolibrary.org/obo/UBERON_0013757 capillary blood http://purl.obolibrary.org/obo/UBERON_0000178 blood A blood that is part of a capillary. http://purl.obolibrary.org/obo/UBERON_3000016 anterior nasal wall http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity Paired, vertical, and relatively straight plates that form the anterior limit of the nasal capsule. http://purl.obolibrary.org/obo/APOLLO_SV_00000033 counting http://purl.obolibrary.org/obo/OBI_0000011 planned process The planned process of finding the number of elements in a finite set of objects. http://purl.obolibrary.org/obo/CHEBI_15377 water http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms. http://purl.obolibrary.org/obo/CHEBI_15422 ATP http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity An adenosine 5'-phosphate in which the 5'-phosphate is a triphosphate group. It is involved in the transportation of chemical energy during metabolic pathways. http://purl.obolibrary.org/obo/CHEBI_53526 tritiated thymidine http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity Thymidine linked to the radioisotope tritium. Used to label DNA in the study of cellular and viral DNA synthesis. http://purl.obolibrary.org/obo/SO_0001410 experimental_feature http://purl.obolibrary.org/obo/SO_0000001 region A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. http://purl.obolibrary.org/obo/OMRSE_00000012 health care provider role http://purl.obolibrary.org/obo/BFO_0000023 role A human health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism. http://purl.obolibrary.org/obo/OBI_0000969 dose specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity a directive information entity that describes the dose that will be administered to a target http://purl.obolibrary.org/obo/OBI_0001509 Edman degradation assay measuring MHC ligand processing and presentation http://purl.obolibrary.org/obo/OBI_1110125 assay measuring MHC ligand processing and presentation A MHC ligand processing and presentation assay that uses Edman degradation to identify the eluted ligands http://purl.obolibrary.org/obo/OBI_0002565 adapter-sequence trimming http://purl.obolibrary.org/obo/OBI_0002585 sequence trimming A data transformation in which adapter sequences at the end of a molecular sequence are cut (removed). http://purl.obolibrary.org/obo/GO_0000785 chromatin http://purl.obolibrary.org/obo/GO_0005575 cellular_component The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. http://purl.obolibrary.org/obo/GO_0001046 core promoter sequence-specific DNA binding http://purl.obolibrary.org/obo/GO_0043565 sequence-specific DNA binding Interacting selectively and non-covalently with a sequence of DNA that is part of a core promoter region. The core promoter is composed of the transcription start site and binding sites for the RNA polymerase and the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon. http://purl.obolibrary.org/obo/GO_0001172 transcription, RNA-templated http://purl.obolibrary.org/obo/GO_0009987 cellular process The cellular synthesis of RNA on a template of RNA. http://purl.obolibrary.org/obo/GO_0001508 action potential http://purl.obolibrary.org/obo/GO_0008150 biological_process A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities. http://purl.obolibrary.org/obo/GO_0001788 antibody-dependent cellular cytotoxicity http://purl.obolibrary.org/obo/GO_0008150 biological_process Cytolysis of target cells by natural killer cells, eosinophils, neutrophils, monocytes, or macrophages following engagement of antibodies bound to the target cells by Fc receptors on the effector cells. http://purl.obolibrary.org/obo/GO_0001806 type IV hypersensitivity http://purl.obolibrary.org/obo/GO_0002524 hypersensitivity An inflammatory response driven by T cell recognition of processed soluble or cell-associated antigens leading to cytokine release and leukocyte activation. http://purl.obolibrary.org/obo/GO_0001816 cytokine production http://purl.obolibrary.org/obo/GO_0008150 biological_process The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0001906 cell killing http://purl.obolibrary.org/obo/GO_0008150 biological_process Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions. http://purl.obolibrary.org/obo/GO_0001913 T cell mediated cytotoxicity http://purl.obolibrary.org/obo/GO_0001906 cell killing The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors. http://purl.obolibrary.org/obo/GO_0002250 adaptive immune response http://purl.obolibrary.org/obo/GO_0006955 immune response An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory). http://purl.obolibrary.org/obo/GO_0002367 cytokine production involved in immune response http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus contributing to an immune response, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0002390 platelet activating factor production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The synthesis or release of platelet activating factor following a stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0002507 tolerance induction http://purl.obolibrary.org/obo/GO_0008150 biological_process A process that directly activates any of the steps required for tolerance, a physiologic state in which the immune system does not react destructively against the components of an organism that harbors it or against antigens that are introduced to it. http://purl.obolibrary.org/obo/GO_0002514 B cell tolerance induction http://purl.obolibrary.org/obo/GO_0002507 tolerance induction A process involving any mechanism for tolerance induction in B cells. http://purl.obolibrary.org/obo/GO_0002517 T cell tolerance induction http://purl.obolibrary.org/obo/GO_0002507 tolerance induction A process involving any mechanism for tolerance induction in T cells. http://purl.obolibrary.org/obo/GO_0002524 hypersensitivity http://purl.obolibrary.org/obo/GO_0008150 biological_process An inflammatory response to an exogenous environmental antigen or an endogenous antigen initiated by the adaptive immune system. http://purl.obolibrary.org/obo/GO_0002534 cytokine production involved in inflammatory response http://purl.obolibrary.org/obo/GO_0001816 cytokine production The synthesis or release of a cytokine following a inflammatory stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0003674 molecular_function http://purl.obolibrary.org/obo/BFO_0000015 process A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. http://purl.obolibrary.org/obo/GO_0003823 antigen binding http://purl.obolibrary.org/obo/GO_0003674 molecular_function Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. http://purl.obolibrary.org/obo/GO_0003824 catalytic activity http://purl.obolibrary.org/obo/GO_0003674 molecular_function Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. http://purl.obolibrary.org/obo/GO_0003964 RNA-directed DNA polymerase activity http://purl.obolibrary.org/obo/GO_0003824 catalytic activity Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time. http://purl.obolibrary.org/obo/GO_0003990 acetylcholinesterase activity http://purl.obolibrary.org/obo/GO_0003824 catalytic activity Catalysis of the reaction: acetylcholine + H2O = choline + acetate. http://purl.obolibrary.org/obo/GO_0004364 glutathione transferase activity http://purl.obolibrary.org/obo/GO_0003824 catalytic activity Catalysis of the reaction: R-X + glutathione = H-X + R-S-glutathione. R may be an aliphatic, aromatic or heterocyclic group; X may be a sulfate, nitrile or halide group. http://purl.obolibrary.org/obo/GO_0005694 chromosome http://purl.obolibrary.org/obo/GO_0005575 cellular_component A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. http://purl.obolibrary.org/obo/GO_0005739 mitochondrion http://purl.obolibrary.org/obo/GO_0043227 membrane-bounded organelle A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. http://purl.obolibrary.org/obo/GO_0006260 DNA replication http://purl.obolibrary.org/obo/GO_0008150 biological_process The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. http://purl.obolibrary.org/obo/GO_0006909 phagocytosis http://purl.obolibrary.org/obo/GO_0008150 biological_process A vesicle-mediated transport process that results in the engulfment of external particulate material by phagocytes and their delivery to the lysosome. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles. http://purl.obolibrary.org/obo/GO_0006955 immune response http://purl.obolibrary.org/obo/GO_0050896 response to stimulus Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. http://purl.obolibrary.org/obo/GO_0006974 cellular response to DNA damage stimulus http://purl.obolibrary.org/obo/GO_0050896 response to stimulus Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism. http://purl.obolibrary.org/obo/GO_0007049 cell cycle http://purl.obolibrary.org/obo/GO_0008150 biological_process The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. http://purl.obolibrary.org/obo/GO_0008150 biological_process http://purl.obolibrary.org/obo/BFO_0000015 process A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. http://purl.obolibrary.org/obo/GO_0008283 cell population proliferation http://purl.obolibrary.org/obo/GO_0008150 biological_process The multiplication or reproduction of cells, resulting in the expansion of a cell population. http://purl.obolibrary.org/obo/GO_0009987 cellular process http://purl.obolibrary.org/obo/GO_0008150 biological_process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. http://purl.obolibrary.org/obo/GO_0010467 gene expression http://purl.obolibrary.org/obo/GO_0008150 biological_process The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. http://purl.obolibrary.org/obo/GO_0016064 immunoglobulin mediated immune response http://purl.obolibrary.org/obo/GO_0008150 biological_process An immune response mediated by immunoglobulins, whether cell-bound or in solution. http://purl.obolibrary.org/obo/GO_0016570 histone modification http://purl.obolibrary.org/obo/GO_0008150 biological_process The covalent alteration of one or more amino acid residues within a histone protein. http://purl.obolibrary.org/obo/GO_0019882 antigen processing and presentation http://purl.obolibrary.org/obo/GO_0008150 biological_process The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. http://purl.obolibrary.org/obo/GO_0030097 hemopoiesis http://purl.obolibrary.org/obo/GO_0008150 biological_process The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates. http://purl.obolibrary.org/obo/GO_0034061 DNA polymerase activity http://purl.obolibrary.org/obo/GO_0003824 catalytic activity Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group. http://purl.obolibrary.org/obo/GO_0042098 T cell proliferation http://purl.obolibrary.org/obo/GO_0008283 cell population proliferation The expansion of a T cell population by cell division. Follows T cell activation. http://purl.obolibrary.org/obo/GO_0042110 T cell activation http://purl.obolibrary.org/obo/GO_0008150 biological_process The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. http://purl.obolibrary.org/obo/GO_0042575 DNA polymerase complex http://purl.obolibrary.org/obo/GO_0032991 protein-containing complex A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA. http://purl.obolibrary.org/obo/GO_0048869 cellular developmental process http://purl.obolibrary.org/obo/GO_0008150 biological_process A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. http://purl.obolibrary.org/obo/GO_0051276 chromosome organization http://purl.obolibrary.org/obo/GO_0008150 biological_process A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. http://purl.obolibrary.org/obo/GO_0052689 carboxylic ester hydrolase activity http://purl.obolibrary.org/obo/GO_0003824 catalytic activity Catalysis of the hydrolysis of a carboxylic ester bond. http://purl.obolibrary.org/obo/GO_0019814 immunoglobulin complex http://purl.obolibrary.org/obo/GO_0032991 protein-containing complex A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. http://purl.obolibrary.org/obo/GO_0019815 B cell receptor complex http://purl.obolibrary.org/obo/OBI_1110022 adaptive immune receptor An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. http://purl.obolibrary.org/obo/GO_0030041 actin filament polymerization http://purl.obolibrary.org/obo/GO_0008150 biological_process Assembly of actin filaments by the addition of actin monomers to a filament. http://purl.obolibrary.org/obo/GO_0032601 connective tissue growth factor production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of connective tissue growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032602 chemokine production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032604 granulocyte macrophage colony-stimulating factor production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of granulocyte macrophage colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032605 hepatocyte growth factor production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of hepatocyte growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032606 type I interferon production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of type I interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families. http://purl.obolibrary.org/obo/GO_0032607 interferon-alpha production http://purl.obolibrary.org/obo/GO_0032606 type I interferon production The appearance of interferon-alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032608 interferon-beta production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interferon-beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032609 interferon-gamma production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon. http://purl.obolibrary.org/obo/GO_0032610 interleukin-1 alpha production http://purl.obolibrary.org/obo/GO_0032612 interleukin-1 production The appearance of interleukin-1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032611 interleukin-1 beta production http://purl.obolibrary.org/obo/GO_0032612 interleukin-1 production The appearance of interleukin-1 beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032612 interleukin-1 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032613 interleukin-10 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032614 interleukin-11 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-11 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032615 interleukin-12 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-12 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032616 interleukin-13 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-13 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032617 interleukin-14 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-14 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032618 interleukin-15 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-15 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032619 interleukin-16 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-16 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032620 interleukin-17 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of any member of the interleukin-17 family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032621 interleukin-18 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-18 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032622 interleukin-19 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-19 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032623 interleukin-2 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032624 interleukin-20 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-20 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032625 interleukin-21 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-21 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032626 interleukin-22 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-22 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032627 interleukin-23 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-23 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032628 interleukin-24 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-24 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032629 interleukin-25 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-25 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032630 interleukin-26 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-26 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032631 interleukin-27 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-27 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032632 interleukin-3 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032633 interleukin-4 