Term IRI Term label Parent term IRI Parent term label Alternative term Definition http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity http://purl.obolibrary.org/obo/BFO_0000040 material entity molecular 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/OBIB_0000068 collection packet identifier http://purl.obolibrary.org/obo/IAO_0020000 proper name Kit ID An identifier that refers to a collection packet used in a specimen collection process. http://purl.obolibrary.org/obo/OBIB_0000070 standard operating procedure http://purl.obolibrary.org/obo/OBI_0000272 protocol SOP A protocol that is a set of step-by-step instructions compiled by an organization for carrying out routine operations. http://purl.obolibrary.org/obo/OBIB_0000073 case report form completion SOP http://purl.obolibrary.org/obo/OBIB_0000070 standard operating procedure CRF completion protocol A standard operating procedure for properly and completely filling out a case report form. http://purl.obolibrary.org/obo/OBIB_0000086 specimen collected with specific collection packet http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism specimen collected with specific kit A specimen from organism that is collected with a collection packet that is designed to collect specimens of a particular type for a particular purpose. http://purl.obolibrary.org/obo/OBIB_0000250 conical centrifuge tube identifier http://purl.obolibrary.org/obo/IAO_0020000 proper name Conical centrifuge Tube code An identifier that specifically identifies a particular conical centrifuge tube. 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/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 a data item is 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_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_0000300 textual entity http://semanticscience.org/resource/SIO_000078 language 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_0000317 methods section http://purl.obolibrary.org/obo/IAO_0000314 document part 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_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/OBI_0000018 material supplier role http://purl.obolibrary.org/obo/OBI_0000947 service provider role material provider role 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_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_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_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_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_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/NGBO_6000353 omics data generation assay transcription profiling An assay that determines gene expression and transcription activity using ribonucleic acids collected from a material entity. 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_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_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_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 which is manufactured by 454 Life Science Corporation 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_0000702 454 Genome Sequencer FLX http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer GS-FLX is a DNA sequencer which is manufactured by 454 Life Science Corporation 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_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_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_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_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_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_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_0000893 real time polymerase chain reaction assay http://purl.obolibrary.org/obo/NGBO_6000264 validation of known variant 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_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_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_0001271 RNA-seq assay http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay transcription profiling by high throughput sequencing An transcription profiling 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_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_0001616 specimen identifier http://semanticscience.org/resource/SIO_000115 identifier 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_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_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_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_0600047 sequencing 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_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_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_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_0001922 microRNA profiling by high throughput sequencing assay http://purl.obolibrary.org/obo/OBI_0001926 microRNA profiling assay miRNA-HTS 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_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_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_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_0002004 surgical cancer treatment http://purl.obolibrary.org/obo/OBI_0001870 Illumina methylation BeadChip Illumina Infinium Human Methylation 450K BeadChip A cancer therapeutic procedure that involves a surgical procedure as a main part. http://purl.obolibrary.org/obo/OBI_0002005 specimen gross appearance of metastatic tumor http://purl.obolibrary.org/obo/OBI_0001870 Illumina methylation BeadChip Illumina Infinium Human Methylation 27K BeadChip A specimen gross appearance of a tumor that has spread from its original site by discontinuous (not direct) spread, e.g. by blood or lymphatics. http://purl.obolibrary.org/obo/OBI_0002006 specimen gross appearance of tumor center http://purl.obolibrary.org/obo/OBI_0001869 Illumina BeadChip Illumina Human 1M-Duo Infinium HD BeadChip A specimen gross appearance of the most internal topographic location of the tumor. http://purl.obolibrary.org/obo/OBI_0002007 specimen gross appearance of tumor edge http://purl.obolibrary.org/obo/OBI_0000696 AB SOLiD System Applied Biosystems SOLiD 3 Plus System A specimen gross appearance of the border of the tumor with non-tumorous tissue. http://purl.obolibrary.org/obo/OBI_0002008 research authorization for post mortem specimen donation for a specific tissue or fluid http://purl.obolibrary.org/obo/OBI_0001307 tiling microarray Nimblegen Mouse 385K Whole Genome CGH Tiling Array A research authorization documentation for postmortem specimen donation in which the authorization is for a specified tissue or biological fluid. http://purl.obolibrary.org/obo/OBI_0002009 0-non autolyis http://purl.obolibrary.org/obo/OBI_0001307 tiling microarray Nimblegen Mouse 3x720K Whole Genome CGH Tiling Array An autolysis value specification that indicates no apparent autolytic destruction of an organism cells or tissues. http://purl.obolibrary.org/obo/OBI_0002010 1-slight autolysis http://purl.obolibrary.org/obo/OBI_0001307 tiling microarray Nimblegen Human 3x720K Whole Genome CGH Tiling Array An autolysis value specification that indicates slight autolytic destruction of an organism cells or tissues. http://purl.obolibrary.org/obo/OBI_0002011 2-moderate autolysis http://purl.obolibrary.org/obo/OBI_0001307 tiling microarray Nimblegen Human 2.1M Whole-Genome CGH Tiling Array v2.0 An autolysis value specification that indicates moderate autolytic destruction of an organism cells or tissues. http://purl.obolibrary.org/obo/OBI_0002012 3-severe autolysis http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer Pacific Biosciences RS II An autolysis value specification that indicates severe autolytic destruction of an organism cells or tissues. 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_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_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_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_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_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 poly(A)-site sequencing assay http://purl.obolibrary.org/obo/OBI_0001271 RNA-seq assay Poly(A)-site sequencing A RNA-seq assay that quantitatively profiles RNA polyadenylation at the transcriptome level. 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_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_0002112 small RNA sequencing assay http://purl.obolibrary.org/obo/OBI_0001271 RNA-seq assay short 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_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_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_0100067 bronchial alveolar lavage http://purl.obolibrary.org/obo/OBI_0000953 processed 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_0200000 data transformation http://purl.obolibrary.org/obo/OBI_0000011 planned process data processing A data transformation is a process which produces output data from input data 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_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_0200111 data visualization http://purl.obolibrary.org/obo/OBI_0000011 planned process data encoding as image An planned process that creates images, diagrams or animations from the input data. http://purl.obolibrary.org/obo/OBI_0200178 class discovery objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective clustering 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 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_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_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_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_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_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/REO_0000171 molecular label role http://purl.obolibrary.org/obo/BFO_0000023 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/SO_0000001 region http://purl.obolibrary.org/obo/BFO_0000031 generically dependent continuant primary structure of sequence macromolecule 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/OMIABIS_0000003 biobank proper name http://purl.obolibrary.org/obo/IAO_0020000 proper name Name of biobank An identifier in natural language referring to a biobank. http://purl.obolibrary.org/obo/OMIABIS_0000005 biobank idenfier with ISO 3166-1 alpha-2 code http://purl.obolibrary.org/obo/OMIABIS_0000003 biobank proper name Biobank ID A biobank identifier that has an ISO 3166-1 alpha-2 code as a part. http://purl.obolibrary.org/obo/OMIABIS_0000007 ISO 3166-1 alpha-2 code for sample collection or study contact http://purl.obolibrary.org/obo/OMIABIS_0000004 ISO 3166-1 alpha-2 code Sample Collection/Study contact country The ISO 3166-1 alpha-2 code that is part of the sample collection or study contact's postal address. http://purl.obolibrary.org/obo/OMIABIS_0000014 