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032634 interleukin-5 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032635 interleukin-6 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032636 interleukin-7 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-7 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032637 interleukin-8 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032638 interleukin-9 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032639 TRAIL production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of TRAIL due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032905 transforming growth factor beta1 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of transforming growth factor-beta1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032906 transforming growth factor beta2 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of transforming growth factor-beta2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032907 transforming growth factor beta3 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of transforming growth factor-beta3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0042611 MHC protein complex http://purl.obolibrary.org/obo/GO_0032991 protein-containing complex A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen. http://purl.obolibrary.org/obo/GO_0043227 membrane-bounded organelle http://purl.obolibrary.org/obo/GO_0005575 cellular_component Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. http://purl.obolibrary.org/obo/GO_0071604 transforming growth factor beta production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of any member of the transforming growth factor-beta family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Transforming growth factor-beta family members include TGF-B1, TGF-B2, and TGF-B3. http://purl.obolibrary.org/obo/GO_0071706 tumor necrosis factor superfamily cytokine production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of any member of the TNF superfamily due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0034343 type III interferon production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of type III interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon lambda is the only member of the type III interferon found so far. http://purl.obolibrary.org/obo/GO_0035393 chemokine (C-X-C motif) ligand 9 production http://purl.obolibrary.org/obo/GO_0032602 chemokine production The appearance of chemokine (C-X-C motif) ligand 9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0035397 helper T cell enhancement of adaptive immune response http://purl.obolibrary.org/obo/GO_0002250 adaptive immune response Positive regulation of an adaptive immune response mediated via cytokine production by helper T cell. http://purl.obolibrary.org/obo/GO_0035398 helper T cell enhancement of T cell mediated immune response http://purl.obolibrary.org/obo/GO_0035397 helper T cell enhancement of adaptive immune response Positive regulation of a T cell mediated immune response mediated via cytokine production by a helper T cell. http://purl.obolibrary.org/obo/GO_0035399 helper T cell enhancement of B cell mediated immune response http://purl.obolibrary.org/obo/GO_0035397 helper T cell enhancement of adaptive immune response Positive regulation of a B cell mediated immune response mediated via cytokine production by a helper T cell. http://purl.obolibrary.org/obo/GO_0035746 granzyme A production http://purl.obolibrary.org/obo/GO_0008150 biological_process The appearance of granzyme A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0035944 perforin production http://purl.obolibrary.org/obo/GO_0008150 biological_process The appearance of a perforin protein due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0036262 granulysin production http://purl.obolibrary.org/obo/GO_0008150 biological_process The appearance of granulysin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0036392 chemokine (C-C motif) ligand 20 production http://purl.obolibrary.org/obo/GO_0032602 chemokine production The appearance of chemokine (C-C motif) ligand 20 (CCL20) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0040030 regulation of molecular function, epigenetic http://purl.obolibrary.org/obo/GO_0008150 biological_process Any heritable epigenetic process that modulates the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya. http://purl.obolibrary.org/obo/GO_0042101 T cell receptor complex http://purl.obolibrary.org/obo/OBI_1110022 adaptive immune receptor A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains. http://purl.obolibrary.org/obo/GO_0042605 peptide antigen binding http://purl.obolibrary.org/obo/GO_0003823 antigen binding Interacting selectively and non-covalently with an antigen peptide. http://purl.obolibrary.org/obo/GO_0043316 cytotoxic T cell degranulation http://purl.obolibrary.org/obo/GO_0001906 cell killing The regulated exocytosis of secretory granules containing preformed mediators such as perforin and granzymes by a cytotoxic T cell. http://purl.obolibrary.org/obo/GO_0044030 regulation of DNA methylation http://purl.obolibrary.org/obo/GO_0040030 regulation of molecular function, epigenetic Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. http://purl.obolibrary.org/obo/GO_0044807 macrophage migration inhibitory factor production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of macrophage migration inhibitory factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0044808 Oncostatin M production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of Oncostatin M due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0044809 chemokine (C-C motif) ligand 17 production http://purl.obolibrary.org/obo/GO_0032602 chemokine production The appearance of chemokine (C-C motif) ligand 17 (CCL17) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0097087 interleukin-17A production http://purl.obolibrary.org/obo/GO_0032620 interleukin-17 production The appearance of interleukin-17A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0097088 interleukin-17F production http://purl.obolibrary.org/obo/GO_0032620 interleukin-17 production The appearance of interleukin-17F due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0097278 complement-dependent cytotoxicity http://purl.obolibrary.org/obo/GO_0001906 cell killing Cell killing caused by the membrane attack complex formed following complement activation. http://purl.obolibrary.org/obo/GO_0097280 histamine secretion mediated by immunoglobulin http://purl.obolibrary.org/obo/GO_0006955 immune response Histamine release triggered by the binding of an antigen to an immunoglobulin bound to the cell surface. http://purl.obolibrary.org/obo/GO_0097281 immune complex formation http://purl.obolibrary.org/obo/GO_0016064 immunoglobulin mediated immune response The process that gives rise to an immune complex. Immune complexes are clusters of antibodies bound to antigen, to which complement may also be fixed, and which may precipitate or remain in solution. Examples are the clumping of cells such as bacteria or red blood cells in the presence of an antibody, precipitation of a toxin after an antibody binds to it, and clumping of viral particles as a result of antibody binding to the virus. http://purl.obolibrary.org/obo/GO_0097282 immunoglobulin-mediated neutralization http://purl.obolibrary.org/obo/GO_0016064 immunoglobulin mediated immune response The inhibition of an antigen's biological effects by antibody binding to it. An example is neutralization of diphtheria toxin by preventing its entry into human cells via the binding of antibody specific for diphtheria toxin. http://purl.obolibrary.org/obo/GO_0097388 chemokine (C-C motif) ligand 19 production http://purl.obolibrary.org/obo/GO_0032602 chemokine production The appearance of chemokine (C-C motif) ligand 19 (CCL19) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0097389 chemokine (C-C motif) ligand 21 production http://purl.obolibrary.org/obo/GO_0032602 chemokine production The appearance of chemokine (C-C motif) ligand 21 (CCL21) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0097390 chemokine (C-X-C motif) ligand 12 production http://purl.obolibrary.org/obo/GO_0032602 chemokine production The appearance of chemokine (C-X-C motif) ligand 12 (CXCL12) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0097391 chemokine (C-X-C motif) ligand 13 production http://purl.obolibrary.org/obo/GO_0032602 chemokine production The appearance of chemokine (C-X-C motif) ligand 13 (CXCL13) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0097392 chemokine (C-X-C motif) ligand 16 production http://purl.obolibrary.org/obo/GO_0032602 chemokine production The appearance of chemokine (C-X-C motif) ligand 16 (CXCL16) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/OBI_0002145 antigen specific antibodies assay http://purl.obolibrary.org/obo/OBI_0000443 analyte assay An analyte assay that measures the presence or amount of antibodies to a specified antigen. http://purl.obolibrary.org/obo/ONE_0003001 food-based dietary guideline http://purl.obolibrary.org/obo/IAO_0000311 publication A publication that provides science-based dietary advice to promote healthy eating of the general public. http://purl.obolibrary.org/obo/ONE_0003002 qualitative food-based dietary guideline http://purl.obolibrary.org/obo/ONE_0003001 food-based dietary guideline A food-based dietary guideline that provides qualitative dietary advice. http://purl.obolibrary.org/obo/ONE_0003003 quantitative food-based dietary guideline http://purl.obolibrary.org/obo/ONE_0003001 food-based dietary guideline A food-based dietary guideline that provides quantitative dietary advice. http://purl.obolibrary.org/obo/ONE_0003004 food-based dietary guideline for infants http://purl.obolibrary.org/obo/ONE_0003001 food-based dietary guideline A food-based dietary guideline that provides a guide about breastfeeding, baby food and nutrition. http://purl.obolibrary.org/obo/ONE_0003005 food-based dietary guideline for children http://purl.obolibrary.org/obo/ONE_0003001 food-based dietary guideline A food-based dietary guideline that provides dietary advice for children. http://purl.obolibrary.org/obo/ONE_0003006 food-based dietary guideline for adolescents http://purl.obolibrary.org/obo/ONE_0003001 food-based dietary guideline A food-based dietary guideline that provides dietary advice for adolescents. http://purl.obolibrary.org/obo/ONE_0003008 food-based dietary guideline for elderly people http://purl.obolibrary.org/obo/ONE_0003001 food-based dietary guideline A food-based dietary guideline that provides dietary advice for elderly people. http://purl.obolibrary.org/obo/ONE_0003010 food-based dietary guideline regarding food diversity http://purl.obolibrary.org/obo/ONE_0003001 food-based dietary guideline A food-based dietary guideline that provides dietary advice regarding food diversity. http://purl.obolibrary.org/obo/GO_0008228 opsonization http://purl.obolibrary.org/obo/GO_0006909 phagocytosis The process in which a microorganism (or other particulate material) is rendered more susceptible to phagocytosis by coating with an opsonin, a blood serum protein such as a complement component or antibody. http://purl.obolibrary.org/obo/GO_0010573 vascular endothelial growth factor production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of vascular endothelial growth factor production due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0019904 protein domain specific binding http://purl.obolibrary.org/obo/OBI_0001588 binding Interacting selectively and non-covalently with a specific domain of a protein. http://purl.obolibrary.org/obo/GO_0043565 sequence-specific DNA binding http://purl.obolibrary.org/obo/OBI_0001588 binding Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. http://purl.obolibrary.org/obo/GO_0070358 actin polymerization-dependent cell motility http://purl.obolibrary.org/obo/GO_0008150 biological_process A process involved in the controlled movement of a bacterial cell powered by the continuous polymerization of actin at one pole of the cell. http://purl.obolibrary.org/obo/GO_0071605 monocyte chemotactic protein-1 production http://purl.obolibrary.org/obo/GO_0032602 chemokine production The appearance of monocyte chemotactic protein-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0071606 chemokine (C-C motif) ligand 4 production http://purl.obolibrary.org/obo/GO_0032602 chemokine production The appearance of chemokine (C-C motif) ligand 4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0071607 macrophage inflammatory protein-1 gamma production http://purl.obolibrary.org/obo/GO_0032602 chemokine production The appearance of macrophage inflammatory protein-1 gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0071608 macrophage inflammatory protein-1 alpha production http://purl.obolibrary.org/obo/GO_0032602 chemokine production The appearance of macrophage inflammatory protein 1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0071609 chemokine (C-C motif) ligand 5 production http://purl.obolibrary.org/obo/GO_0032602 chemokine production The appearance of chemokine (C-C motif) ligand 5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0071610 chemokine (C-C motif) ligand 1 production http://purl.obolibrary.org/obo/GO_0032602 chemokine production The appearance of chemokine (C-C motif) ligand 1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0071611 granulocyte colony-stimulating factor production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of granulocyte colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0071612 IP-10 production http://purl.obolibrary.org/obo/GO_0032602 chemokine production The appearance of IP-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0071613 granzyme B production http://purl.obolibrary.org/obo/GO_0008150 biological_process The appearance of granzyme B due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0071924 chemokine (C-C motif) ligand 22 production http://purl.obolibrary.org/obo/GO_0032602 chemokine production The appearance of chemokine (C-C motif) ligand 22 (CCL22) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0072535 tumor necrosis factor (ligand) superfamily member 11 production http://purl.obolibrary.org/obo/GO_0071706 tumor necrosis factor superfamily cytokine production The appearance of tumor necrosis factor superfamily member 11 (TNFSF11; RANKL) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/OBI_0002650 biopsy http://purl.obolibrary.org/obo/OBI_0600005 collecting specimen from organism A specimen collection that obtains a sample of tissue or cell from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive. http://purl.obolibrary.org/obo/OBI_0002653 ultrasound-guided needle biopsy http://purl.obolibrary.org/obo/OBI_0002651 image guided biopsy A needle biopsy guided by ultrasound visualization. http://purl.obolibrary.org/obo/OBI_0002654 needle biopsy http://purl.obolibrary.org/obo/OBI_0002650 biopsy A biopsy that uses a hollow needle to extract cells. http://purl.obolibrary.org/obo/OBI_0002662 bone marrow biopsy http://purl.obolibrary.org/obo/OBI_0002650 biopsy A biopsy where a small amount of bone and a small amount of fluid and bone marrow are collected. http://purl.obolibrary.org/obo/OBI_0002679 vacuum-assisted biopsy needle http://purl.obolibrary.org/obo/OBI_0000436 needle A core biopsy needle integrated with a vacuum system which facilitates the collection of specimen material. http://purl.obolibrary.org/obo/OBI_0002746 induced sputum specimen http://purl.obolibrary.org/obo/OBI_0002508 sputum specimen A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution. http://purl.obolibrary.org/obo/OBI_0002747 passage process http://purl.obolibrary.org/obo/OBI_0000094 material processing A material processing that consists of first growing an organism in an environmental system and then removing the organism to be grown in another environmental system, a process which may be repeated with the objective of altering the organism or increasing its number. http://purl.obolibrary.org/obo/OBI_0002748 passage history record http://purl.obolibrary.org/obo/IAO_0000027 data item A data item that is about the sequence of environmental systems in each of which is grown an organism in a passage process. http://purl.obolibrary.org/obo/OBI_0002754 cDNA library http://purl.obolibrary.org/obo/OBI_0000047 processed material A collection of DNA molecules with sequences complementary to a specified set of mRNA molecules and commonly developed by enzymatic reverse transcription. http://purl.obolibrary.org/obo/OBI_0002756 ordinal value specification http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification A categorical value specification in which the available categories were created with an explicit order. http://purl.obolibrary.org/obo/OBI_0002760 metatranscriptome sequencing assay http://purl.obolibrary.org/obo/OBI_0001271 RNA-seq assay An RNA-seq assay that determines the RNA sequence of microbial transcripts from a microbioal community of mixed species from a given microbiome. http://purl.obolibrary.org/obo/OBI_0002766 cytokine assay http://purl.obolibrary.org/obo/OBI_0000443 analyte assay An analyte assay to study presence, concentration, or amount of cytokines. http://purl.obolibrary.org/obo/OBI_0002767 amplicon sequencing assay http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced. http://purl.obolibrary.org/obo/OBI_0002768 whole virome sequencing assay http://purl.obolibrary.org/obo/OBI_0002623 whole metagenome sequencing assay A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample. http://purl.obolibrary.org/obo/OBI_0002769 karyotype information http://purl.obolibrary.org/obo/OBI_0001404 genetic characteristics information A genetic characteristics information that is about the number and appearance of chromosomes in the nucleus of an eukaryotic cell. http://purl.obolibrary.org/obo/OBI_0002770 partial karyotype information http://purl.obolibrary.org/obo/OBI_0002769 karyotype information A karyotype information that is about the structural variation of partial genome rather than whole genome. http://purl.obolibrary.org/obo/OBI_0002771 full karyotype information http://purl.obolibrary.org/obo/OBI_0002769 karyotype information A karyotype information that is about the structural variation of the whole genome. http://purl.obolibrary.org/obo/OBI_0002772 presence or over-threshold value specification http://purl.obolibrary.org/obo/OBI_0002756 ordinal value specification An ordinal value specification that indicates that either a) an analyte or mesaurand is present in an evaluant, or b) that the amount of analyte/measurand detected is over some predetermined threshold. http://purl.obolibrary.org/obo/OBI_0002774 platelet-poor plasma specimen http://purl.obolibrary.org/obo/OBI_0100016 blood plasma specimen A blood plasma specimen that is the output of some platelet-poor plasma preparation and is the portion of plasma that contains fewer than 10,000 platelets per microliter. http://purl.obolibrary.org/obo/OBI_0002775 platelet-poor plasma preparation process http://purl.obolibrary.org/obo/OBI_0600014 material component separation A material component separation process in which (1) whole blood is first centrifuged to separate red blood cells from blood plasma, which forms the supernatant, and (2) the blood plasma is then centrifuged to separate platelets from the plasm. http://purl.obolibrary.org/obo/OBI_2000000 uterine cervix specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from some uterine cervix http://purl.obolibrary.org/obo/OBI_2000001 urethra specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from some urethra http://purl.obolibrary.org/obo/OBI_2000002 cervical mucus specimen http://purl.obolibrary.org/obo/OBI_2000009 bodily fluid specimen A specimen that is derived from some cervical mucus http://purl.obolibrary.org/obo/OBI_2000003 throat specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from some throat http://purl.obolibrary.org/obo/OBI_2000004 eye specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from some eye http://purl.obolibrary.org/obo/OBI_2000005 respiratory system specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from some respiratory system http://purl.obolibrary.org/obo/OBI_2000006 upper respiratory tract specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from some upper respiratory tract http://purl.obolibrary.org/obo/OBI_2000007 nasopharynx specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from some nasopharynx http://purl.obolibrary.org/obo/OBI_2000008 semen specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from some semen http://purl.obolibrary.org/obo/OBI_2000009 bodily fluid specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from some bodily fluid http://purl.obolibrary.org/obo/OBI_2000010 chorionic villus specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from some chorionic villus http://purl.obolibrary.org/obo/OBI_2000011 meconium specimen http://purl.obolibrary.org/obo/OBI_0002503 feces specimen A specimen that is derived from some meconium http://purl.obolibrary.org/obo/OBI_2000012 umbilical cord blood specimen http://purl.obolibrary.org/obo/OBI_2000009 bodily fluid specimen A specimen that is derived from some umbilical cord blood http://purl.obolibrary.org/obo/OBI_2000013 arterial blood specimen http://purl.obolibrary.org/obo/OBI_2000009 bodily fluid specimen A specimen that is derived from some arterial blood http://purl.obolibrary.org/obo/OBI_2000014 venous blood specimen http://purl.obolibrary.org/obo/OBI_2000009 bodily fluid specimen A specimen that is derived from some venous blood http://purl.obolibrary.org/obo/OBI_2000015 capillary blood specimen http://purl.obolibrary.org/obo/OBI_2000009 bodily fluid specimen A specimen that is derived from some capillary blood http://purl.obolibrary.org/obo/OBI_2000016 erythrocyte specimen http://purl.obolibrary.org/obo/OBI_0002599 swab specimen A specimen that is derived from some erythrocytes http://purl.obolibrary.org/obo/OBI_2000017 reticulocyte specimen http://purl.obolibrary.org/obo/OBI_0002599 swab specimen A specimen that is derived from some reticulocytes http://purl.obolibrary.org/obo/OBI_2000018 leukocyte specimen http://purl.obolibrary.org/obo/OBI_0002599 swab specimen A specimen that is derived from some leukocytes http://purl.obolibrary.org/obo/IDO_0000450 pathogenic disposition http://purl.obolibrary.org/obo/BFO_0000016 disposition A disposition to initiate processes that result in a disorder. http://purl.obolibrary.org/obo/IDO_0000528 pathogen http://purl.obolibrary.org/obo/BFO_0000040 material entity A material entity with a pathogenic disposition. http://purl.obolibrary.org/obo/OGMS_0000073 diagnosis http://purl.obolibrary.org/obo/IAO_0000027 data item The representation of a conclusion of a diagnostic process. http://purl.obolibrary.org/obo/OBI_0002444 measurand role http://purl.obolibrary.org/obo/BFO_0000023 role A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role. http://purl.obolibrary.org/obo/OBI_0002445 transcription start site mapping by primer extension assay http://purl.obolibrary.org/obo/OBI_0000424 transcription profiling assay A transcription profiling assay in which the transcription start site for a gene is determined by identifying the 5' end of mRNA. A radio-labeled primer is annealed to a complementary mRNA sequence near the 3' end, then cDNA is synthesized until the 5' end is reached. http://purl.obolibrary.org/obo/OBI_0002446 proteomic profiling design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which proteins in a sample are detected, quantified or otherwise analysed. http://purl.obolibrary.org/obo/OBI_0002449 footprinting assay measuring binding of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0001703 assay measuring qualitiative binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a footprinting assay. http://purl.obolibrary.org/obo/OBI_0002450 hydroxyl-radical footprinting assay measuring binding of a B cell epitope:antibody complex http://purl.obolibrary.org/obo/OBI_0002449 footprinting assay measuring binding of a B cell epitope:antibody complex A footprinting assay that uses hydroxyl-radical footprinting to measure B cell epitope qualitative binding to antibody. http://purl.obolibrary.org/obo/OBI_0002451 ELISA measuring epitope specific interferon-alpha production by T cells http://purl.obolibrary.org/obo/OBI_0002452 biological activity assay measuring epitope specific interferon-alpha production by T cells An assay of epitope specific interferon-alpha production by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0002452 biological activity assay measuring epitope specific interferon-alpha production by T cells http://purl.obolibrary.org/obo/OBI_1110129 biological activity assay measuring epitope specific cytokine production by T cells A T cell epitope specific cytokine production assay that detects interferon-alpha production by T cells. http://purl.obolibrary.org/obo/OBI_0002453 health status inclusion criterion http://purl.obolibrary.org/obo/OBI_0500027 inclusion criterion An inclusion criterion that defines and states one or more clinically significant bodily components, dispositions, and/or bodily processes of an entity that are inferred from relevant clinical findings or self-reported, which, if met, makes the entity suitable for a given task or participation in a given process. http://purl.obolibrary.org/obo/OBI_0002454 clinically relevant lifestyle inclusion criterion http://purl.obolibrary.org/obo/OBI_0500027 inclusion criterion An inclusion criterion that defines and states one or more clinically relevant planned processes that a human being actively participates in , which, if met, makes the human being suitable for a given task or participation in a given process. http://purl.obolibrary.org/obo/OBI_0002455 clinically relevant exposure inclusion criterion http://purl.obolibrary.org/obo/OBI_0500027 inclusion criterion An inclusion criterion that defines and states one or more clinically relevant histories of exposure of an entity, which, if met, makes the entity suitable for a given task or participation in a given process. http://purl.obolibrary.org/obo/OBI_0002456 gravidity inclusion criterion http://purl.obolibrary.org/obo/OBI_0500027 inclusion criterion An inclusion criterion that defines and states one or more gravidity statuses of an organism, which, if met, makes the entity suitable for a given task or participation in a given process. http://purl.obolibrary.org/obo/OBI_0002590 molecular interaction identification design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that investigates the features of interaction between molecules. http://purl.obolibrary.org/obo/OBI_0002589 unsupervised machine learning http://purl.obolibrary.org/obo/OBI_0002587 machine learning A machine learning process that infers a function describing the structure of "unlabeled" data (i.e. data that has not been classified or categorized). http://purl.obolibrary.org/obo/OBI_0002492 case role in case-control study http://purl.obolibrary.org/obo/OBI_0000097 participant under investigation role A role that is borne by a case-control study design participant under investigation that is associated with the outcome mentioned in the study design. http://purl.obolibrary.org/obo/OBI_0002493 control role in case-control study http://purl.obolibrary.org/obo/OBI_0000097 participant under investigation role A role that is borne by a case-control study design participant under investigation that is not associated with the outcome mentioned in the study design. http://purl.obolibrary.org/obo/OBI_0002619 site-directed mutagenesis http://purl.obolibrary.org/obo/OBI_0001154 induced mutation An induced mutation in which a specific base change is programmed into the sequence of a synthetic primer. http://purl.obolibrary.org/obo/OBI_0002620 random mutagenesis http://purl.obolibrary.org/obo/OBI_0001154 induced mutation An induced mutation that produces a random mutation, either by introducing the organism to mutagens, or through a process such as error-prone PCR. http://purl.obolibrary.org/obo/OBI_0002622 in vitro transcription reconstitution assay http://purl.obolibrary.org/obo/OBI_0002621 reconstitution assay A reconstitution assay in which RNA synthesis is investigated using RNA polymerase II transcription systems replicated in vitro from their base components. http://purl.obolibrary.org/obo/OBI_0002624 case-control study design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that entails the creation of two types of roles, such that each participant under investigation bears one or the other. What distinguishes the two types of roles is an 'outcome', which is associated with participants that have the case role but not associated with participants that have the control role. A case-control study examines the hypothesis that the presence of the outcome in case participants is associated with an 'exposure' that is not associated with control participants. http://purl.obolibrary.org/obo/OBI_0002627 ribosomal RNA-depleted RNA extract http://purl.obolibrary.org/obo/OBI_0000880 RNA extract An extract of RNA which is produced through rRNA (ribosomal RNA) depletion (the removal of highly abundant rRNA species). http://purl.obolibrary.org/obo/IAO_0000444 publishing process http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free. http://purl.obolibrary.org/obo/IAO_0000445 document in preparation for publication http://purl.obolibrary.org/obo/IAO_0000310 document A document that is in preparation for submission to be published. http://purl.obolibrary.org/obo/IAO_0000701 descriptive data section http://purl.obolibrary.org/obo/IAO_0000314 document part A document part that lists and defines data variables, describes data characteristics (e.g. missing data information) and any assumptions and simplifications made. http://purl.obolibrary.org/obo/IAO_0000702 additional results section http://purl.obolibrary.org/obo/IAO_0000318 results section A results section that reports analyses other than main results of the study (e.g. subgroups analyses, adjusted analyses, sensitivity analyses, etc.) http://purl.obolibrary.org/obo/IAO_0000703 research participants section http://purl.obolibrary.org/obo/IAO_0000314 document part A document part that describes human subject(s) that participated in a study (e.g. inclusion & exclusion criteria, recruitment methods, reasons for non-participation, grouping and randomisation, methods of follow-up, etc.). http://purl.obolibrary.org/obo/IAO_0000704 measurement methods section http://purl.obolibrary.org/obo/IAO_0000317 methods section A methods section that describes details of data assessment methods (data measurement). http://purl.obolibrary.org/obo/IAO_0000705 research settings section http://purl.obolibrary.org/obo/IAO_0000314 document part A document part that describes the physical/social/cultural conditions around a research trial. http://purl.obolibrary.org/obo/IAO_0000706 study bias section http://purl.obolibrary.org/obo/IAO_0000631 study limitations section A study limitations section that describes systematic error introduced into sampling or testing by selecting or encouraging one outcome or answer over others. http://purl.obolibrary.org/obo/IAO_0000605 abbreviation textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity listing abbreviations and their expansions that are used in a document. http://purl.obolibrary.org/obo/IAO_0000608 author information textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. http://purl.obolibrary.org/obo/IAO_0000610 author summary textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). http://purl.obolibrary.org/obo/IAO_0000612 availability textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained. http://purl.obolibrary.org/obo/IAO_0000614 case report textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that expresses a detailed account of a portion of the medical history for a specific patient. http://purl.obolibrary.org/obo/IAO_0000617 conflict of interest textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document. http://purl.obolibrary.org/obo/IAO_0000619 consent textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that documents the consenting process used to enroll patients in a study. http://purl.obolibrary.org/obo/IAO_0000621 ethical approval textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that documents the ethical approval of some study design. http://purl.obolibrary.org/obo/IAO_0000624 funding source declaration textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity documenting the source of funding that supported some study. http://purl.obolibrary.org/obo/IAO_0000626 future directions textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity expressing ideas regarding future work relevant to work described in a document that could be done. http://purl.obolibrary.org/obo/IAO_0000628 genome announcement textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that describes the generation and public release of a novel, draft genome sequence. http://purl.obolibrary.org/obo/IAO_0000629 keyword textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity listing keywords indicating the major theme(s) of a document. http://purl.obolibrary.org/obo/IAO_0000632 