name of biobank contact person http://purl.obolibrary.org/obo/IAO_0020015 personal name Biobank contact person A personal name that designates the person acting as contact for a sample collection or a study. http://purl.obolibrary.org/obo/OMIABIS_0000028 ISO 3166-1 alpha-2 code for biobank contact person http://purl.obolibrary.org/obo/OMIABIS_0000004 ISO 3166-1 alpha-2 code Biobank country code The ISO 3166-1 alpha-2 code that is part of the biobank contact person's postal address. http://purl.obolibrary.org/obo/OMIABIS_0000037 study proper name http://purl.obolibrary.org/obo/IAO_0020000 proper name Study name A proper name that designates a study. http://purl.obolibrary.org/obo/OMIABIS_0000038 name of sample collection responsible or principal investigator http://purl.obolibrary.org/obo/IAO_0020015 personal name Sample Collection Responsible / Principal Investigator A personal name that designates the human being responsible for a sample collection or the human being being the principal investigator in a study. http://purl.obolibrary.org/obo/OMIABIS_0000039 name of sample collection or study contact person http://purl.obolibrary.org/obo/IAO_0020015 personal name Sample Collection/Study contact person A personal name that designates the person acting as contact for a sample collection or a study. http://purl.obolibrary.org/obo/OMIABIS_0000045 biobank location ISO 3166-1 alpha-2 code http://purl.obolibrary.org/obo/OMIABIS_0000004 ISO 3166-1 alpha-2 code Biobank country code An ISO 3166-1 alpha-2 code that designates the country a biobank is located in. http://purl.obolibrary.org/obo/OMIABIS_0001080 sample handling http://purl.obolibrary.org/obo/OBI_0000011 planned process specimen handling A planned process of preparing and submitting specimens to storage. http://purl.obolibrary.org/obo/OBIB_0000272 specimen transporting organization http://purl.obolibrary.org/obo/BFO_0000023 role specimen shipping organization A role borne by an organization that is the provider of a specimen that is transported to another organization. http://purl.obolibrary.org/obo/OBIB_0000274 name of person responsible for specimen transport http://purl.obolibrary.org/obo/IAO_0020015 personal name name of person responsible for specimen shipment A personal name that designates the person who is responsible for the transport of a specimen to another organization. http://purl.obolibrary.org/obo/OBIB_0000275 name of IATA-trained person verifying specimen transport http://purl.obolibrary.org/obo/IAO_0020015 personal name name of IATA-trained person verifying specimen shipment A personal name that designates the person who verified the specimen transport was according to best practice, international standards, and industry regulations as trained by the IATA. http://purl.obolibrary.org/obo/OBIB_0000318 name of specimen slide preparation technician http://purl.obolibrary.org/obo/IAO_0020015 personal name Slide Prep Technician Name A personal name that designates the person who performed a specimen slide preparation. http://purl.obolibrary.org/obo/OBIB_0000360 collection packet component ID http://purl.obolibrary.org/obo/IAO_0020000 proper name kit component ID An identifier that specifically identifies a particular component of a collection packet. http://purl.obolibrary.org/obo/OBIB_0000387 name of submitter of pathology case summary report. http://purl.obolibrary.org/obo/IAO_0020015 personal name name of submitting pathologist name of submitter of pathology case summary report. http://purl.obolibrary.org/obo/OBIB_0000389 name of reviewer of pathology case summary report. http://purl.obolibrary.org/obo/IAO_0020015 personal name name of submitting pathologist A personal name that designates the person who served as the reviewer for quality assurance purposes of a pathology case summary report. http://purl.obolibrary.org/obo/OBIB_0000474 identification number of a protocol at a particular site http://purl.obolibrary.org/obo/IAO_0000577 centrally registered identifier symbol protocol number at a site An centrally registered identifier symbol assigned by an Institutional Review Board (IRB) that identifies a particular protocol at a given site. http://purl.obolibrary.org/obo/OBIB_0000477 name of person screening specimen donors http://purl.obolibrary.org/obo/IAO_0020015 personal name specimen donor screener A personal name that designates who performed the screening of a potential specimen donor for a research study. http://purl.obolibrary.org/obo/OBIB_0000478 name of person obtaining authorization from legally authorized representative for post-mortem specimen donation http://purl.obolibrary.org/obo/IAO_0020015 personal name Research authorization obtainer for post-mortem specimen donation A personal name of an individual with research obtainer role who approaches a person's legal representative and informs them of key facts about potential risks and benefits, and asks them for authorization for post-mortem specimen donation for research for the person they legally represent. http://purl.obolibrary.org/obo/OBIB_0000480 identifier for legally authorized representative http://purl.obolibrary.org/obo/IAO_0020000 proper name legal representative identifier An identifier that uniquely identifies a particular legally authorized representative in a research study. http://purl.obolibrary.org/obo/DOID_162 cancer http://purl.obolibrary.org/obo/OGMS_0000031 disease malignant tumor A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis. http://purl.obolibrary.org/obo/OBI_0002457 precision nuclear run-on sequencing assay http://purl.obolibrary.org/obo/OBI_0001271 RNA-seq 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_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/OMRSE_00000010 human health care role http://purl.obolibrary.org/obo/OMRSE_00000024 role in human social processes health care role A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis. http://www.ebi.ac.uk/efo/EFO_0003919 risk factor http://purl.obolibrary.org/obo/BFO_0000016 disposition Risk Factors An aspect of personal behavior or lifestyle, environmental exposure, or inborn or inherited characteristic, which, on the basis of epidemiologic evidence, is known to be associated with a health-related condition considered important to prevent. http://purl.obolibrary.org/obo/NCIT_C81229 Alcohol Use History http://semanticscience.org/resource/SIO_001196 history Alcohol Use History A description of an individual's current and past experience with alcoholic beverage consumption. 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/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_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 ethical approval 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_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_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/NCIT_C29719 Smoking History http://semanticscience.org/resource/SIO_001196 history Smoking History A record of an individual's background in regard to smoking tobacco. This would include such factors as start date, end date (if applicable), number of cigarette smoked, attempts to quit, and others. http://purl.obolibrary.org/obo/GENO_0000902 genomic feature location http://purl.obolibrary.org/obo/GENO_0000815 sequence feature location genomic location The location of a sequence feature in a genome, defined by its start and end position on some reference genomic coordinate system 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_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_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_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/ICO_0000088 participation duration http://purl.obolibrary.org/obo/BFO_0000038 one-dimensional temporal region a temporal interval that represent the time of someone (for example the study subject) participating the study or the research. 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_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_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_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_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_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/OBIB_0000060 time in fixative measurement http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum that states the duration during which a specimen was submerged in fixative. http://purl.obolibrary.org/obo/OBIB_0000071 specimen transport SOP http://purl.obolibrary.org/obo/OBIB_0000070 standard operating procedure A standard operating procedure for the transportation of specimens. http://purl.obolibrary.org/obo/OBIB_0000072 tissue procurement SOP http://purl.obolibrary.org/obo/OBIB_0000070 standard operating procedure A standard operating procedure for collecting specimens from organism. http://purl.obolibrary.org/obo/OBIB_0000093 time donor body refrigerated measurement http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum that states the duration during which the specimen donor's body was refrigerated. http://purl.obolibrary.org/obo/OBIB_0000131 in vivo intraoperative ischemic period http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum of the period between organ resection and the time of first clamping perfomed in vivo. http://purl.obolibrary.org/obo/OBIB_0000150 Duration of fasting by specimen donor prior to surgery http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum of the duration of fasting by the specimen donor prior to surgery. http://purl.obolibrary.org/obo/OBIB_0000200 receipt and dissection of surgical specimen SOP http://purl.obolibrary.org/obo/OBIB_0000070 standard operating procedure A standard operating procedure for the receipt and dissection of surgical tissue in a biobank. http://purl.obolibrary.org/obo/OBIB_0000202 name of biobank person receiving specimen http://purl.obolibrary.org/obo/IAO_0020015 personal name A personal name that designates the person who received a specimen in the biobank. http://purl.obolibrary.org/obo/OBIB_0000204 parent specimen ID http://purl.obolibrary.org/obo/OBI_0001616 specimen identifier A specimen ID denoting a specimen that is used to create a specimen family. http://purl.obolibrary.org/obo/OBIB_0000205 name of dissector of parent specimen http://purl.obolibrary.org/obo/IAO_0020015 personal name A personal name that designates the person who performed the dissection of a surgical specimen to create a specimen family. http://purl.obolibrary.org/obo/OBIB_0000220 buffered formalin condition http://purl.obolibrary.org/obo/BFO_0000019 quality A quality that inheres in buffered formalin by virtue of its usage and processing. http://purl.obolibrary.org/obo/OBIB_0000222 blood specimen collection and processing SOP http://purl.obolibrary.org/obo/OBIB_0000070 standard operating procedure A standard operating procedure for collection and processing of blood specimens. http://purl.obolibrary.org/obo/OBIB_0000232 name of person performing blood draw http://purl.obolibrary.org/obo/IAO_0020015 personal name A personal name that designates the person who performed the collection of a blood specimen. http://purl.obolibrary.org/obo/OBIB_0000240 name of person receiving blood specimen in laboratory http://purl.obolibrary.org/obo/IAO_0020015 personal name A personal name that designates the person who received a blood specimen in the laboratory. http://purl.obolibrary.org/obo/OBIB_0000243 vacutainer specimen barcode http://purl.obolibrary.org/obo/FLU_0001019 specimen barcode A specimen barcode that is associated with a vacutainer. http://purl.obolibrary.org/obo/OBIB_0000246 name of person storing specimen http://purl.obolibrary.org/obo/IAO_0020015 personal name A personal name that designates the person who stored a specimen. http://purl.obolibrary.org/obo/OBIB_0000252 blood plasma specimen barcode http://purl.obolibrary.org/obo/FLU_0001019 specimen barcode A specimen barcode that is associated with a blood plasma specimen. http://purl.obolibrary.org/obo/OBIB_0000255 cryovial specimen barcode http://purl.obolibrary.org/obo/FLU_0001019 specimen barcode A specimen barcode that is associated with a cryovial. http://purl.obolibrary.org/obo/OBIB_0000257 name of person processing blood plasma specimen aliquots http://purl.obolibrary.org/obo/IAO_0020015 personal name A personal name that designates the person who processed a blood specimen to generate aliquots of blood plasma specimens. http://purl.obolibrary.org/obo/OBIB_0000258 name of person transferring blood plasma specimens to freezer http://purl.obolibrary.org/obo/IAO_0020015 personal name A personal name that designates the person who transferred blood plasma specimens to freezer. http://purl.obolibrary.org/obo/OBIB_0000263 cell pellet specimen barcode http://purl.obolibrary.org/obo/FLU_0001019 specimen barcode A specimen barcode that is associated with a cell pellet specimen. http://purl.obolibrary.org/obo/OBIB_0000266 name of person processing blood cell pellet specimen http://purl.obolibrary.org/obo/IAO_0020015 personal name A personal name that designates the person who performed processing of the blood cell pellet specimen. 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/NGBO_6000179 alignment 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_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_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_0002585 sequence trimming http://purl.obolibrary.org/obo/NGBO_6000122 bioinformatics analysis A data transformation in which subsequences of a molecular sequence are cut (removed). http://purl.obolibrary.org/obo/PATO_0000128 weight http://purl.obolibrary.org/obo/PATO_0001018 physical quality A physical quality inhering in a bearer that has mass near a gravitational body. 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_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_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_0001827 pseudohermaphrodite http://purl.obolibrary.org/obo/PATO_0001894 phenotypic sex A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of one sex and external sexual characteristics of the other sex. 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_0015009 humidity http://purl.obolibrary.org/obo/PATO_0000146 temperature A quality inhering in air by virtue of the partial pressure exerted by the bearer's water vapour content. http://purl.obolibrary.org/obo/PO_0004010 meristematic cell http://purl.obolibrary.org/obo/PO_0025606 native plant cell A native plant cell (PO:0025606) synthesizing protoplasm and producing new cells by division and with only a primary cell wall. http://purl.obolibrary.org/obo/PO_0006204 sporocyte http://purl.obolibrary.org/obo/PO_0025606 native plant cell A native plant cell (PO:0025606) which is diploid (2n), and undergoes meiosis (GO:0007126) to produce four haploid (1n) plant spores (PO:0025017). http://purl.obolibrary.org/obo/PO_0009002 plant cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A cell which is a plant structure (PO:0009011). http://purl.obolibrary.org/obo/PO_0020099 microgametophyte vegetative cell http://purl.obolibrary.org/obo/PO_0025606 native plant cell A native plant cell (PO:0025606) that is the larger cell of a microgametophyte (PO:0025280) in seed plants. It does not divide further and develops into a pollen tube cell (PO:0025195). http://purl.obolibrary.org/obo/PO_0020132 columella root cap cell http://purl.obolibrary.org/obo/PO_0025606 native plant cell Cell that constitutes the central part of the root cap, arranged in longitudinal files. http://purl.obolibrary.org/obo/PO_0025606 native plant cell http://purl.obolibrary.org/obo/PO_0009002 plant cell A plant cell (PO:0009002) that is either part of a multicellular whole plant (PO:0000003) 'in vivo' or a unicellular organism 'in natura' (i.e. part of a natural environment). http://purl.obolibrary.org/obo/PO_0030007 meristematic apical cell http://purl.obolibrary.org/obo/PO_0004010 meristematic cell A single meristematic cell (PO:0004010) at the tip of a plant structure where apical growth occurs. http://purl.obolibrary.org/obo/PO_0030014 gametophyte meristematic apical cell http://purl.obolibrary.org/obo/PO_0030007 meristematic apical cell An apical cell that is part of a whole plant in the gametophytic phase. http://purl.obolibrary.org/obo/PO_0030015 sporophyte meristematic apical cell http://purl.obolibrary.org/obo/PO_0030007 meristematic apical cell A meristematic apical cell that is part of a whole plant in the sporophytic phase. http://purl.obolibrary.org/obo/BTO_0000238 cerebrovascular endothelial cell http://purl.obolibrary.org/obo/CL_0000115 endothelial cell Endothelial cell of or involving the cerebrum and the blood vessels supplying it. http://purl.obolibrary.org/obo/BTO_0000426 erythroleukemia cell http://www.ebi.ac.uk/efo/EFO_0005934 disease cell type Cancer cell of the blood-forming tissues in which large numbers of immature, abnormal red blood cells are found in the blood and bone marrow. http://purl.obolibrary.org/obo/BTO_0000551 lung cancer cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type Cancer cell of the major organ of respiration the lung. http://purl.obolibrary.org/obo/BTO_0001130 prostate gland cancer cell http://www.ebi.ac.uk/efo/EFO_0005934 disease cell type A malignant tumour cell of glandular origin in the prostate. Over 95% are adenocarcinomas. http://purl.obolibrary.org/obo/BTO_0001899 stationary phase culture http://www.ebi.ac.uk/efo/EFO_0002958 experimental cell A cell culture at the plateau of the growth curve after log growth in a culture, during which cell number remains constant. New cells are produced at the same rate as older cells die. http://purl.obolibrary.org/obo/BTO_0001903 logarithmic phase culture http://www.ebi.ac.uk/efo/EFO_0002958 experimental cell A cell culture at the steepest slope of the growth curve of a culture-- at the phase of vigorous growth during which cell number doubles every 20-30 minutes. http://purl.obolibrary.org/obo/BTO_0002842 cholangioma cell http://www.ebi.ac.uk/efo/EFO_0005934 disease cell type A rare type of hepatocellular carcinoma arising from the cholangioles, composed of tumor cells resembling the epithelial cells of the cholangioles arranged in cords consisting of two layers of cells surrounding a minute lumen. http://purl.obolibrary.org/obo/BTO_0002844 breast invasive ductal carcinoma cell http://www.ebi.ac.uk/efo/EFO_0005934 disease cell type Infiltrating ductal carcinoma is one of several recognized specific patterns of cancer of the breast. It is so named because it begins in the cells forming the ducts of the breast. It is the most common form of breast cancer, comprising 65-85% of all cases. http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://purl.obolibrary.org/obo/BFO_0000040 material entity A cell type is a distinct morphological or functional form of cell. Examples are epithelial, glial etc. http://www.ebi.ac.uk/efo/EFO_0002958 experimental cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type experimental cell is a cell which is experimentally derived such as a cell line cell, or a cell differentiated in culture. Experimentally derived cells may have diffrent properties from the cell from which they originally derived, such as through gene expression changes. 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_0002526 skin of body specimen 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/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_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_0000015 process http://purl.obolibrary.org/obo/BFO_0000003 occurrent p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) 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/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_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_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_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_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_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_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_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_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_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_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_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_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_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_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/OBI_0000011 planned process http://purl.obolibrary.org/obo/BFO_0000015 process A processual entity 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_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_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_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_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_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_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_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_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_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_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_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_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_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_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 organization is a continuant entity which can play 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_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_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_0000338 drawing a conclusion based on data http://purl.obolibrary.org/obo/NGBO_6000122 bioinformatics analysis 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_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_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_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_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_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_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_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_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_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_0000433 DNA sequence feature detection assay http://purl.obolibrary.org/obo/OBI_0200187 sequence analysis data transformation 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_0200187 sequence analysis data transformation An assay that measures changes (expansion, amplification, deletion, mutation) in the sequence of a DNA molecule. 