study limitations textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity addressing a shortcoming or bias of a study design or execution. http://purl.obolibrary.org/obo/IAO_0000635 patients section http://purl.obolibrary.org/obo/IAO_0000314 document part A part of a document about the patients that participated in a study. http://purl.obolibrary.org/obo/IAO_0000636 patients textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity expressing information regarding the patients used in a study. http://purl.obolibrary.org/obo/IAO_0000638 pre-publication history textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information. http://purl.obolibrary.org/obo/IAO_0000640 related work textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that discusses work from other publications and expresses their relevancy to the content of a document. http://purl.obolibrary.org/obo/IAO_0000642 requirements textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that expresses the requirements necessary to use a resource, e.g. software. http://purl.obolibrary.org/obo/IAO_0000643 statistical analysis textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity documenting statistical analysis tools and techniques employed. http://purl.obolibrary.org/obo/IAO_8000001 base ontology module http://purl.obolibrary.org/obo/IAO_8000000 ontology module An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. http://purl.obolibrary.org/obo/IAO_8000003 main release ontology module http://purl.obolibrary.org/obo/IAO_8000000 ontology module An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. http://purl.obolibrary.org/obo/IAO_8000004 bridge ontology module http://purl.obolibrary.org/obo/IAO_8000000 ontology module An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. http://purl.obolibrary.org/obo/IAO_8000007 curation subset ontology module http://purl.obolibrary.org/obo/IAO_8000006 subset ontology module A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. http://purl.obolibrary.org/obo/IAO_8000008 analysis subset ontology module http://purl.obolibrary.org/obo/IAO_8000006 subset ontology module An ontology module that is intended for usage in analysis or discovery applications. http://purl.obolibrary.org/obo/IAO_8000013 reasoned ontology module http://purl.obolibrary.org/obo/IAO_8000000 ontology module An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. http://purl.obolibrary.org/obo/IAO_8000014 generated ontology module http://purl.obolibrary.org/obo/IAO_8000000 ontology module An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. http://purl.obolibrary.org/obo/IAO_8000015 template generated ontology module http://purl.obolibrary.org/obo/IAO_8000014 generated ontology module An ontology module that is automatically generated from a template specification and fillers for slots in that template. http://purl.obolibrary.org/obo/IAO_8000018 obo basic subset ontology module http://purl.obolibrary.org/obo/IAO_8000017 ontology module subsetted by expressivity A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports http://purl.obolibrary.org/obo/OBI_0002570 nCounter Mouse miRNA Expression array http://purl.obolibrary.org/obo/OBI_0001865 assay array A mouse array which is manufacutred by NanoString Technologies. Built upon color-coded molecular barcodes technology, the array profiles miRNA with increased specificity and sensitivty than microarrays. http://purl.obolibrary.org/obo/APOLLO_SV_00000522 source code repository http://purl.obolibrary.org/obo/IAO_0000310 document A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc. http://purl.obolibrary.org/obo/APOLLO_SV_00000524 compiling software http://purl.obolibrary.org/obo/APOLLO_SV_00000008 software development A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions. http://purl.obolibrary.org/obo/OBI_0002554 vagina specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from vagina. http://purl.obolibrary.org/obo/OBI_0002191 courier tracking number http://purl.obolibrary.org/obo/IAO_0000577 centrally registered identifier symbol A centrally registered identifier symbol assigned by a courier organization in order to track the delivery of an item. http://purl.obolibrary.org/obo/OBI_0002192 Leica Peloris rapid tissue processor http://purl.obolibrary.org/obo/OBI_0001064 automatic tissue processor An automatic tissue processor that is a dual retort tissue processor manufactured by the Leica company to provide fast, high quality tissue processing for histology laboratories. http://purl.obolibrary.org/obo/OBI_0002194 Microm Ergostar HM200 http://purl.obolibrary.org/obo/OBI_0400168 microtome A microtome that is manufactured by Microm and uses a vertical cutting stroke common to all rotary microtomes engaged by a horizontal sliding movement. An operating arm replaces the handwheel and is attached to both sides of the instrument for greater convenience to permit control of sectioning from the left or right. http://purl.obolibrary.org/obo/OBI_0002195 microtome blade http://purl.obolibrary.org/obo/OBI_0000968 device A device that is the part of a microtome used to slice specimens to a desired thickness. http://purl.obolibrary.org/obo/OBI_0002196 Sakura Low profile Accu-Edge microtome blade http://purl.obolibrary.org/obo/OBI_0002195 microtome blade A microtome blade that is manufactured by Feather and is disposable. The ultra-sharp blades section specimens without striations, distortion or chattering. http://purl.obolibrary.org/obo/OBI_0002197 tissue section thickness http://purl.obolibrary.org/obo/IAO_0000408 length measurement datum A length measurement datum that is the result of an assay measuring the thickness of a tissue section. http://purl.obolibrary.org/obo/OBI_0002199 reason for lack of data item http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity that provides an explanation why a data item is not provided. http://purl.obolibrary.org/obo/OBI_0002201 determination if assay will provide reliable results http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process that is used to assess whether an assay will provide reliable results based on the conditions or qualities of the inputs, devices, and other participants of the assay. http://purl.obolibrary.org/obo/OBI_0002202 GX http://purl.obolibrary.org/obo/OBI_0002200 cannot be assessed determination A cannot be assessed determination for histologic tumor grade. http://purl.obolibrary.org/obo/OBI_0002203 pTX http://purl.obolibrary.org/obo/OBI_0002200 cannot be assessed determination A cannot be assessed determination for pathologic primary tumor staging. http://purl.obolibrary.org/obo/OBI_0002204 pNX http://purl.obolibrary.org/obo/OBI_0002200 cannot be assessed determination A cannot be assessed determination of pathologic staging of lymph nodes. http://purl.obolibrary.org/obo/OBI_0002205 histologic grade according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system. http://purl.obolibrary.org/obo/OBI_0002215 histologic grade for ovarian tumor http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification A categorical value specification that is a histologic grade assigned to a ovarian tumor. http://purl.obolibrary.org/obo/OBI_0002216 histologic grade for ovarian tumor according to a two-tier grading system http://purl.obolibrary.org/obo/OBI_0002215 histologic grade for ovarian tumor A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors. http://purl.obolibrary.org/obo/OBI_0002219 histologic grade for ovarian tumor according to the World Health Organization http://purl.obolibrary.org/obo/OBI_0002215 histologic grade for ovarian tumor A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO). http://purl.obolibrary.org/obo/OBI_0002368 clinical history of cancer http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a diagnosis of cancer. http://purl.obolibrary.org/obo/OBI_0002370 unknown clinical history of cancer http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which it is not known whether there was a diagnosis of cancer. http://purl.obolibrary.org/obo/OBI_0002373 aunt clinical history of cancer http://purl.obolibrary.org/obo/OBI_0002372 family clinical history of cancer A clinical history in which there is a diagnosis of cancer in the female sibling of a parent. http://purl.obolibrary.org/obo/OBI_0002374 brother clinical history of cancer http://purl.obolibrary.org/obo/OBI_0002372 family clinical history of cancer A clinical history in which there is a diagnosis of cancer in a male sibling. http://purl.obolibrary.org/obo/OBI_0002375 daughter clinical history of cancer http://purl.obolibrary.org/obo/OBI_0002372 family clinical history of cancer A clinical history in which there is a diagnosis of cancer in a person's female child. http://purl.obolibrary.org/obo/OBI_0002376 father clinical history of cancer http://purl.obolibrary.org/obo/OBI_0002372 family clinical history of cancer A clinical history in which there is a diagnosis of cancer in a male parent. http://purl.obolibrary.org/obo/OBI_0002377 mother clinical history of cancer http://purl.obolibrary.org/obo/OBI_0002372 family clinical history of cancer A clinical history in which there is a diagnosis of cancer in a female parent. http://purl.obolibrary.org/obo/OBI_0002378 sister clinical history of cancer http://purl.obolibrary.org/obo/OBI_0002372 family clinical history of cancer A clinical history in which there is a diagnosis of cancer in a female sibling. http://purl.obolibrary.org/obo/OBI_0002379 son clinical history of cancer http://purl.obolibrary.org/obo/OBI_0002372 family clinical history of cancer A clinical history in which there is a diagnosis of cancer in a person's male child. http://purl.obolibrary.org/obo/OBI_0002380 uncle clinical history of cancer http://purl.obolibrary.org/obo/OBI_0002372 family clinical history of cancer A clinical history in which there is a diagnosis of cancer in a male sibling of a parent. http://purl.obolibrary.org/obo/OBI_0002381 grandmother clinical history of cancer http://purl.obolibrary.org/obo/OBI_0002372 family clinical history of cancer A clinical history in which there is a diagnosis of cancer in a female parent of a parent. http://purl.obolibrary.org/obo/OBI_0002382 grandfather clinical history of cancer http://purl.obolibrary.org/obo/OBI_0002372 family clinical history of cancer A clinical history in which there is a diagnosis of cancer in a male parent of a parent. http://purl.obolibrary.org/obo/OBI_0002383 nephew clinical history of cancer http://purl.obolibrary.org/obo/OBI_0002372 family clinical history of cancer A clinical history in which there is a diagnosis of cancer in a male child of a sibling. http://purl.obolibrary.org/obo/OBI_0002384 niece clinical history of cancer http://purl.obolibrary.org/obo/OBI_0002372 family clinical history of cancer A clinical history in which there is a diagnosis of cancer in a female child of a sibling. http://purl.obolibrary.org/obo/OBI_0002385 diagnosis of infectious disease http://purl.obolibrary.org/obo/OGMS_0000073 diagnosis A diagnosis that is an assertion that a patient who is the subject of a diagnostic process has an infectious disease. http://purl.obolibrary.org/obo/OBI_0002386 diagnosis of hepatitis B http://purl.obolibrary.org/obo/OBI_0002385 diagnosis of infectious disease A diagnosis of infectious disease caused by the hepatitis B virus. http://purl.obolibrary.org/obo/OBI_0002387 diagnosis of hepatitis C http://purl.obolibrary.org/obo/OBI_0002385 diagnosis of infectious disease A diagnosis of infectious disease caused by the hepatitis C virus. http://purl.obolibrary.org/obo/OBI_0002388 diagnosis of HIV http://purl.obolibrary.org/obo/OBI_0002385 diagnosis of infectious disease A diagnosis of infectious disease caused by the human immunodeficiency virus (1 or 2). http://purl.obolibrary.org/obo/OBI_0002389 clinical history of repeated HIV assays http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is repeated reactive screening assays for human immunodeficiency virus (1 or 2) antibodies regardless of the results of supplemental assays. http://purl.obolibrary.org/obo/OBI_0002390 exposure to second hand smoke http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there has been second hand exposure to tobacco smoking. http://purl.obolibrary.org/obo/OBI_0002391 exposure to second hand smoke in household during childhood http://purl.obolibrary.org/obo/OBI_0002390 exposure to second hand smoke An exposure to second hand smoke that occurred in the (patient's) household when the person was a child. http://purl.obolibrary.org/obo/OBI_0002392 exposure to second hand smoke in current household http://purl.obolibrary.org/obo/OBI_0002390 exposure to second hand smoke An exposure to second hand smoke in person's current household. http://purl.obolibrary.org/obo/OBI_0002393 pregnancy history http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which a female has had a pregnancy. http://purl.obolibrary.org/obo/OBI_0002394 number of pregnancies http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement datum of the total number of pregnancies a woman has had. http://purl.obolibrary.org/obo/OBI_0002395 number of live births http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement datum of the total number of live births a female has had. http://purl.obolibrary.org/obo/OBI_0002396 age when gave birth to first child http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum performed on a female when her first biological child was born. http://purl.obolibrary.org/obo/OBI_0002397 gynecologic surgery history http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which a woman has had gynecologic surgery in the past. http://purl.obolibrary.org/obo/OBI_0002398 hysterectomy history http://purl.obolibrary.org/obo/OBI_0002397 gynecologic surgery history A gynecologic surgery history in which a woman has had a hysterectomy. http://purl.obolibrary.org/obo/OBI_0002399 unilateral oophorectomy history http://purl.obolibrary.org/obo/OBI_0002397 gynecologic surgery history A gynecologic surgery history in which a woman has had a unilateral oophorectomy. http://purl.obolibrary.org/obo/OBI_0002400 neither hysterectomy nor oophorectomy history http://purl.obolibrary.org/obo/OBI_0002397 gynecologic surgery history A gynecologic surgery history in which a woman has not had either a hysterectomy or an oophorectomy. http://purl.obolibrary.org/obo/OBI_0002401 hormonal birth control use history http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity that indicates whether a woman has ever used oral contraceptives in order to block ovulation and prevent the occurrence of pregnancy. http://purl.obolibrary.org/obo/OBI_0002402 hormonal birth control former use history http://purl.obolibrary.org/obo/OBI_0002401 hormonal birth control use history A hormonal birth control use history that indicates an individual has previously been a hormonal birth control user but is not a current user. http://purl.obolibrary.org/obo/OBI_0002403 hormonal birth control current use history http://purl.obolibrary.org/obo/OBI_0002401 hormonal birth control use history A hormonal birth control use history that indicates an individual is currently a hormonal birth control user. http://purl.obolibrary.org/obo/OBI_0002404 no hormonal birth control use history http://purl.obolibrary.org/obo/OBI_0002401 hormonal birth control use history A hormonal birth control use history that indicates an individual has not ever been a hormonal birth control user. http://purl.obolibrary.org/obo/OBI_0002405 hormonal replacement therapy history http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which an individual has had hormonal replacement therapy in the past. http://purl.obolibrary.org/obo/OBI_0002407 pill delivery form for hormonal replacement therapy http://purl.obolibrary.org/obo/OBI_0002406 delivery form for hormonal replacement therapy A delivery form for hormonal replacement therapy that is a pill for oral administration. http://purl.obolibrary.org/obo/OBI_0002408 patch delivery form for hormonal replacement therapy http://purl.obolibrary.org/obo/OBI_0002406 delivery form for hormonal replacement therapy A delivery form for hormonal replacement therapy that is a patch for transdermal administration. http://purl.obolibrary.org/obo/OBI_0002409 cream delivery form for hormonal replacement therapy http://purl.obolibrary.org/obo/OBI_0002406 delivery form for hormonal replacement therapy A delivery form for hormonal replacement therapy that is a cream for transdermal administration. http://purl.obolibrary.org/obo/OBI_0002410 menopausal status http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity that indicates the state of a female's cessation