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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_0000655 blood specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism a material entity derived from a portion of blood collected from an organism 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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_0000880 RNA extract http://purl.obolibrary.org/obo/NGBO_6000106 specimen derivative 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_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_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_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_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_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_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_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_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_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_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_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_0000989 PCR instrument http://purl.obolibrary.org/obo/OBI_0000968 device 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_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_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_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_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_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/NGBO_6000106 specimen derivative 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_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_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_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_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_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_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_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_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_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_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_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_0001166 validation by real time PCR design http://purl.obolibrary.org/obo/NGBO_6000362 validation of known variant protocol 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_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_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_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_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_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_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_0001361 transcription profiling by RT-PCR assay http://purl.obolibrary.org/obo/OBI_0000424 transcription profiling assay A transcription profiling assay that uses reverse transcription PCR (RT-PCR). 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_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_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_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_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_0001615 investigation description http://purl.obolibrary.org/obo/IAO_0000300 textual entity 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_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_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_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_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_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_0001872 sequence assembly process http://purl.obolibrary.org/obo/OBI_0200187 sequence analysis 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_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_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_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/OBI_0000684 specimen collection objective 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_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_0001900 specimen identifier assigned by specimen repository http://purl.obolibrary.org/obo/NGBO_6000161 personally identifiable information 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/NGBO_6000161 personally identifiable information A specimen identifier which is assigned by a sequencing facility 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_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_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_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/NGBO_6000122 bioinformatics analysis A sequence annotation bioinformatics analysis that identifies and reports sequence features (e.g. protein coding regions) in sequence data. 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_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_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_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_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_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_0001479 specimen from organism A specimen that is derived from bile. http://purl.obolibrary.org/obo/OBI_0002502 cerebrospinal fluid specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from cerbrospinal fluid. http://purl.obolibrary.org/obo/OBI_0002505 milk specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism A specimen that is derived from milk. http://purl.obolibrary.org/obo/OBI_0002506 pericardial fluid specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism 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_0001479 specimen from organism A specimen that is derived from sweat. http://purl.obolibrary.org/obo/OBI_0002510 synovial fluid specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism 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_0001479 specimen from organism A specimen that is derived from peritoneal fluid. http://purl.obolibrary.org/obo/OBI_0002515 pleural fluid specimen http://purl.obolibrary.org/obo/OBI_0001479 specimen from organism 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_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_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_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_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_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_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_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_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_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_0200183 scaling objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective is a data transformation objective where all, or some of a data set is adjusted by some data transformation according to some scale, for example a user defined minimum or maximum http://purl.obolibrary.org/obo/OBI_0200186 error correction objective http://purl.obolibrary.org/obo/OBI_0200168 correction objective An error correction objective is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself. http://purl.obolibrary.org/obo/OBI_0200187 sequence analysis data transformation http://purl.obolibrary.org/obo/NGBO_6000122 bioinformatics analysis A sequence analysis data transformation is a data transformation that has objective sequence analysis and has the aim of analysing ordered biological data for sequential patterns. http://purl.obolibrary.org/obo/OBI_0200196 correlation study objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A data transformation objective in which correlation is obtained (often measured as a correlation coefficient, ρ) which indicates the strength and direction of a relationship between two random variables. http://purl.obolibrary.org/obo/OBI_0200197 spectrum analysis objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective is a data transformation objective where the aim is to analyse some aspect of spectral data by some data transformation process. http://purl.obolibrary.org/obo/OBI_0302884 extraction http://purl.obolibrary.org/obo/OBI_0600014 material component separation A material separation in which a desired component of an input material is separated from the remainder http://purl.obolibrary.org/obo/OBI_0302885 filtration http://purl.obolibrary.org/obo/OBI_0600014 material component separation filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device http://purl.obolibrary.org/obo/OBI_0302886 centrifugation http://purl.obolibrary.org/obo/OBI_0600014 material component separation centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation http://purl.obolibrary.org/obo/OBI_0302888 washing http://purl.obolibrary.org/obo/OBI_0000094 material processing washing is a process by which a material entity acting as contaminant (e.g. excess staining reagent) is removed by application of one or more cycles of solution in flow. http://purl.obolibrary.org/obo/OBI_0302903 nucleic acid hybridization http://purl.obolibrary.org/obo/OBI_0000094 material processing a planned process by which totally or partially complementary, single-stranded nucleic acids are combined into a single molecule called heteroduplex or homoduplex to an extent depending on the amount of complementarity. http://purl.obolibrary.org/obo/OBI_0302906 DNA Subtraction http://purl.obolibrary.org/obo/OBI_0600014 material component separation a material separation process by which repetitive genomic DNA is removed during the construction of cDNA library. http://purl.obolibrary.org/obo/OBI_0302908 document editing http://purl.obolibrary.org/obo/OBI_0000011 planned process is a planned process with specified input original document and specified output edited document http://purl.obolibrary.org/obo/OBI_0400045 fluid pressure regulator http://purl.obolibrary.org/obo/OBI_0000832 measurement device Part of the fluidic subsystem. The fluid pressure regulator maintains constant pressure within the sheath and or sample lines by filling the lines with enough gas to push the fluid at the desired rate. The gas is usually air, and less frequently nitrogen. In the sheath line, the gas is pushed into the sheath tank. In the sample line the gas is pushed into the collection tube. Fluid pressure regulators maintain great enough pressure to push sample fluid out of the tube and sheath fluid out of the sheath tank. http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer http://purl.obolibrary.org/obo/OBI_0000832 measurement device A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. http://purl.obolibrary.org/obo/OBI_0400105 arrayer http://purl.obolibrary.org/obo/OBI_0000968 device a device which deposits biological material onto a substrate in a defined pattern. http://purl.obolibrary.org/obo/OBI_0400106 centrifuge http://purl.obolibrary.org/obo/OBI_0000832 measurement device A device with a rapidly rotating container that applies centrifugal force to its contents http://purl.obolibrary.org/obo/OBI_0400107 computer http://purl.obolibrary.org/obo/OBI_0000968 device A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions. http://purl.obolibrary.org/obo/OBI_0400147 microarray http://purl.obolibrary.org/obo/OBI_0001865 assay array A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position. http://purl.obolibrary.org/obo/OBI_0400149 protein microarray http://purl.obolibrary.org/obo/OBI_0400147 microarray A protein-microarray is a microarray, ususlly a piece of glass, on which different molecules of protein have been affixed at separate locations in an ordered manner. These are used to identify protein-protein or protein-small molecule interactions. http://purl.obolibrary.org/obo/OBI_0400170 microscope slide http://purl.obolibrary.org/obo/OBI_0000968 device a microscope slide is a device usually made of glass which is used as a solid matrix for (biological) material deposited on its surface and which is compatible for use with a microscope instrument http://purl.obolibrary.org/obo/OBI_0600004 human subject enrollment http://purl.obolibrary.org/obo/OBI_0001928 selection A planned process with the objective to obtain a population of human subjects to participate in an investigation by determining eligibility of subjects and obtaining informed consent. http://purl.obolibrary.org/obo/OBI_0600005 collecting specimen from organism http://purl.obolibrary.org/obo/OBI_0000659 specimen collection process a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation http://purl.obolibrary.org/obo/OBI_0600014 material component separation http://purl.obolibrary.org/obo/OBI_0000094 material processing a material processing in which components of an input material become segregated in space 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_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_0600047 sequencing assay http://purl.obolibrary.org/obo/NGBO_6000353 omics data generation assay An assay the uses chemical or biochemical means to infer the sequence of a biomaterial 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_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_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_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_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_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/OGMS_0000015 clinical history http://semanticscience.org/resource/SIO_001196 history 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/PATO_0000011 age http://purl.obolibrary.org/obo/PATO_0001237 quality of a single physical entity A time quality inhering in a bearer by virtue of how long the bearer has existed. http://purl.obolibrary.org/obo/PATO_0000047 biological sex http://purl.obolibrary.org/obo/PATO_0001995 organismal quality Term applied to any organism able to undergo sexual reproduction in order to differentiate the individuals or types involved. Sexual reproduction is defined as the ability to exchange genetic material with the potential of recombinant progeny. http://purl.obolibrary.org/obo/PATO_0000122 length http://purl.obolibrary.org/obo/BFO_0000019 quality 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/BFO_0000019 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_0001237 quality of a single physical entity A physical quality of the thermal energy of a system. http://purl.obolibrary.org/obo/PATO_0000383 female http://purl.obolibrary.org/obo/PATO_0000047 biological 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_0000047 biological 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_0001237 quality of a single physical entity 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_0001237 quality of a single physical entity http://purl.obolibrary.org/obo/BFO_0000019 quality A physical object quality which inheres in a single-bearer. http://purl.obolibrary.org/obo/PATO_0001340 hermaphrodite http://purl.obolibrary.org/obo/PATO_0000047 biological 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_0001985 frozen http://purl.obolibrary.org/obo/NGBO_6000294 specimen shipping 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/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. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (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_0001248 assembly http://purl.obolibrary.org/obo/SO_0000001 region 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/IAO_0020000 proper name http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant A proper name 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/IAO_0020015 personal name http://purl.obolibrary.org/obo/IAO_0020000 proper name A personal name is a proper name identifying an individual person. http://purl.obolibrary.org/obo/ICO_0000001 informed consent form http://purl.obolibrary.org/obo/IAO_0000310 document A document that explains all relevant study information to assist a human subject in understanding the expectations and requirements of participation in a research study. This form document is presented to and signed by the study subject. http://purl.obolibrary.org/obo/ICO_0000023 completely filled informed consent form http://purl.obolibrary.org/obo/ICO_0000001 informed consent form an informed consent form that has been filled with all required contents. http://purl.obolibrary.org/obo/ICO_0000024 partially filled informed consent form http://purl.obolibrary.org/obo/ICO_0000001 informed consent form an informed consent form that has been partically filled with required contents. http://purl.obolibrary.org/obo/OBIB_0000029 medication material http://purl.obolibrary.org/obo/BFO_0000040 material entity A material entity that is bearer of a medication role. http://purl.obolibrary.org/obo/OBIB_0000033 specimen receiving http://purl.obolibrary.org/obo/OMIABIS_0001080 sample handling A planned process for receiving specimens such as into a laboratory. http://purl.obolibrary.org/obo/OBIB_0000034 adding specimen into a container http://purl.obolibrary.org/obo/OBI_0000274 adding a material entity into a target An adding a material entity into a target process where a collected specimen is added to a specimen container. (note, not used for other specimen process that produce new specimens) http://purl.obolibrary.org/obo/OBIB_0000035 blood spotting http://purl.obolibrary.org/obo/OBIB_0000034 adding specimen into a container An adding specimen into a container process that spots the blood from an organism on the blood spot card. http://purl.obolibrary.org/obo/OBIB_0000036 buffy coat specimen http://purl.obolibrary.org/obo/OBI_0000953 processed specimen A processed specimen which is the output of a density gradient centrifugation of an anticoagulated blood specimen that contains most of the white blood cells and platelets. http://purl.obolibrary.org/obo/OBIB_0000039 blood specimen on blood spot card http://purl.obolibrary.org/obo/OBI_0000953 processed specimen A blood specimen that is located on a blood spot card. http://purl.obolibrary.org/obo/OBIB_0000041 duration time of smoking regularly http://purl.obolibrary.org/obo/OBIB_0000053 duration time of smoking A duration time of smoking about how long a person has been smoking regularly. (better to have criteria of regularly mean, such as smoke everyday) http://purl.obolibrary.org/obo/OBIB_0000051 smoking start date http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum which is the start date of a smoking behavior. http://purl.obolibrary.org/obo/OBIB_0000053 duration time of smoking http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum about how long a person has been smoking. http://purl.obolibrary.org/obo/OBIB_0000054 smoking end date http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum which is the end date of a smoking behavior. http://purl.obolibrary.org/obo/OMIABIS_0000000 biobank http://purl.obolibrary.org/obo/BFO_0000027 object aggregate A biobank is a collections of samples of biological substances (e.g. tissue, blood, DNA) which are linked to data about the samples and their donors. They have a dual nature as collections of samples and data. http://purl.obolibrary.org/obo/OMIABIS_0000004 ISO 3166-1 alpha-2 code http://purl.obolibrary.org/obo/IAO_0020000 proper name An identifier that consists of two letters, is part of the ISO 3166-1, and designates countries, dependent territories, and special areas of geographical interest. http://purl.obolibrary.org/obo/OMIABIS_0000012 contact role http://purl.obolibrary.org/obo/OMRSE_00000024 role in human social processes A role borne by a human being that is part of an group of individuals and acts as contact person for the group. This role gets realized by the bearer being a participant in a contacting process. http://purl.obolibrary.org/obo/OMIABIS_0000024 post-office box http://purl.obolibrary.org/obo/OBI_0000245 organization A post-office box is material entity that is a box on the premises of a post office station and is uniquely addressable. http://purl.obolibrary.org/obo/OMIABIS_0000046 CTEP organization identifier http://purl.obolibrary.org/obo/IAO_0020000 proper name An identifier for an organization that is assigned to that organization by the Cancer Therapy Evaluation Program. http://purl.obolibrary.org/obo/OMIABIS_0000047 biobank identifier with ISO 3166-1 alpha-2 code and CTEP organization identifier http://purl.obolibrary.org/obo/OMIABIS_0000005 biobank idenfier with ISO 3166-1 alpha-2 code A biobank identifier that has both an ISO 3166-1 alpha-2 code and a CTEP organization code. 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_0000051 fixed tissue block specimen http://purl.obolibrary.org/obo/OMIABIS_0000050 fixed tissue specimen A fixed tissue specimen that is in block form. 