of menstruation. http://purl.obolibrary.org/obo/OBI_0002411 indeterminate menopausal status http://purl.obolibrary.org/obo/OBI_0002410 menopausal status A menopausal status that is neither pre- nor post-menopausal. http://purl.obolibrary.org/obo/OBI_0002412 premenopausal status http://purl.obolibrary.org/obo/OBI_0002410 menopausal status A menopausal status indicating that less than 6 months has passed since the last menstrual period and there has not been prior bilateral oophorectomy and not on estrogen replacement. http://purl.obolibrary.org/obo/OBI_0002413 perimenopausal status http://purl.obolibrary.org/obo/OBI_0002410 menopausal status A menopausal status indicating that it has been 6-12 months since last menstrual period. http://purl.obolibrary.org/obo/OBI_0002414 postmenopausal status http://purl.obolibrary.org/obo/OBI_0002410 menopausal status A menopausal status indicating that it has been more than 12 months since the last menstrual period with no prior hysterectomy or that there has been a prior bilateral oophorectomy. http://purl.obolibrary.org/obo/OBI_0002415 exposure to environmental and workplace carcinogens history http://purl.obolibrary.org/obo/IAO_0000030 information content entity A information content entity that indicates the exposure of an individual to carcinogens in the workplace or environment. http://purl.obolibrary.org/obo/OBI_0002416 exposure to arsenic history http://purl.obolibrary.org/obo/OBI_0002415 exposure to environmental and workplace carcinogens history An exposure to environmental and workplace carcinogens history where the carcinogen is arsenic. http://purl.obolibrary.org/obo/OBI_0002417 exposure to asbestos history http://purl.obolibrary.org/obo/OBI_0002415 exposure to environmental and workplace carcinogens history An exposure to environmental and workplace carcinogens history where the carcinogen is asbestos. http://purl.obolibrary.org/obo/OBI_0002418 exposure to diesel exhaust history http://purl.obolibrary.org/obo/OBI_0002415 exposure to environmental and workplace carcinogens history An exposure to environmental and workplace carcinogens history where the carcinogen is diesel exhaust. http://purl.obolibrary.org/obo/OBI_0002419 exposure to chromium history http://purl.obolibrary.org/obo/OBI_0002415 exposure to environmental and workplace carcinogens history An exposure to environmental and workplace carcinogens history where the carcinogen is chromium. http://purl.obolibrary.org/obo/OBI_0002420 exposure to silica history http://purl.obolibrary.org/obo/OBI_0002415 exposure to environmental and workplace carcinogens history An exposure to environmental and workplace carcinogens history where the carcinogen is silica. http://purl.obolibrary.org/obo/OBI_0002423 age of majority inclusion criterion http://purl.obolibrary.org/obo/OBI_0500027 inclusion criterion An inclusion criterion that uses the age of majority for a state or institution, where one is generally considered to be an adult, which if met, makes an individual suitable for a given task or participation in a given process. http://purl.obolibrary.org/obo/OBI_0002424 chemotherapy treatment exclusion criterion http://purl.obolibrary.org/obo/OBI_0500028 exclusion criterion An exclusion criterion that defines whether chemotherapy was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process http://purl.obolibrary.org/obo/OBI_0002425 radiation treatment exclusion criteria http://purl.obolibrary.org/obo/OBI_0500028 exclusion criterion An exclusion criterion that defines whether radiation was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process http://purl.obolibrary.org/obo/OBI_0002426 chemotherapy treatment within the recent past exclusion criterion http://purl.obolibrary.org/obo/OBI_0500028 exclusion criterion An exclusion criterion that defines whether chemotherapy was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process. http://purl.obolibrary.org/obo/OBI_0002427 radiation treatment within the recent past exclusion criterion http://purl.obolibrary.org/obo/OBI_0500028 exclusion criterion An exclusion criterion that defines whether radiation was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process. http://purl.obolibrary.org/obo/OBI_0002428 BMI range inclusion criterion http://purl.obolibrary.org/obo/OBI_0500027 inclusion criterion An inclusion criterion that defines and states a Body Mass Index range, which if met, makes an individual suitable for a given task or participation in a given process. http://purl.obolibrary.org/obo/OBI_0002429 blood transfusion exclusion criterion http://purl.obolibrary.org/obo/OBI_0500028 exclusion criterion An exclusion criterion that is defined by whether the specimen donor received a whole blood transfusion within a specified time frame prior to death, which if met, makes a specimen donor unsuitable for a given task or participation in a given process. http://purl.obolibrary.org/obo/OBI_0002430 history of metastatic cancer exclusion criterion http://purl.obolibrary.org/obo/OBI_0500028 exclusion criterion An exclusion criterion defined as whether an individual has ever been diagnosed with metastatic cancer (cancer that spread beyond the initial site such as to other organs like brain bone or liver), which if met, makes the individual unsuitable for a given task or participation in a given process. http://purl.obolibrary.org/obo/OBI_0002431 intravenous drug use exclusion criterion http://purl.obolibrary.org/obo/OBI_0500028 exclusion criterion An exclusion criterion defined as when an individual has a history of intravenous drug abuse for a specific timeframe, which if met, makes the individual unsuitable for a given task or participation in a given process. http://purl.obolibrary.org/obo/OBI_0002432 history of sex with someone with a history of blood borne infection exclusion criterion http://purl.obolibrary.org/obo/OBI_0500028 exclusion criterion An exclusion criterion defined as whether an individual has a history of sex with someone who has been diagnosed or at risk for a blood borne infections disease in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process. http://purl.obolibrary.org/obo/OBI_0002433 history of sex with someone with a history of intravenous drugs exclusion criterion http://purl.obolibrary.org/obo/OBI_0500028 exclusion criterion An exclusion criterion defined as whether an individual has a history of sex with someone who has used intravenous drugs in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process. http://purl.obolibrary.org/obo/OBI_0002434 HIV exclusion criterion http://purl.obolibrary.org/obo/OBI_0500028 exclusion criterion An exclusion criterion defined as whether an individual has a history of repeatedly reactive screening assays for HIV-1 or HIV-2 antibody regardless of the results of supplemental assays, which if met, makes the individual unsuitable for a given task or participation in a given process. http://purl.obolibrary.org/obo/OBI_0002435 exposure to blood borne infectious disease exclusion criterion http://purl.obolibrary.org/obo/OBI_0500028 exclusion criterion An exclusion criterion defined as whether an individual has been exposed to a blood borne infections disease through needle sticks and/or contact with non-intact skin and/or contact with open wounds and/or contact with mucous membranes, which if met, makes the individual unsuitable for a given task or participation in a given process. http://purl.obolibrary.org/obo/OBI_0002436 RNA interactome capture http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that identifies RNA binding proteins by cross-linking RNA and proteins with UV light, then purifying the bound complexes by oligo(dT) capture. Finally, the complexes are analyzed by mass spectrometry. http://purl.obolibrary.org/obo/OBI_0002438 nuclear ligation assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that detects the proximity of chromosomal DNA through the use of a ligation reaction in isolated nuclei. http://purl.obolibrary.org/obo/OBI_0002440 Hi-C assay http://purl.obolibrary.org/obo/OBI_0002439 chromosome conformation capture assay A chromosome conformation capture assay that detects genome-wide chromosomal interactions. High-throughput techniques are used to sequence the ligated fragments after cross-linking and cutting with restriction enzymes. http://purl.obolibrary.org/obo/OBI_0002441 physical examination of individual http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that produces a description of the qualities of an entity that has not been transformed, through observation and physical, non-invasive techniques. http://purl.obolibrary.org/obo/OBI_0002442 hydroxyl-radical footprinting assay http://purl.obolibrary.org/obo/OBI_0002162 footprinting assay A footprinting assay that uses the reaction of hydroxyl radicals with side-chain sites in molecules (proteins, DNA, etc)_ with the resultant mass shift demonstrating the site of modification, used to_ to asses the accessibility of that site. http://purl.obolibrary.org/obo/OBI_0002634 in vivo assay measuring B cell epitope specific disease exacerbation resulting from the adoptive transfer of epitope specific antibodies or B cells http://purl.obolibrary.org/obo/OBI_0002677 in vivo assay measuring a B cell epitope specific response after adoptive transfer of epitope specific antibodies or B cells An efficacy of B cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment after adoptive transfer of epitope specific antibodies or B cells. http://purl.obolibrary.org/obo/OBI_0002635 in vivo assay measuring T cell epitope specific disease reduction resulting from the adoptive transfer of epitope specific T cells http://purl.obolibrary.org/obo/OBI_0002676 in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells An efficacy of T cell epitope intervention experiment that detects a decrease in disease after adoptive transfer of epitope specfic T cells. http://purl.obolibrary.org/obo/OBI_0002636 in vivo assay measuring B cell epitope specific disease reduction resulting from adoptive transfer of epitope specific antibodies or B cells http://purl.obolibrary.org/obo/OBI_0002677 in vivo assay measuring a B cell epitope specific response after adoptive transfer of epitope specific antibodies or B cells An efficacy of B cell epitope intervention experiment that detects a decrease in disease after adoptive transfer of epitope specific antibodies or B cells. http://purl.obolibrary.org/obo/OBI_0002637 in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells http://purl.obolibrary.org/obo/OBI_0002676 in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells An efficacy of T cell epitope intervention experiment that uses a epitope protection experiment after adoptive transfer of epitope specfic T cells. http://purl.obolibrary.org/obo/OBI_0002638 in vivo assay measuring B cell epitope specific protection from challenge resulting from adoptive transfer of epitope specific antibodies or B cells http://purl.obolibrary.org/obo/OBI_0002677 in vivo assay measuring a B cell epitope specific response after adoptive transfer of epitope specific antibodies or B cells An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment after adoptive transfer of epitope specific antibodies or B cells. http://purl.obolibrary.org/obo/OBI_0002639 in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on pathogen burden http://purl.obolibrary.org/obo/OBI_0002637 in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on pathogen burden after adoptive transfer of epitope specfic T cells. http://purl.obolibrary.org/obo/OBI_0002640 in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on pathogen burden http://purl.obolibrary.org/obo/OBI_0002638 in vivo assay measuring B cell epitope specific protection from challenge resulting from adoptive transfer of epitope specific antibodies or B cells A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on pathogen burden after adoptive transfer of epitope specific antibodies or B cells. http://purl.obolibrary.org/obo/OBI_0002641 in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on survival http://purl.obolibrary.org/obo/OBI_0002637 in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on survival after adoptive transfer of epitope specfic T cells. http://purl.obolibrary.org/obo/OBI_0002642 in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival http://purl.obolibrary.org/obo/OBI_0002638 in vivo assay measuring B cell epitope specific protection from challenge resulting from adoptive transfer of epitope specific antibodies or B cells A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on survival after adoptive transfer of epitope specific antibodies or B cells. http://purl.obolibrary.org/obo/OBI_0002643 in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells http://purl.obolibrary.org/obo/OBI_0002637 in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on tumor burden after adoptive transfer of epitope specfic T cells. http://purl.obolibrary.org/obo/OBI_0002644 in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells http://purl.obolibrary.org/obo/OBI_0002638 in vivo assay measuring B cell epitope specific protection from challenge resulting from adoptive transfer of epitope specific antibodies or B cells A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on tumor burden after adoptive transfer of epitope specific antibodies or B cells. http://purl.obolibrary.org/obo/OBI_0002645 in vivo assay measuring T cell epitope specific tolerance induction resulting from the adoptive transfer of epitope specific T cells http://purl.obolibrary.org/obo/OBI_0002676 in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment after adoptive transfer of epitope specfic T cells. http://purl.obolibrary.org/obo/OBI_0002646 in vivo assay measuring B cell epitope specific tolerance induction resulting from the adoptive transfer of epitope specific antibodies or B cells http://purl.obolibrary.org/obo/OBI_0002677 in vivo assay measuring a B cell epitope specific response after adoptive transfer of epitope specific antibodies or B cells An efficacy of B cell epitope intervention experiment that uses a tolerance induction intervention experiment after adoptive transfer of epitope specific antibodies or B cells. http://purl.obolibrary.org/obo/OBI_0002647 Giemsa stain assay http://purl.obolibrary.org/obo/OBI_0001977 cytometry assay An assay that uses a Giemsa stain to characterize cells. http://purl.obolibrary.org/obo/OBI_0002648 individual organism specimen http://purl.obolibrary.org/obo/OBI_0100051 specimen A specimen composed of an individual organism to be studied in an investigation. http://purl.obolibrary.org/obo/OBI_0002649 blood microbiology assay http://purl.obolibrary.org/obo/OBI_0001624 organism identification assay An organism identification assay that identifies a microorganism in a blood specimen. http://purl.obolibrary.org/obo/OBI_0002664 cytometric bead array assay measuring epitope specific interleukin-15 production by T cells http://purl.obolibrary.org/obo/OBI_0001292 biological activity assay measuring epitope specific interleukin-15 production by T cells An assay of epitope specific interleukin-15 production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0002665 cytometric bead array assay measuring epitope specific interleukin-16 production by T cells http://purl.obolibrary.org/obo/OBI_0001280 biological activity assay measuring epitope specific interleukin-16 production by T cells An assay of epitope specific interleukin-16 production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0002666 in vivo assay measuring B cell epitope specific induction of hypersensitivity resulting from the adoptive transfer of epitope specific antibodies or B cells http://purl.obolibrary.org/obo/OBI_0002677 in vivo assay measuring a B cell epitope specific response after adoptive transfer of epitope specific antibodies or B cells An efficacy of B cell epitope intervention experiment that detects a hypersensitivity response by monitoring skin reactions after adoptive transfer of epitope specific antibodies or B cells. http://purl.obolibrary.org/obo/OBI_0002667 in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity resulting from the adoptive transfer of epitope specific T cells http://purl.obolibrary.org/obo/OBI_0002676 in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity after adoptive transfer of epitope specfic T cells. http://purl.obolibrary.org/obo/OBI_0002668 in vivo assay measuring epitope specific proliferation of T cells resulting from the adoptive transfer of epitope specific T cells http://purl.obolibrary.org/obo/OBI_0002676 in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells A T cell