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/OMIABIS_0000057 microdissected specimen http://purl.obolibrary.org/obo/OBI_0100051 specimen A specimen that has been procured from a histology slide under direct microscopic visualization. http://purl.obolibrary.org/obo/OMIABIS_0000093 biobank contact role http://purl.obolibrary.org/obo/OMIABIS_0000012 contact role A contact role borne by a member of a sample collection or study organization and realized by serving as the contact for the collection or the study. http://purl.obolibrary.org/obo/OMIABIS_0000911 fixation http://purl.obolibrary.org/obo/OBI_0000094 material processing A material processing that uses chemical process by which biological tissues are preserved from decay. Fixation terminates any ongoing biochemical reactions and may increase stability of the treated tissues. http://purl.obolibrary.org/obo/OMIABIS_0001042 specimen preparation contact http://purl.obolibrary.org/obo/IAO_0020015 personal name A personal name that designates the person who prepared the specimen. http://purl.obolibrary.org/obo/OMIABIS_0001043 time in formalin measurement http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum that states the duration during which a specimen was submerged in formalin. http://purl.obolibrary.org/obo/OMIABIS_0001047 case ID http://purl.obolibrary.org/obo/IAO_0020000 proper name An identifier that refers to a specimen donor who is participating in specimen collection process for tissue procurement purposes and is usually assigned at the time of donor procurement. http://purl.obolibrary.org/obo/OMIABIS_0001054 normal specimen http://purl.obolibrary.org/obo/OBI_0100051 specimen A specimen that is normal. http://purl.obolibrary.org/obo/OMRSE_00000024 role in human social processes http://purl.obolibrary.org/obo/BFO_0000023 role A role inhering in an entity realized by social interactions in human society. http://purl.obolibrary.org/obo/OMRSE_00000038 legal person role http://purl.obolibrary.org/obo/OMRSE_00000024 role in human social processes A role borne by a human individual or by a collection of humans regarded as possessing rights and duties enforeable at law. http://purl.obolibrary.org/obo/FLU_0001019 specimen barcode http://purl.obolibrary.org/obo/OBI_0001616 specimen identifier A specimen barcode is a specimen identification number formatted as an optical machine-readable representation. http://purl.obolibrary.org/obo/OMIT_0025630 DNA Fragmentation http://purl.obolibrary.org/obo/OBI_0000094 material processing DNA fragmentation is the separation or breaking of DNA strands into pieces. It can be done intentionally by laboratory personnel or by cells, or can occur spontaneously http://purl.obolibrary.org/obo/CL_0001063 neoplastic cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type An abnormal cell exhibiting dysregulation of cell proliferation or programmed cell death and capable of forming a neoplasm, an aggregate of cells in the form of a tumor mass or an excess number of abnormal cells (liquid tumor) within an organism. http://purl.obolibrary.org/obo/OBIB_0000273 specimen receiving organization http://purl.obolibrary.org/obo/BFO_0000023 role A role borne by an organization that is the recipient of a specimen that is transported from another organization. http://purl.obolibrary.org/obo/OBIB_0000285 name of quality control inspector of specimen http://purl.obolibrary.org/obo/IAO_0020015 personal name A personal name that designates the person who performed a quality control inspection of the specimen that is to be transported to another organization. http://purl.obolibrary.org/obo/OBIB_0000286 name of data entry person for tissue recovery form http://purl.obolibrary.org/obo/IAO_0020015 personal name A personal name that designates the person who performed the data entry process for filling in a tissue recovery case report form. http://purl.obolibrary.org/obo/OBIB_0000287 name of team leader for filling out tissue recovery form http://purl.obolibrary.org/obo/IAO_0020015 personal name A personal name that designates the person who is the leader of the team responsible for entering the tissue recovery form data. http://purl.obolibrary.org/obo/OBIB_0000288 FFPE tissue processing SOP http://purl.obolibrary.org/obo/OBIB_0000070 standard operating procedure A standard operating procedure for fixation of a tissue to the state where it is completely infiltrated with a suitable histological wax and can be embedded ready for section cutting on the microtome for a formalin-fixed paraffin-embedded (FFPE) process. http://purl.obolibrary.org/obo/OBIB_0000292 adherence of alcohol stage duration to FFPE tissue processing SOP http://purl.obolibrary.org/obo/NGBO_6000148 paraffin embedding and Fixation quality check report An information content entity that indicates whether duration of the alcohol stage followed that prescribed in the FFPE tissue processing SOP. http://purl.obolibrary.org/obo/OBIB_0000293 FFPE alcohol stage duration http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum that is the result of measuring the duration of the alcohol stage in a formalin-fixed paraffin-embedded (FFPE) process. http://purl.obolibrary.org/obo/OBIB_0000294 adherence of dehydration process duration to FFPE tissue processing SOP http://purl.obolibrary.org/obo/NGBO_6000148 paraffin embedding and Fixation quality check report An information content entity that indicates whether duration of the dehydration process followed that prescribed in the FFPE tissue processing SOP. http://purl.obolibrary.org/obo/OBIB_0000295 FFPE dehydration process duration http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum that is the result of measuring the duration of the dehydration process in the formalin-fixed paraffin-embedded (FFPE) process. http://purl.obolibrary.org/obo/OBIB_0000296 adherence of dehydration process temperature to FFPE tissue processing SOP http://purl.obolibrary.org/obo/NGBO_6000148 paraffin embedding and Fixation quality check report An information content entity that indicates whether temperature of the dehydration process followed that prescribed in the FFPE tissue processing SOP. http://purl.obolibrary.org/obo/OBIB_0000298 adherence of stage and replicate numbers to FFPE tissue processing SOP http://purl.obolibrary.org/obo/NGBO_6000148 paraffin embedding and Fixation quality check report An information content entity that indicates whether the number of stages and replicates followed that prescribed in the FFPE tissue processing SOP. http://purl.obolibrary.org/obo/OBIB_0000300 adherence of duration in clearing agent to FFPE tissue processing SOP http://purl.obolibrary.org/obo/NGBO_6000148 paraffin embedding and Fixation quality check report An information content entity that indicates whether the duration in clearing agent followed that prescribed in the FFPE tissue processing SOP. http://purl.obolibrary.org/obo/OBIB_0000301 FFPE clearing agent duration http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum that is the result of measuring the duration in clearing agent in the formalin-fixed paraffin-embedded (FFPE) process. http://purl.obolibrary.org/obo/OBIB_0000302 adherence of temperature of clearing agent to FFPE tissue processing SOP http://purl.obolibrary.org/obo/NGBO_6000148 paraffin embedding and Fixation quality check report An information content entity that indicates whether the temperature of clearing agent followed that prescribed in the FFPE tissue processing SOP. http://purl.obolibrary.org/obo/OBIB_0000304 adherence to paraffin impregnation method in FFPE tissue processing SOP http://purl.obolibrary.org/obo/NGBO_6000148 paraffin embedding and Fixation quality check report An information content entity that indicates whether the paraffin impregnation method followed that prescribed in the FFPE tissue processing SOP. http://purl.obolibrary.org/obo/OBIB_0000306 adherence of paraffin temperature to FFPE tissue processing SOP http://purl.obolibrary.org/obo/NGBO_6000148 paraffin embedding and Fixation quality check report An information content entity that indicates whether the paraffin temperature followed that prescribed in the FFPE tissue processing SOP. http://purl.obolibrary.org/obo/OBIB_0000309 FFPE tissue paraffin embedding SOP http://purl.obolibrary.org/obo/OBIB_0000070 standard operating procedure A standard operating procedure for the paraffin embedding of a formalin-fixed paraffin-embedded (FFPE) tissue. http://purl.obolibrary.org/obo/OBIB_0000313 total time FFPE freshly poured blocks were cooled http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum that is the result of measuring the total time that freshly poured blocks were cooled in the formalin-fixed paraffin-embedded (FFPE) process. http://purl.obolibrary.org/obo/OBIB_0000314 FFPE tissue block handling, tracking, and storage SOP http://purl.obolibrary.org/obo/OBIB_0000070 standard operating procedure A standard operating procedure for the handling, tracking, and storing of a formalin-fixed paraffin-embedded (FFPE) tissue block. http://purl.obolibrary.org/obo/OBIB_0000315 adherence to FFPE tissue block storage SOP http://purl.obolibrary.org/obo/NGBO_6000148 paraffin embedding and Fixation quality check report An information content entity that indicates whether the FFPE tissue block storage SOP was followed. http://purl.obolibrary.org/obo/OBIB_0000319 FFPE tissue section preparation SOP http://purl.obolibrary.org/obo/OBIB_0000070 standard operating procedure A standard operating procedure for the preparation of a formalin-fixed paraffin-embedded (FFPE) tissue section. http://purl.obolibrary.org/obo/OBIB_0000320 microtome blade age http://purl.obolibrary.org/obo/PATO_0000011 age An age that inheres in a microtome blade. http://purl.obolibrary.org/obo/OBIB_0000321 fresh microtome blade http://purl.obolibrary.org/obo/OBIB_0000320 microtome blade age A microtome blade age that indicates that the microtome blade is as new as possible. http://purl.obolibrary.org/obo/OBIB_0000334 FFPE tissue section H&E staining and mounting SOP http://purl.obolibrary.org/obo/OBIB_0000070 standard operating procedure A standard operating procedure for the hematoxylin and eosin (H&E) staining and slide mounting of a formalin-fixed paraffin-embedded (FFPE) tissue section. http://purl.obolibrary.org/obo/OBIB_0000335 FFPE tissue section H&E staining in oven duration http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum that is the result of measuring the duration in an oven for the hematoxylin and eosin staining of a formalin-fixed paraffin-embedded (FFPE) tissue section. http://purl.obolibrary.org/obo/OBIB_0000341 manual FFPE tissue section H&E deparaffinization http://purl.obolibrary.org/obo/OMIABIS_0000911 fixation A planned