epitope specific proliferation assay that is performed in vivo after adoptive transfer of epitope specfic T cells. http://purl.obolibrary.org/obo/OBI_0002669 biological activity assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response resulting from the adoptive transfer of epitope specific T cells http://purl.obolibrary.org/obo/OBI_0002676 in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance an antibody response after adoptive transfer of epitope specfic T cells. http://purl.obolibrary.org/obo/OBI_0002670 biological activity assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response resulting from the adoptive transfer of epitope specific T cells http://purl.obolibrary.org/obo/OBI_0002676 in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell response after adoptive transfer of epitope specfic T cells. http://purl.obolibrary.org/obo/OBI_0002671 in vivo assay measuring epitope specific T cell killing resulting from the adoptive transfer of epitope specific T cells http://purl.obolibrary.org/obo/OBI_0002676 in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells A T cell epitope specific killing assay that uses an in vivo cell mediated cell killing assay after adoptive transfer of epitope specfic T cells. http://purl.obolibrary.org/obo/OBI_0002672 ELISA measuring epitope specific perforin release by T cells http://purl.obolibrary.org/obo/OBI_0001497 biological activity assay measuring epitope specific perforin release by T cells An assay of epitope specific perforin release by T cells that uses an ELISA. http://purl.obolibrary.org/obo/OBI_0002674 case series design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that samples only subjects who have experienced a particular event (outcome or exposure). Such a design, in contrast to a cohort study, does not permit calculation of absolute risk as non-case subjects are not included. http://purl.obolibrary.org/obo/OBI_0002676 in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells http://purl.obolibrary.org/obo/OBI_0001484 biological activity assay measuring T cell epitope specific in vivo activity An efficacy of T cell epitope intervention experiment that is performed after adoptive transfer of epitope specfic T cells. http://purl.obolibrary.org/obo/OBI_0002677 in vivo assay measuring a B cell epitope specific response after adoptive transfer of epitope specific antibodies or B cells http://purl.obolibrary.org/obo/OBI_0001698 biological activity assay measuring B cell epitope specific in vivo activity An efficacy of B cell epitope intervention experiment that is performed after adoptive transfer of epitope specific antibodies or B cells. http://purl.obolibrary.org/obo/OBI_0002678 in vivo assay measuring T cell epitope specific disease exacerbation resulting from the adoptive transfer of epitope specific T cells http://purl.obolibrary.org/obo/OBI_0002676 in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells An efficacy of T cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment after adoptive transfer of epitope specfic T cells. http://purl.obolibrary.org/obo/OBI_0002681 glass bottle http://purl.obolibrary.org/obo/OBI_0000967 container A container with a narrow neck that is made of glass. http://purl.obolibrary.org/obo/OBI_0002682 glass bottle coated with insecticides http://purl.obolibrary.org/obo/OBI_0002681 glass bottle A glass bottle that coated with material designed to control insects. http://purl.obolibrary.org/obo/OBI_0002686 counter current immunoelectrophoresis http://purl.obolibrary.org/obo/OBI_0600053 electrophoresis An electrophoresis in which antigen and antibody move in opposite directions and form precipitates in the area between the cells where they meet in concentrations of optimal proportions. http://purl.obolibrary.org/obo/OBI_0002689 detection of pathogenic organisms objective http://purl.obolibrary.org/obo/OBI_0000268 organism feature identification objective An organism feature identification objective that aims to detect whether an organism contains pathogenic organisms. http://purl.obolibrary.org/obo/OBI_0002690 insecticide resistance detection objective http://purl.obolibrary.org/obo/OBI_0000268 organism feature identification objective An organism feature identification objective that aims to detect insecticide resistance of an insect. http://purl.obolibrary.org/obo/OBI_0002692 polymerase chain reaction assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that uses polymerase chain reaction technique to amplify DNA. http://purl.obolibrary.org/obo/OBI_0002722 insecticide resistance by ligase detection reaction assay http://purl.obolibrary.org/obo/OBI_0002696 insecticide resistance by monitoring known mutations assay An insecticide resistance assay that is based on monitoring known mutations using ligase detection reaction exquisitely discriminate between a mismatched and complementary DNA helix. http://purl.obolibrary.org/obo/OBI_0002725 insecticide resistance by fluorogenic PCR assay http://purl.obolibrary.org/obo/OBI_0002696 insecticide resistance by monitoring known mutations assay An insecticide resistance assay that is based on monitoring known mutations by PCR technique that uses target specific probes labeled with fluorogenic chromophores to detect gene mutation. http://purl.obolibrary.org/obo/ONE_0003011 food-based dietary guideline regarding processed food http://purl.obolibrary.org/obo/ONE_0003001 food-based dietary guideline A food-based dietary guideline that provides dietary advice regarding the eating frequency/quantity of processed food. http://purl.obolibrary.org/obo/ONE_0003007 food-based dietary guideline for adults http://purl.obolibrary.org/obo/ONE_0003001 food-based dietary guideline A food-based dietary guideline that provides dietary advice for adults. http://purl.obolibrary.org/obo/OBI_0002133 cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells http://purl.obolibrary.org/obo/OBI_0002134 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells An assay of epitope specific chemokine (C-C motif) ligand 20 production by T cells that uses a cytometric bead array assay. http://purl.obolibrary.org/obo/OBI_0002123 IHC slide staining http://purl.obolibrary.org/obo/OBI_0302887 staining A staining using labeled antibodies, i.e. the analytical part of immunohistochemistry. The staining is applied to fixed specimens on slides to identify biomarkers in tissues. http://purl.obolibrary.org/obo/OBI_0002124 H&E slide staining http://purl.obolibrary.org/obo/OBI_0302887 staining A staining using hematoxylin and eosin. The staining is applied to fixed specimens on slides to observe the whole structure and morphology of cells in a tissue; nuclei are stained dark blue/purple while cytoplasm is stained pink. http://purl.obolibrary.org/obo/OBI_0002125 H&E-stained fixed tissue slide specimen http://purl.obolibrary.org/obo/OMIABIS_0000052 fixed tissue slide specimen A fixed tissue slide specimen that is the output of H&E slide staining. http://purl.obolibrary.org/obo/OBI_0002127 single cell specimen http://purl.obolibrary.org/obo/OBI_0001468 cell specimen A cell specimen that contains only one cell. http://purl.obolibrary.org/obo/OBI_0002130 Illumina Infinium Omni5Exome-4 Kit http://purl.obolibrary.org/obo/OBI_0001869 Illumina BeadChip An Illumina BeadChip which is an array that interrogates over 4.3 million whole-genome variants for genotyping and copy number variation. http://purl.obolibrary.org/obo/OBI_0002131 Illumina Infinium MethylationEPIC BeadChip http://purl.obolibrary.org/obo/OBI_0001870 Illumina methylation BeadChip An Illumina methylation BeadChip which is an array that interrogates ~ 850,000 methylation sites per sample at single-nucleotide resolution. http://purl.obolibrary.org/obo/OBI_0002591 colocalization identification design http://purl.obolibrary.org/obo/OBI_0002590 molecular interaction identification design A molecular interaction identification design that investigates the co-occurence and correlation of two or more molecules. http://purl.obolibrary.org/obo/OBI_0002592 genetic interaction identification design http://purl.obolibrary.org/obo/OBI_0002590 molecular interaction identification design A molecular interaction identification design that investigates a phenotype that is the result of two or more genetic perturbations, and is not explained by the individual genetic perturbations alone. http://purl.obolibrary.org/obo/OBI_0002593 functional association identification design http://purl.obolibrary.org/obo/OBI_0002590 molecular interaction identification design A molecular interaction identification design that investigates a relationship that is the result of intermediate steps between two or more molecules that are not necessarily in direct contact with each other. http://purl.obolibrary.org/obo/OBI_0002595 enzymatic reaction identification design http://purl.obolibrary.org/obo/OBI_0002594 direct interaction identification design A direct interaction identification design that investigations a biological reaction on a molecule which has been triggered by an enzyme. http://purl.obolibrary.org/obo/OBI_0002596 self interaction identification design http://purl.obolibrary.org/obo/OBI_0002590 molecular interaction identification design A molecular interaction identification design that investigates intra-molecular interactions between two or more regions of a single molecule. http://purl.obolibrary.org/obo/OBI_0002599 swab specimen http://purl.obolibrary.org/obo/OBI_0100051 specimen A specimen that is stored on a swab as the output of a collecting specimen with swab process. http://purl.obolibrary.org/obo/OBI_0002600 collecting specimen with swab http://purl.obolibrary.org/obo/OBI_0000659 specimen collection process A specimen collection process that uses a swab as the collection device. A swab is an absorbent material (e.g. cotton) on a rod (e.g., wooden stick). http://purl.obolibrary.org/obo/OBI_0002601 demultiplexed sequence data http://purl.obolibrary.org/obo/OBI_0000973 sequence data Sequence data in which an identifier subsequence has been used to categorize each reads by source. http://purl.obolibrary.org/obo/OBI_0002602 multiplexed sequence data http://purl.obolibrary.org/obo/OBI_0000973 sequence data Sequence data from a sequence library generated from at least two different sources, where each read in the sequence data includes base calls from a multiplex identifier sequence that can be used to trace the source of the read to its source. http://purl.obolibrary.org/obo/OBI_0002603 areolar swab specimen http://purl.obolibrary.org/obo/OBI_0002599 swab specimen A specimen that is collected with a swab from the surface of an areola of a breast. http://purl.obolibrary.org/obo/OBI_0002604 breast swab specimen http://purl.obolibrary.org/obo/OBI_0002599 swab specimen A specimen that is collected with a swab from the surface of a breast. http://purl.obolibrary.org/obo/OBI_0002605 cheek swab specimen http://purl.obolibrary.org/obo/OBI_0002599 swab specimen A specimen that is collected with a swab from the cheek portion of the inside surface of a mouth. http://purl.obolibrary.org/obo/OBI_0002606 nasopharyngeal swab specimen http://purl.obolibrary.org/obo/OBI_0002599 swab specimen A specimen that is collected with a swab from the surface of a nasopharynx. http://purl.obolibrary.org/obo/OBI_0002607 oral swab specimen http://purl.obolibrary.org/obo/OBI_0002599 swab specimen A specimen that is collected with a swab from the inside surface of a mouth. http://purl.obolibrary.org/obo/OBI_0002608 oropharyngeal swab specimen http://purl.obolibrary.org/obo/OBI_0002599 swab specimen A specimen that is collected with a swab from the surface of a oropharynx. http://purl.obolibrary.org/obo/OBI_0002609 rectal swab specimen http://purl.obolibrary.org/obo/OBI_0002599 swab specimen A specimen that is collected with a swab from the surface of a rectum. http://purl.obolibrary.org/obo/OBI_0002610 tongue swab specimen http://purl.obolibrary.org/obo/OBI_0002599 swab specimen A specimen that is collected with a swab from the surface of a tongue. http://purl.obolibrary.org/obo/OBI_0002611 vagina swab specimen http://purl.obolibrary.org/obo/OBI_0002599 swab specimen A specimen that is collected with a swab from the surface of a vagina. http://purl.obolibrary.org/obo/OBI_0002613 environmental swab specimen http://purl.obolibrary.org/obo/OBI_0002599 swab specimen A specimen that is collected with a swab from the surface of an environmenal material. http://purl.obolibrary.org/obo/OBI_0002614 birth cohort study design http://purl.obolibrary.org/obo/OBI_0500000 study design A cohort study design for which the subjects are followed from the time of birth usually including information about gestation and follow up. http://purl.obolibrary.org/obo/OBI_0002615 disease specific study design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design for which material and information is collected from subjects that have already developed a particular disease. http://purl.obolibrary.org/obo/OBI_0002616 genealogical record http://purl.obolibrary.org/obo/IAO_0000310 document A document about the family relationships of persons related as members of a domestic group linked through descent from a common ancestor, marriage, or adoption. http://purl.obolibrary.org/obo/OBI_0002617 national registry http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity that contains information about a nationwide group of individuals. http://purl.obolibrary.org/obo/OBI_0002618 national biomedical registry http://purl.obolibrary.org/obo/OBI_0002617 national registry A national registry that contains information about individuals that was accumulated for a biomedical purpose, such as diagnoses, treatments, or outcomes. http://purl.obolibrary.org/obo/OBI_0002779 mid-turbinate nasal swab specimen http://purl.obolibrary.org/obo/OBI_0002599 swab specimen A specimen that is collected with a mid-turbinate nasal swab from the turbinate area of the nasal cavity. http://purl.obolibrary.org/obo/OBI_0002782 upper respiratory specimen http://purl.obolibrary.org/obo/OBI_0002599 swab specimen A specimen that is derived from the upper respiratory tract http://purl.obolibrary.org/obo/OBI_0002783 lower respiratory tract specimen http://purl.obolibrary.org/obo/OBI_0002599 swab specimen A specimen that is derived from the lower respiratory tract. http://purl.obolibrary.org/obo/OBI_0002784 anterior nasal swab specimen http://purl.obolibrary.org/obo/OBI_0002599 swab specimen A specimen that is derived from the anterior nasal wall http://purl.obolibrary.org/obo/OBI_0002897 surveillance process http://purl.obolibrary.org/obo/OBI_0000066 investigation An investigation in which some entity is monitored, and data concerning that entity collected, interpreted, and disseminated, for the purpose of managing, directing, or protecting that entity, or some other entity. http://purl.obolibrary.org/obo/OBI_0002901 visible light source http://purl.obolibrary.org/obo/OBI_0400065 light source A light source that provides visible light for use in a distant area using a delivery system. http://purl.obolibrary.org/obo/OBI_0002902 solar light source http://purl.obolibrary.org/obo/OBI_0400065 light source A light source that light is produced from solar energy. http://purl.obolibrary.org/obo/OBI_0002921 artificial pit shelter http://purl.obolibrary.org/obo/OBI_0002939 resting arthropod trap An arthropod trap, consisting of a pit dug in the ground to provide a space for arthropods to rest and be collected. http://purl.obolibrary.org/obo/OBI_0002922 baited net trap http://purl.obolibrary.org/obo/OBI_0002920 arthropod trap An arthropod trap designed to work with an animal (which could be human) inside a netted structure. This structure is designed so that an arthropod, attracted by the animal, can fly into the netted structure but can neither escape nor reach the animal. http://purl.obolibrary.org/obo/OBI_0002934 MosquiTRAP http://purl.obolibrary.org/obo/OBI_0002929 gravid trap A gravid trap consisting of an arthropod attractant and adhesive surface. http://purl.obolibrary.org/obo/OBI_0002939 resting arthropod trap http://purl.obolibrary.org/obo/OBI_0002920 arthropod trap An arthropod trap that is designed to be attractive to an arthropod as a place to rest during a period of inactivity. http://purl.obolibrary.org/obo/OBI_0002945 population based design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design where the selection of the individuals that are included into the study are intended to be representative of all individuals in the a priori defined specific population and is done at the population level or among the population groups, generally to find