process involving the manual performance of the FFPE tissue section H&E deparaffinization protocol. http://purl.obolibrary.org/obo/OBIB_0000342 manual FFPE tissue section H&E staining http://purl.obolibrary.org/obo/OMIABIS_0000911 fixation A planned process involving the manual performance of the FFPE tissue section H&E staining protocol. http://purl.obolibrary.org/obo/OBIB_0000343 manual FFPE tissue section H&E clearing http://purl.obolibrary.org/obo/OMIABIS_0000911 fixation A planned process involving the manual performance of the FFPE tissue section H&E clearing protocol. http://purl.obolibrary.org/obo/OBIB_0000344 manual FFPE tissue section H&E cover slipping http://purl.obolibrary.org/obo/OMIABIS_0000911 fixation A planned process involving the manual performance of the FFPE tissue section H&E cover slip protocol. http://purl.obolibrary.org/obo/OBIB_0000349 specimen randomization key ID http://purl.obolibrary.org/obo/FLU_0001019 specimen barcode A specimen barcode associated with the specific chart (key) used to randomly assign specimens to one of several distinct experimental protocols. http://purl.obolibrary.org/obo/OBIB_0000365 FFPE tissue cassette ID http://purl.obolibrary.org/obo/OBI_0001616 specimen identifier A specimen ID that specifically identifies a particular tissue cassete used in a formalin-fixed paraffin-embedded (FFPE) process. http://purl.obolibrary.org/obo/OBIB_0000368 placement of tissue cassette in FFPE fixative delay duration http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum that is the result of measuring the duration of the the planned delay of placing the tissue cassette in fixative in the formalin-fixed paraffin-embedded (FFPE) process. http://purl.obolibrary.org/obo/OBIB_0000374 measurement of time between FFPE tissue processor cycle completion and embedding http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum that is the result of measuring the time between FFPE tissue processor cycle completion and embedding in a formalin-fixed paraffin-embedded (FFPE) process. http://purl.obolibrary.org/obo/OBIB_0000380 name of dissector of normal adjacent tissue to tumor for FFPE http://purl.obolibrary.org/obo/IAO_0020015 personal name A personal name that designates the person who performed the dissection of a normal tissue adjacent to a tumor for a formalin-fixed paraffin-embedded (FFPE) process. http://purl.obolibrary.org/obo/OBIB_0000385 specimen image ID http://purl.obolibrary.org/obo/IAO_0020000 proper name An identifier that specifically identifies a particular specimen image. http://purl.obolibrary.org/obo/OBIB_0000402 confirmation of histologic type of FFPE H&E tumor slide http://purl.obolibrary.org/obo/NGBO_6000148 paraffin embedding and Fixation quality check report An information content entity that is an indicator of whether the local pathology review of a formalin-fixed paraffin-embedded (FFPE) hematoxylin and eosin (H&E)-stained tumor tissue slide confirmed the histological type. http://purl.obolibrary.org/obo/OBIB_0000408 name of reviewing pathologist at organization conducting specimen collection http://purl.obolibrary.org/obo/IAO_0020015 personal name A personal name that designates the person who served as the pathologist reviewing a specimen slide at an organization conducting specimen collection from organisms. http://purl.obolibrary.org/obo/OBIB_0000410 name of data entry person for local pathology review form http://purl.obolibrary.org/obo/IAO_0020015 personal name A personal name that designates the person who performed the data entry process for filling in a local pathology review form. http://purl.obolibrary.org/obo/OBIB_0000413 name of person in gross room receiving OR specimen http://purl.obolibrary.org/obo/IAO_0020015 personal name A personal name that designates the person who received a specimen in a pathology gross room from an associated operating room (OR). http://purl.obolibrary.org/obo/OBIB_0000414 specimen transport from OR to gross room SOP http://purl.obolibrary.org/obo/OBIB_0000071 specimen transport SOP A specimen transport SOP governing the transport of tissue from the operating room (OR) to the pathology gross room. http://purl.obolibrary.org/obo/OBIB_0000419 name of performer of gross evaluation of resected tissue specimen http://purl.obolibrary.org/obo/IAO_0020015 personal name A personal name that designates the person who performed the gross evaluation of a resected tissue specimen. http://purl.obolibrary.org/obo/OBIB_0000445 additional tumor specimen was obtained and processed with a particular FFPE fixation delay protocol http://purl.obolibrary.org/obo/NGBO_6000148 paraffin embedding and Fixation quality check report An information content entity that is an indicator of whether a tumor specimen was obtained and processed with a particular FFPE fixation delay protocol other than meeting the top priority for tissue procurement. http://purl.obolibrary.org/obo/OBIB_0000481 relationship between person signing research authorization and specimen donor http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant A relationship that may be biological or legal, between the specimen donor and the legally authorized representative who signed the research authorization. http://purl.obolibrary.org/obo/OBIB_0000499 time since radiation therapy was received prior to surgery http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum that is the result of measuring the time elapsed since radiation therapy prior to surgery. http://purl.obolibrary.org/obo/OBIB_0000500 time since chemotherapy was received prior to surgery http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum that is the result of measuring the time elapsed since chemotherapy prior to surgery. http://purl.obolibrary.org/obo/OBIB_0000501 time since immunotherapy was received prior to surgery http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum that is the result of measuring the time elapsed since immunotherapy prior to surgery. http://purl.obolibrary.org/obo/OBIB_0000502 time since hormonal therapy was received prior to surgery http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum that is the result of measuring the time elapsed since hormonal therapy prior to surgery. http://purl.obolibrary.org/obo/OBIB_0000507 lifelong non-drinker of alcohol http://purl.obolibrary.org/obo/NCIT_C81229 Alcohol Use History An Alcohol Use History in which there is no alcohol consumption. http://purl.obolibrary.org/obo/OBIB_0000508 current non-drinker of alcohol http://purl.obolibrary.org/obo/NCIT_C81229 Alcohol Use History An Alcohol Use History in which there was alcohol consumption in the past but is currently a non-drinker of alcohol. http://purl.obolibrary.org/obo/OBIB_0000509 moderate alcohol consumption history http://purl.obolibrary.org/obo/NCIT_C81229 Alcohol Use History An Alcohol Use History in which alcohol consumption was equal to or less than 2 drinks per day for men and 1 drink or less per day for women. http://purl.obolibrary.org/obo/OBIB_0000510 greater than moderate alcohol consumption history http://purl.obolibrary.org/obo/NCIT_C81229 Alcohol Use History An Alcohol Use History in which alcohol consumption was more than 2 drinks per day for men and more than 1 drink per day for women. http://purl.obolibrary.org/obo/OBIB_0000511 duration of greater than moderate alcohol consumption prior to enrollment http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum that is the result of measuring the duration of greater than moderate alcohol consumption (more than 2 drinks per day for a man or more than 1 drink per day for a woman) prior to study enrollment. http://purl.obolibrary.org/obo/OBIB_0000512 lifelong non-smoker history http://purl.obolibrary.org/obo/NCIT_C29719 Smoking History A Smoking History in which there was no or an insignificant level of smoking. http://purl.obolibrary.org/obo/OBIB_0000513 current smoker history http://purl.obolibrary.org/obo/NCIT_C29719 Smoking History A Smoking History in which there is current smoking either on a daily or non-daily basis. http://purl.obolibrary.org/obo/OBIB_0000514 current reformed smoker for more than 15 years history http://purl.obolibrary.org/obo/NCIT_C29719 Smoking History A Smoking History in which there is no current smoking and has not been smoking for more than 15 years. http://purl.obolibrary.org/obo/OBIB_0000515 current reformed smoker for less than 15 years history http://purl.obolibrary.org/obo/NCIT_C29719 Smoking History A Smoking History in which there is no current smoking and has not been smoking for less than 15 years. http://purl.obolibrary.org/obo/OBIB_0000526 duration of hormonal birth control use prior to enrollment http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum that is the result of measuring the duration of use of hormonally based birth control prior to enrollment in a study. http://purl.obolibrary.org/obo/OBIB_0000527 time since last usage of hormonal birth control http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum that is the result of measuring the time elapsed since the participant last used hormonally based birth control. http://purl.obolibrary.org/obo/OBIB_0000529 duration of hormone replacement therapy prior to enrollment http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum that is the result of measuring the duration of hormone replacement therapy prior to enrollment in a study. http://purl.obolibrary.org/obo/OBIB_0000530 time since last usage of hormone replacement therapy http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum that is the result of measuring the time elapsed since the participant last used hormonally replacement therapy. http://purl.obolibrary.org/obo/OBIB_0000543 clinical history of sepsis http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of sepsis. http://purl.obolibrary.org/obo/OBIB_0000544 clinical history of pneumonia http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of pneumonia. http://purl.obolibrary.org/obo/OBIB_0000545 clinical history of open wounds http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of open wounds. http://purl.obolibrary.org/obo/OBIB_0000546 clinical history of high unexplained fever http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of a high unexplained fever . http://purl.obolibrary.org/obo/OBIB_0000547 clinical history of positive blood cultures http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of positive blood cultures. http://purl.obolibrary.org/obo/OBIB_0000548 clinical history of abnormal white blood cell levels http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of abnormal white blood cell levels. http://purl.obolibrary.org/obo/OBIB_0000549 clinical history of fungal infections http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of fungal