the cause, incidence or spread of the disease or to see the response to the treatment, nutrition or environment. http://purl.obolibrary.org/obo/OBI_0002971 endotracheal tube specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected upon removal of the tube from the trachea. http://purl.obolibrary.org/obo/OBI_0002972 endotracheal aspirate specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected by suction without removing the tube. http://purl.obolibrary.org/obo/BFO_0000148 zero-dimensional temporal region http://purl.obolibrary.org/obo/BFO_0000008 temporal region temporal instant. http://purl.obolibrary.org/obo/NCBITaxon_3702 Arabidopsis thaliana http://purl.obolibrary.org/obo/NCBITaxon_2759 Eukaryota thale-cress http://purl.obolibrary.org/obo/NCBITaxon_4896 Schizosaccharomyces pombe http://purl.obolibrary.org/obo/NCBITaxon_4890 Ascomycota fission yeast http://purl.obolibrary.org/obo/NCBITaxon_4932 Saccharomyces cerevisiae http://purl.obolibrary.org/obo/NCBITaxon_716545 saccharomyceta S. cerevisiae http://purl.obolibrary.org/obo/NCBITaxon_6239 Caenorhabditis elegans http://purl.obolibrary.org/obo/NCBITaxon_1206794 Ecdysozoa roundworm http://purl.obolibrary.org/obo/NCBITaxon_6668 Daphnia http://purl.obolibrary.org/obo/NCBITaxon_197562 Pancrustacea common water fleas http://purl.obolibrary.org/obo/NCBITaxon_7227 Drosophila melanogaster http://purl.obolibrary.org/obo/NCBITaxon_197562 Pancrustacea fruit fly http://purl.obolibrary.org/obo/NCBITaxon_8353 Xenopus http://purl.obolibrary.org/obo/NCBITaxon_32523 Tetrapoda Xenopus http://purl.obolibrary.org/obo/NCBITaxon_9606 Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_314146 Euarchontoglires man http://purl.obolibrary.org/obo/NCBITaxon_10090 Mus musculus http://purl.obolibrary.org/obo/NCBITaxon_39107 Murinae mouse http://purl.obolibrary.org/obo/NCBITaxon_10116 Rattus norvegicus http://purl.obolibrary.org/obo/NCBITaxon_39107 Murinae rats http://purl.obolibrary.org/obo/NCBITaxon_10376 Human gammaherpesvirus 4 http://purl.obolibrary.org/obo/NCBITaxon_10292 Herpesviridae Epstein-Barr virus http://purl.obolibrary.org/obo/NCBITaxon_2 Bacteria http://purl.obolibrary.org/obo/OBI_0100026 organism eubacteria http://purl.obolibrary.org/obo/NCBITaxon_4890 Ascomycota http://purl.obolibrary.org/obo/NCBITaxon_33154 Opisthokonta sac fungi http://purl.obolibrary.org/obo/NCBITaxon_117571 Euteleostomi http://purl.obolibrary.org/obo/NCBITaxon_7742 Vertebrata bony vertebrates http://purl.obolibrary.org/obo/NCBITaxon_2759 Eukaryota http://purl.obolibrary.org/obo/OBI_0100026 organism eukaryotes http://purl.obolibrary.org/obo/NCBITaxon_32523 Tetrapoda http://purl.obolibrary.org/obo/NCBITaxon_117571 Euteleostomi tetrapods http://purl.obolibrary.org/obo/NCBITaxon_32524 Amniota http://purl.obolibrary.org/obo/NCBITaxon_32523 Tetrapoda amniotes http://purl.obolibrary.org/obo/NCBITaxon_40674 Mammalia http://purl.obolibrary.org/obo/NCBITaxon_32524 Amniota mammals http://purl.obolibrary.org/obo/NCBITaxon_7742 Vertebrata http://purl.obolibrary.org/obo/NCBITaxon_33213 Bilateria vertebrates http://purl.obolibrary.org/obo/NCBITaxon_7955 Danio rerio http://purl.obolibrary.org/obo/NCBITaxon_117571 Euteleostomi zebrafish http://purl.obolibrary.org/obo/NCBITaxon_9031 Gallus gallus http://purl.obolibrary.org/obo/NCBITaxon_32524 Amniota Gallus domesticus http://purl.obolibrary.org/obo/NCBITaxon_9989 Rodentia http://purl.obolibrary.org/obo/NCBITaxon_314146 Euarchontoglires rodent http://purl.obolibrary.org/obo/IAO_8000000 ontology module http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part ontology file http://purl.obolibrary.org/obo/IAO_8000017 ontology module subsetted by expressivity http://purl.obolibrary.org/obo/IAO_8000006 subset ontology module http://purl.obolibrary.org/obo/CHEBI_23528 cytochalasin http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity http://purl.obolibrary.org/obo/CHEBI_29191 hydroxyl http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity http://purl.obolibrary.org/obo/CHEBI_17137 hydrogensulfite http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity http://purl.obolibrary.org/obo/CHEBI_42191 ethylenediaminetetraacetic acid http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity http://purl.obolibrary.org/obo/CHEBI_30682 ruthenium atom http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity http://purl.obolibrary.org/obo/CHEBI_33375 gadolinium atom http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity http://purl.obolibrary.org/obo/CHEBI_33376 terbium atom http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity http://purl.obolibrary.org/obo/CHEBI_27889 lead(0) http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity http://purl.obolibrary.org/obo/CHEBI_35729 gadolinium molecular entity http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity http://purl.obolibrary.org/obo/CHEBI_37586 sodium phosphate http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity http://purl.obolibrary.org/obo/CHEBI_33321 rare earth metal atom http://purl.obolibrary.org/obo/CHEBI_33250 atom http://purl.obolibrary.org/obo/NCBITaxon_10407 Hepatitis B virus http://purl.obolibrary.org/obo/NCBITaxon_10239 Viruses http://purl.obolibrary.org/obo/NCBITaxon_11103 Hepacivirus C http://purl.obolibrary.org/obo/NCBITaxon_10239 Viruses http://purl.obolibrary.org/obo/NCBITaxon_10292 Herpesviridae http://purl.obolibrary.org/obo/NCBITaxon_10239 Viruses http://purl.obolibrary.org/obo/NCBITaxon_11646 Lentivirus http://purl.obolibrary.org/obo/NCBITaxon_10239 Viruses http://purl.obolibrary.org/obo/NCBITaxon_388799 HIV-1 group O http://purl.obolibrary.org/obo/NCBITaxon_11676 Human immunodeficiency virus 1 http://purl.obolibrary.org/obo/BFO_0000008 temporal region http://purl.obolibrary.org/obo/BFO_0000003 occurrent http://purl.obolibrary.org/obo/BFO_0000011 spatiotemporal region http://purl.obolibrary.org/obo/BFO_0000003 occurrent http://purl.obolibrary.org/obo/BFO_0000141 immaterial entity http://purl.obolibrary.org/obo/BFO_0000004 independent continuant http://purl.obolibrary.org/obo/BFO_0000009 two-dimensional spatial region http://purl.obolibrary.org/obo/BFO_0000006 spatial region http://purl.obolibrary.org/obo/BFO_0000018 zero-dimensional spatial region http://purl.obolibrary.org/obo/BFO_0000006 spatial region http://purl.obolibrary.org/obo/BFO_0000026 one-dimensional spatial region http://purl.obolibrary.org/obo/BFO_0000006 spatial region http://purl.obolibrary.org/obo/BFO_0000028 three-dimensional spatial region http://purl.obolibrary.org/obo/BFO_0000006 spatial region http://purl.obolibrary.org/obo/BFO_0000038 one-dimensional temporal region http://purl.obolibrary.org/obo/BFO_0000008 temporal region http://purl.obolibrary.org/obo/BFO_0000182 history http://purl.obolibrary.org/obo/BFO_0000015 process http://purl.obolibrary.org/obo/BFO_0000034 function http://purl.obolibrary.org/obo/BFO_0000016 disposition http://purl.obolibrary.org/obo/BFO_0000016 disposition http://purl.obolibrary.org/obo/BFO_0000017 realizable entity http://purl.obolibrary.org/obo/BFO_0000019 quality http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant http://purl.obolibrary.org/obo/BFO_0000024 fiat object part http://purl.obolibrary.org/obo/BFO_0000040 material entity http://purl.obolibrary.org/obo/BFO_0000027 object aggregate http://purl.obolibrary.org/obo/BFO_0000040 material entity http://purl.obolibrary.org/obo/BFO_0000030 object http://purl.obolibrary.org/obo/BFO_0000040 material entity http://purl.obolibrary.org/obo/BFO_0000142 one-dimensional continuant fiat boundary http://purl.obolibrary.org/obo/BFO_0000140 continuant fiat boundary http://purl.obolibrary.org/obo/BFO_0000146 two-dimensional continuant fiat boundary http://purl.obolibrary.org/obo/BFO_0000140 continuant fiat boundary http://purl.obolibrary.org/obo/BFO_0000147 zero-dimensional continuant fiat boundary http://purl.obolibrary.org/obo/BFO_0000140 continuant fiat boundary http://purl.obolibrary.org/obo/BFO_0000006 spatial region http://purl.obolibrary.org/obo/BFO_0000141 immaterial entity http://purl.obolibrary.org/obo/BFO_0000029 site http://purl.obolibrary.org/obo/BFO_0000141 immaterial entity http://purl.obolibrary.org/obo/IAO_0000034 time trigger http://purl.obolibrary.org/obo/IAO_0000001 conditional specification http://purl.obolibrary.org/obo/UO_0000005 temperature unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label http://purl.obolibrary.org/obo/UO_0000006 substance unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label http://purl.obolibrary.org/obo/UO_0000051 concentration unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label http://purl.obolibrary.org/obo/UO_0000095 volume unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label http://purl.obolibrary.org/obo/UO_0000105 frequency unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label http://purl.obolibrary.org/obo/UO_0000109 pressure unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label http://purl.obolibrary.org/obo/UO_0000270 volumetric flow rate unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label http://purl.obolibrary.org/obo/UO_0000280 rate unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label http://purl.obolibrary.org/obo/IAO_0000429 email address http://purl.obolibrary.org/obo/IAO_0000030 information content entity http://purl.obolibrary.org/obo/IAO_0000057 contour plot http://purl.obolibrary.org/obo/IAO_0000038 graph http://purl.obolibrary.org/obo/IAO_0000582 time stamped measurement datum http://purl.obolibrary.org/obo/IAO_0000109 measurement datum http://purl.obolibrary.org/obo/OBI_0000794 transcription factor binding site http://purl.obolibrary.org/obo/OBI_0000905 sequence feature annotation http://purl.obolibrary.org/obo/NCBITaxon_10239 Viruses http://purl.obolibrary.org/obo/OBI_0100026 organism http://purl.obolibrary.org/obo/NCBITaxon_2157 Archaea http://purl.obolibrary.org/obo/OBI_0100026 organism http://purl.obolibrary.org/obo/OBI_0200001 geometric mean calculation http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating http://purl.obolibrary.org/obo/IAO_0000008 obsolete_artifact http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://purl.obolibrary.org/obo/IAO_0000018 obsolete_material_entity http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://purl.obolibrary.org/obo/IAO_0000128 obsolete_identifier http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://purl.obolibrary.org/obo/IAO_0000141 obsolete_digital quality http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://purl.obolibrary.org/obo/OBI_0000340 obsolete_documenting http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://purl.obolibrary.org/obo/OBI_0000851 obsolete_diethyl pyrocarbonate http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://purl.obolibrary.org/obo/OBI_0000926 obsolete_ambidexterious handedness http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://purl.obolibrary.org/obo/OBI_0000937 obsolete_left handedness http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://purl.obolibrary.org/obo/OBI_0000956 obsolete_handedness http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://purl.obolibrary.org/obo/OBI_0000974 obsolete_right handedness http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://purl.obolibrary.org/obo/OBI_0000987 obsolete_general scalar measurement datum http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://purl.obolibrary.org/obo/CHEBI_4705 double-stranded DNA http://purl.obolibrary.org/obo/CHEBI_16991 deoxyribonucleic acid http://purl.obolibrary.org/obo/NCBITaxon_160 Treponema pallidum http://purl.obolibrary.org/obo/NCBITaxon_2 Bacteria http://purl.obolibrary.org/obo/NCBITaxon_716545 saccharomyceta http://purl.obolibrary.org/obo/NCBITaxon_4890 Ascomycota http://purl.obolibrary.org/obo/NCBITaxon_10358 Cytomegalovirus http://purl.obolibrary.org/obo/NCBITaxon_10292 Herpesviridae http://purl.obolibrary.org/obo/NCBITaxon_11676 Human immunodeficiency virus 1 http://purl.obolibrary.org/obo/NCBITaxon_11646 Lentivirus http://purl.obolibrary.org/obo/NCBITaxon_11709 Human immunodeficiency virus 2 http://purl.obolibrary.org/obo/NCBITaxon_11646 Lentivirus http://purl.obolibrary.org/obo/NCBITaxon_197562 Pancrustacea http://purl.obolibrary.org/obo/NCBITaxon_1206794 Ecdysozoa http://purl.obolibrary.org/obo/NCBITaxon_44689 Dictyostelium discoideum http://purl.obolibrary.org/obo/NCBITaxon_2759 Eukaryota http://purl.obolibrary.org/obo/NCBITaxon_33154 Opisthokonta http://purl.obolibrary.org/obo/NCBITaxon_2759 Eukaryota http://purl.obolibrary.org/obo/NCBITaxon_33213 Bilateria http://purl.obolibrary.org/obo/NCBITaxon_33154 Opisthokonta http://purl.obolibrary.org/obo/NCBITaxon_1206794 Ecdysozoa http://purl.obolibrary.org/obo/NCBITaxon_33213 Bilateria http://purl.obolibrary.org/obo/NCBITaxon_314146 Euarchontoglires http://purl.obolibrary.org/obo/NCBITaxon_40674 Mammalia http://purl.obolibrary.org/obo/NCBITaxon_5140 Neurospora http://purl.obolibrary.org/obo/NCBITaxon_716545 saccharomyceta http://purl.obolibrary.org/obo/NCBITaxon_39107 Murinae http://purl.obolibrary.org/obo/NCBITaxon_9989 Rodentia http://purl.obolibrary.org/obo/UBERON_0006911 digestive system secreted substance http://purl.obolibrary.org/obo/UBERON_0000463 organism substance http://purl.obolibrary.org/obo/IAO_8000016 taxonomic bridge ontology module http://purl.obolibrary.org/obo/IAO_8000004 bridge ontology module http://purl.obolibrary.org/obo/IAO_8000019 ontology module subsetted by OWL profile http://purl.obolibrary.org/obo/IAO_8000017 ontology module subsetted by expressivity http://purl.obolibrary.org/obo/IAO_8000020 EL++ ontology module http://purl.obolibrary.org/obo/IAO_8000019 ontology module subsetted by OWL profile http://purl.obolibrary.org/obo/CHEBI_37987 Cy3 dye http://purl.obolibrary.org/obo/OBI_0002744 molecular label http://purl.obolibrary.org/obo/CHEBI_37989 Cy5 dye http://purl.obolibrary.org/obo/OBI_0002744 molecular label http://purl.obolibrary.org/obo/CHEBI_51756 Alexa Fluor 532 http://purl.obolibrary.org/obo/OBI_0002744 molecular label http://purl.obolibrary.org/obo/CHEBI_51760 Alexa Fluor 546 http://purl.obolibrary.org/obo/OBI_0002744 molecular label http://purl.obolibrary.org/obo/UBERON_0001707 nasal cavity An anatomical cavity that is part of the olfactory apparatus. This includes the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present. http://purl.obolibrary.org/obo/BFO_0000001 entity http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://purl.obolibrary.org/obo/RO_0000079 function of http://purl.obolibrary.org/obo/RO_0000052 inheres in is function of a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000080 quality of http://purl.obolibrary.org/obo/RO_0000052 inheres in quality_of a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000085 has function http://purl.obolibrary.org/obo/RO_0000053 bearer of has_function a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000086 has quality http://purl.obolibrary.org/obo/RO_0000053 bearer of has_quality a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0002350 member of http://purl.obolibrary.org/obo/BFO_0000050 part of member part of is member of is a mereological relation between a item and a collection. http://purl.obolibrary.org/obo/RO_0000087 has role http://purl.obolibrary.org/obo/RO_0000053 bearer of has_role a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000081 role of http://purl.obolibrary.org/obo/RO_0000052 inheres in role_of a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/IAO_0000142 mentions http://purl.obolibrary.org/obo/IAO_0000136 is about An information artifact IA mentions an entity E exactly when it has a component/part that denotes E http://purl.obolibrary.org/obo/IAO_0000219 denotes http://purl.obolibrary.org/obo/IAO_0000136 is about A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically http://purl.obolibrary.org/obo/IAO_0000221 is quality measurement of http://purl.obolibrary.org/obo/IAO_0000136 is about m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q http://purl.obolibrary.org/obo/IAO_0000413 is duration of http://purl.obolibrary.org/obo/IAO_0000136 is about relates a process to a time-measurement-datum that represents the duration of the process http://purl.obolibrary.org/obo/IAO_0000418 is quality specification of http://purl.obolibrary.org/obo/IAO_0000136 is about A relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality. http://purl.obolibrary.org/obo/IAO_0000581 has time stamp http://purl.obolibrary.org/obo/BFO_0000051 has part relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken http://purl.obolibrary.org/obo/IAO_0000583 has measurement datum http://purl.obolibrary.org/obo/BFO_0000051 has part relates a time stamped measurement datum to the measurement datum that was measured http://purl.obolibrary.org/obo/OBI_0000107 provides_service_consumer_with http://purl.obolibrary.org/obo/BFO_0000051 has part A relation between a service and the primary processual part of the service that is performed by the provider for the consumer. http://purl.obolibrary.org/obo/OBI_0000293 has_specified_input http://purl.obolibrary.org/obo/RO_0000057 has participant A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. http://purl.obolibrary.org/obo/OBI_0000295 is_specified_input_of http://purl.obolibrary.org/obo/RO_0000056 participates in A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. http://purl.obolibrary.org/obo/OBI_0000299 has_specified_output http://purl.obolibrary.org/obo/RO_0000057 has participant A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. http://purl.obolibrary.org/obo/OBI_0000312 is_specified_output_of http://purl.obolibrary.org/obo/RO_0000056 participates in A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. http://purl.obolibrary.org/obo/OBI_0000643 has grain http://purl.obolibrary.org/obo/BFO_0000051 has part the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car. http://purl.obolibrary.org/obo/OBI_0000645 is grain of http://purl.obolibrary.org/obo/BFO_0000050 part of A relation between granular parts and the whole of which they are a part. Granular parts have indeterminate number such that removing one granular part does not necessarily damage or diminish the whole. http://purl.obolibrary.org/obo/OBI_0000999 has category label http://purl.obolibrary.org/obo/BFO_0000051 has part A relation between a categorical measurement data item and the categorical label that indicates the value of that data item on the categorical scale. http://purl.obolibrary.org/obo/OBI_0001927 specifies value of http://purl.obolibrary.org/obo/IAO_0000136 is about A relation between a value specification and an entity which the specification is about. http://purl.obolibrary.org/obo/OBI_0001937 has specified numeric value http://purl.obolibrary.org/obo/OBI_0002135 has specified value A relation between a value specification and a number that quantifies it. http://purl.obolibrary.org/obo/OBI_0001938 has value specification http://purl.obolibrary.org/obo/BFO_0000051 has part A relation between an information content entity and a value specification that specifies its value. http://purl.obolibrary.org/obo/OBI_1110060 process is result of http://purl.obolibrary.org/obo/RO_0002087 immediately preceded by is a relationship between a process and a preceding occurrent that directly caused the later one to occur http://purl.obolibrary.org/obo/RO_0002219 surrounded by http://purl.obolibrary.org/obo/RO_0002220 adjacent to x surrounded_by y if and only if x is adjacent to y and for every region r that is adjacent to x, r overlaps y http://purl.obolibrary.org/obo/RO_0002223 starts http://purl.obolibrary.org/obo/BFO_0000050 part of inverse of starts with http://purl.obolibrary.org/obo/RO_0002351 has member http://purl.obolibrary.org/obo/BFO_0000051 has part has member is a mereological relation between a collection and an item. http://purl.obolibrary.org/obo/RO_0000091 has disposition http://purl.obolibrary.org/obo/RO_0000053 bearer of a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/ONE_0003017 promotion method http://purl.obolibrary.org/obo/ONE_0003009 object property of food-based dietary guidelines a relation between a food-based dietary guideline and a promotion method , in which the promotion method encourages individuals to adopt and maintain healthy behaviours indicated in the food-based dietary guideline. http://purl.obolibrary.org/obo/ONE_0003016 target audience http://purl.obolibrary.org/obo/ONE_0003009 object property of food-based dietary guidelines a relation between a food-based dietary guideline and a group of individuals , in which the food-based dietary guideline is developed for the group of individuals. http://purl.obolibrary.org/obo/RO_0002180 has component http://purl.obolibrary.org/obo/BFO_0000051 has part w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. http://purl.obolibrary.org/obo/ONE_0003015 stakeholder http://purl.obolibrary.org/obo/ONE_0003009 object property of food-based dietary guidelines a relation between a food-based dietary guideline and an independent party, in which people from the independent party contributes to the development of the food-based dietary guideline. http://purl.obolibrary.org/obo/ONE_0003018 evidence characteristic http://purl.obolibrary.org/obo/ONE_0003009 object property of food-based dietary guidelines a relation between a food-based dietary guideline and an evidence characteristic , in which the evidence (e.g. scientific reports, articles, etc.) with the characteristic is used to support the food-based dietary guideline. http://purl.obolibrary.org/obo/ONE_0003009 object property of food-based dietary guidelines http://purl.obolibrary.org/obo/ONE_0003009 object property of food-based dietary guidelines a relation between a food-based dietary guideline and an information content entity, in which the information content entity specifies the quality of the food-based dietary guideline. http://purl.obolibrary.org/obo/ONE_0003012 target area http://purl.obolibrary.org/obo/ONE_0003009 object property of food-based dietary guidelines a relation between a food-based dietary guideline and a geographic location, in which the geographic location specifies where to apply the food-based dietary guideline. http://purl.obolibrary.org/obo/ONE_0003014 has update frequency http://purl.obolibrary.org/obo/ONE_0003019 data property of food-based dietary guidelines a relation between a food-based dietary guideline and its update frequency. http://purl.obolibrary.org/obo/RO_0002087 immediately preceded by http://purl.obolibrary.org/obo/BFO_0000062 preceded by starts_at_end_of http://purl.obolibrary.org/obo/RO_0002090 immediately precedes http://purl.obolibrary.org/obo/BFO_0000063 precedes meets http://purl.obolibrary.org/obo/RO_0000092 disposition of http://purl.obolibrary.org/obo/RO_0000052 inheres in http://purl.obolibrary.org/obo/OBI_0001950 has performer http://purl.obolibrary.org/obo/RO_0000057 has participant http://purl.obolibrary.org/obo/IAO_0000039 has measurement unit label http://purl.obolibrary.org/obo/BFO_0000051 has part http://purl.obolibrary.org/obo/IAO_0000407 has coordinate unit label http://purl.obolibrary.org/obo/BFO_0000051 has part http://purl.obolibrary.org/obo/BFO_0000063 precedes http://purl.obolibrary.org/obo/RO_0002222 temporal relation http://purl.obolibrary.org/obo/ONE_0003013 has publication year http://purl.obolibrary.org/obo/ONE_0003019 data property of food-based dietary guidelines http://purl.obolibrary.org/obo/OBI_0000300 obsolete_is_realized_by is_realized_as Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm] http://purl.obolibrary.org/obo/OBI_0000304 is_manufactured_by has_manufacturer c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this. http://purl.obolibrary.org/obo/OBI_0000308 obsolete_realizes is_realization_of Relation between a process and a function, where the unfolding of the process requires the execution of the function. Class level: P realizes F iff: given any p that instantiates P, there exists some f, t such that f instantiates F at t and p *realizes* f. Here, *realizes* is the primitive instance level relation [GOC:cjm] http://purl.obolibrary.org/obo/OBI_0000315 obsoleted_has_specified_input_information consumes data A relation between a process and a participant in that process, that consumes a data set . The process is the realization of a concretization of a directive information entity (objective specification or plan specification). In general, not all data present at the beginning of the process are specified_data. http://purl.obolibrary.org/obo/OBI_0000646 provisions supplies A relation between an organisation or person and a material entity, where the organization or person provides or supplies the material entity for others to use http://purl.obolibrary.org/obo/RO_0000052 inheres in inheres_in a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000053 bearer of is bearer of a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000056 participates in participates_in a relation between a continuant and a process, in which the continuant is somehow involved in the process http://purl.obolibrary.org/obo/RO_0000057 has participant has_participant a relation between a process and a continuant, in which the continuant is somehow involved in the process http://purl.obolibrary.org/obo/RO_0001000 derives from derives_from a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity http://purl.obolibrary.org/obo/RO_0001001 derives into derives_into a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity http://purl.obolibrary.org/obo/RO_0001015 location of location_of a relation between two independent continuants, the location and the target, in which the target is entirely within the location http://purl.obolibrary.org/obo/RO_0002000 2D boundary of is boundary of a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity http://purl.obolibrary.org/obo/RO_0002002 has 2D boundary has_2D_boundary a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity http://purl.obolibrary.org/obo/RO_0001025 located in located_in a relation between two independent continuants, the target and the location, in which the target is entirely within the location http://purl.obolibrary.org/obo/BFO_0000051 has part has_part a core relation that holds between a whole and its part http://purl.obolibrary.org/obo/BFO_0000050 part of part_of a core relation that holds between a part and its whole http://purl.obolibrary.org/obo/BFO_0000066 occurs in unfolds_in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t http://purl.obolibrary.org/obo/OBI_0002135 has specified value A relation between a value specification and a literal. http://purl.obolibrary.org/obo/BFO_0000067 contains process [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t http://purl.obolibrary.org/obo/IAO_0000135 obsolete_specifically denotes c specifically denotes r =def r is a portion of reality & c is a particular quality & c depends specifically on some independent continuant b & b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. Case 1 Memory trace as mark created when reading some description of some friend. The trace can denote. Case 2 Pattern of ink arrayed on paper as mark when writing down a friend's name Case 3 Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file. http://purl.obolibrary.org/obo/IAO_0000136 is about A (currently) primitive relation that relates an information artifact to an entity. http://purl.obolibrary.org/obo/IAO_0000417 is quality measured as inverse of the relation of is quality measurement of http://purl.obolibrary.org/obo/IAO_0000419 quality is specified as inverse of the relation of is quality specification of http://purl.obolibrary.org/obo/OBI_0000124 is_supported_by_data The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process http://purl.obolibrary.org/obo/OBI_0000292 has_feature_value has_feature_value datatype property is used to describe the feature values which the feature class can contain, for example has_base can have feature values of nonNegativeInteger values. http://purl.obolibrary.org/obo/OBI_0000294 obsolete_is_concretization_of Is a relationship between a generically dependent continuant and a specifically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter. http://purl.obolibrary.org/obo/OBI_0000297 obsolete_is_concretized_as Is a relationship between a specifically dependent continuant and a generically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter. http://purl.obolibrary.org/obo/OBI_0000298 obsolete_has_quality A relation between an entity and a quality. For types: E has_quality Q iff: for any eEt, exists qQt such that q inheres_in e at t. For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Quality [GOC:cjm] http://purl.obolibrary.org/obo/OBI_0000301 obsoleted_has_specified_output_information A relation between a participant in a process, that produces a data set . The process is the realization of a concretization of a realizable information entity (objective specification or plan specification). In general, not all data present at the end of the process are specified_data. http://purl.obolibrary.org/obo/OBI_0000306 obsolete_has_function Relation between an independent continuant and a function. http://purl.obolibrary.org/obo/OBI_0000307 obsoleted_is_reagent_in Relationship between a substance and a protocol application in which it participates, where the substance has a ReagentRole http://purl.obolibrary.org/obo/OBI_0000309 obsoleted_utilizes_reagent Relationship between a protocol application and a substance that has role reagent that participates in the protocol application http://purl.obolibrary.org/obo/OBI_0000311 obsoleted_is_device_for Relationship between a device and a protocol application in which it participates http://purl.obolibrary.org/obo/OBI_0000313 obsoleted_utilizes_device Relationship between protocol application and an intrument in which it participates http://purl.obolibrary.org/obo/OBI_0000314 is_proxy_for A relation between continuant instances c1 and c2 where within an experiment/ protocol application, measurement of c1 is used to determine what a measurement of c2 would be. http://purl.obolibrary.org/obo/OBI_0000316 obsolete_has_role A relation between a continuant C and a role R. The reciprocal relation of role_of. http://purl.obolibrary.org/obo/OBI_0000417 achieves_planned_objective This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. http://purl.obolibrary.org/obo/OBI_0000459 obsoleted_is_specified_information_output_of A relation between a data set and the process in which it participates and was produced. Inverse of outputs_specified_data relation. http://purl.obolibrary.org/obo/OBI_0000644 obsoleted_is_specified_information_intput_of Is the inverse relation of has_specfied_input_information http://purl.obolibrary.org/obo/OBI_0000647 has_supplier A relation between a material entity and an organisation or person who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner. http://purl.obolibrary.org/obo/OBI_0000833 objective_achieved_by This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. http://purl.obolibrary.org/obo/OBI_0000846 is member of organization Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization. http://purl.obolibrary.org/obo/OBI_0001637 has disposition to bind A relationship between two material entitites that each have disposition to form a complex with the other. http://purl.obolibrary.org/obo/OBI_0001688 has organization member Relating an organization to a legal person or organization. http://purl.obolibrary.org/obo/OBI_1110119 bound_to A relationship between two material entities that form a complex based on a selective, non-covalent interaction. http://purl.obolibrary.org/obo/RO_0000058 is concretized as A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. http://purl.obolibrary.org/obo/RO_0000059 concretizes A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. http://purl.obolibrary.org/obo/ONE_0003019 data property of food-based dietary guidelines a relation between a food-based dietary guideline and an information content entity, in which the information content entity specifies the quality of the food-based dietary guideline. http://purl.obolibrary.org/obo/IAO_0000235 denoted by inverse of the relation 'denotes' http://purl.obolibrary.org/obo/OBI_0002815 has representation 'has representation' is a data property that attaches between an information content entity and a value that contains linguistically or computationally coded text. http://purl.obolibrary.org/obo/BFO_0000054 realized in realized_in http://purl.obolibrary.org/obo/BFO_0000062 preceded by preceded_by http://purl.obolibrary.org/obo/BFO_0000055 realizes http://purl.obolibrary.org/obo/IAO_0000004 has measurement value http://purl.obolibrary.org/obo/IAO_0000220 obsolete_materially denotes http://purl.obolibrary.org/obo/IAO_0000222 obsolete_describes http://purl.obolibrary.org/obo/IAO_0000223 obsolete_represents http://purl.obolibrary.org/obo/IAO_0000404 has x coordinate value http://purl.obolibrary.org/obo/IAO_0000405 has z coordinate value http://purl.obolibrary.org/obo/IAO_0000406 has y coordinate value http://purl.obolibrary.org/obo/OBI_0000365 obsolete_results_from http://purl.obolibrary.org/obo/OBI_1110112 obsolete_is_described_by http://purl.obolibrary.org/obo/RO_0002220 adjacent to http://purl.obolibrary.org/obo/RO_0002222 temporal relation