infections. http://purl.obolibrary.org/obo/OBIB_0000550 clinical history of ascites http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of the presence of ascites fluid. http://purl.obolibrary.org/obo/OBIB_0000551 clinical history of cellulitis http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of cellulitis. http://purl.obolibrary.org/obo/OBIB_0000552 clinical history of blood transfusion in foreign country http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of receiving a blood transfusion while in another country. http://purl.obolibrary.org/obo/OBIB_0000553 clinical history of human tissue transplant http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of receiving a human tissue or organ transplant . http://purl.obolibrary.org/obo/OBIB_0000554 clinical history of animal tissue xenotransplant http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of receiving an animal tissue or organ xenotransplant. http://purl.obolibrary.org/obo/OBIB_0000555 clinical history of smallpox vaccination http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinic history in which there is a history of a recent of smallpox vaccination. http://purl.obolibrary.org/obo/OBIB_0000556 a clinical history of contact with someone with smallpox http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of contact with someone who recently had smallpox. http://purl.obolibrary.org/obo/OBIB_0000557 clinical history of dialysis http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of significant regular dialysis treatment. http://purl.obolibrary.org/obo/OBIB_0000558 clinical history of cancer at death http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a current diagnosis of cancer at death. http://purl.obolibrary.org/obo/OBIB_0000559 clinical history of cancer within a time period before death http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of cancer diagnosis within a specified time frame. http://purl.obolibrary.org/obo/OBIB_0000560 clinical history of tuberculosis http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of tuberculosis . http://purl.obolibrary.org/obo/OBIB_0000561 clinical history of meningitis at death http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there was active meningitis at death. http://purl.obolibrary.org/obo/OBIB_0000562 clinical history of encephalitis http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there was active encephalitis at death. http://purl.obolibrary.org/obo/OBIB_0000563 clinical history of long term steroid use http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of long term steroid use. http://purl.obolibrary.org/obo/OBIB_0000564 clinical history of osteomyelitis http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of osteomyelitis. http://purl.obolibrary.org/obo/OBIB_0000565 clinical history of unexplained seizures http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of unexplained seizures. http://purl.obolibrary.org/obo/OBIB_0000566 clinical history of unexplained weakness and fatigue http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of unexplained weakness and fatigue described as flu-like symptoms. http://purl.obolibrary.org/obo/OBIB_0000567 clinical history of exposure to toxins http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of exposure to toxic substances that may have led to chronic conditions. http://purl.obolibrary.org/obo/OBIB_0000568 clinical history of exposure to rabies http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of an animal bite in recent past, from an animal suspected to have rabies. http://purl.obolibrary.org/obo/OBIB_0000573 clinical history of clotting disorders http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of clotting disorders, such as hemophilia, requiring treatment with human-derived clotting factors. http://purl.obolibrary.org/obo/OBIB_0000574 clinical history of growth hormone use http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of growth hormone use. http://purl.obolibrary.org/obo/OBIB_0000575 clinical history of inability to have Human Immunodeficiency Virus testing due to hemodilution http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of the donor not being able to be tested for Human Immunodeficiency Virus (HIV) because of hemodilution. http://purl.obolibrary.org/obo/OBIB_0000576 clinical history of unexplained weight loss http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of unexplained weight loss. http://purl.obolibrary.org/obo/OBIB_0000577 clinical history of night sweats http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of night sweats. http://purl.obolibrary.org/obo/OBIB_0000578 clinical history of blue or purple spots on skin or mucous membranes http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a of blue or purple spots on the skin or mucus membranes (typical of Kaposi's sarcoma). http://purl.obolibrary.org/obo/OBIB_0000579 clinical history of unexplained lymphadenopathy http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of unexplained lymphadenopathy of a specific duration. http://purl.obolibrary.org/obo/OBIB_0000580 clinical history of a prolonged fever http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of fever of at least 38.6 Celsius for a specified duration. http://purl.obolibrary.org/obo/OBIB_0000581 clinical history of an unexplained cough or shortness of breath http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is are active signs of unexplained persistent cough and/or shortness of breath. http://purl.obolibrary.org/obo/OBIB_0000582 clinical history of opportunistic infections http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of opportunistic infections. http://purl.obolibrary.org/obo/OBIB_0000583 clinical history of sexually transmitted disease http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of sexually transmitted diseases http://purl.obolibrary.org/obo/OBIB_0000584 clinical history of drug abuse http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of drug abuse. http://purl.obolibrary.org/obo/OBIB_0000585 clinical history of Severe Acute Respiratory Syndrome http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of a Severe Acute Respiratory Syndrome (SARS) diagnosis. http://purl.obolibrary.org/obo/OBIB_0000586 clinical history of exposure to Severe Acute Respiratory Syndrome http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of recent contact with someone who has Severe Acute Respiratory Syndrome (SARS). http://purl.obolibrary.org/obo/OBIB_0000587 clinical history of West Nile Virus http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of West Nile Virus (WNV) infection. http://purl.obolibrary.org/obo/OBIB_0000588 clinical history of West Nile Virus exposure http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of contact with a human or animal who has West Nile Virus (WNV). http://purl.obolibrary.org/obo/OBIB_0000589 clinical history of gonorrhea http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of active gonorrhea infection or treatment for gonorrhea in the recent past. http://purl.obolibrary.org/obo/OBIB_0000590 clinical history of syphilis http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of active syphilis infection or treatment for syphilis in the recent past. http://purl.obolibrary.org/obo/OBIB_0000591 clinical history of Hepatitis B http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of Hepatitis B infection. http://purl.obolibrary.org/obo/OBIB_0000592 clinical history of Hepatitis C http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of Hepatitis C infection. http://purl.obolibrary.org/obo/OBIB_0000593 clinical history of Human Immunodeficiency Virus http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of Human Immunodeficiency Virus (HIV). http://purl.obolibrary.org/obo/OBIB_0000594 clinical history of lupus http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of systemic lupus http://purl.obolibrary.org/obo/OBIB_0000595 clinical history of sarcoidosis http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of sarcoidosis. http://purl.obolibrary.org/obo/OBIB_0000596 clinical history of scleroderma http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of scleroderma. http://purl.obolibrary.org/obo/OBIB_0000597 clinical history of Reye's Syndrome http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of Reye's Syndrome. http://purl.obolibrary.org/obo/OBIB_0000598 clinical history of rheumatoid arthritis http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of rheumatoid arthritis. http://purl.obolibrary.org/obo/OBIB_0000599 clinical history of idiopathic heart disease http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of idiopathic heart disease. http://purl.obolibrary.org/obo/OBIB_0000600 clinical history of Alzheimer's disease http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of Alzheimer's Disease. http://purl.obolibrary.org/obo/OBIB_0000601 clinical history of dementia of unknown cause http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of dementia with unknown cause that is not caused by a previous Cerebrovascular Accident (CVA) infection, head trauma or brain tumor). http://purl.obolibrary.org/obo/OBIB_0000602 clinical history of Multiple Sclerosis http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of Multiple Sclerosis (MS). http://purl.obolibrary.org/obo/OBIB_0000603 clinical history of Amyotrophic Lateral Sclerosis http://purl.obolibrary.org/obo/OGMS_0000015 clinical history A clinical history in which there is a history of Amyotrophic Lateral Sclerosis (ALS) http://purl.obolibrary.org/obo/CL_0000007 early embryonic cell http://purl.obolibrary.org/obo/CL_0002321 embryonic cell A cell found in the embryo before the formation of all the gem layers is complete. http://purl.obolibrary.org/obo/CL_0000023 oocyte http://purl.obolibrary.org/obo/CL_0000586 germ cell A female germ cell that has entered meiosis. http://purl.obolibrary.org/obo/CL_0000034 stem cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. http://purl.obolibrary.org/obo/CL_0000037 hematopoietic stem cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4,CD5,CD8 alpha chain, CD14, CD19, CD20, integrin alpha-M, neural cell adhesion molecule 1, lymphocyte antigen 6G, lymphocyte antigen 76. http://purl.obolibrary.org/obo/CL_0000038 erythroid progenitor cell http://purl.obolibrary.org/obo/CL_0000839 myeloid lineage restricted progenitor cell A progenitor cell committed to the erythroid lineage. This cell is ter119-positive but lacks expression of other hematopoietic lineage markers (lin-negative). http://purl.obolibrary.org/obo/CL_0000047 neuronal stem cell http://purl.obolibrary.org/obo/CL_0000034 stem cell Neural stem cell is characterized as an undifferentiated cell that originates from the neuroectoderm and has the capacity both to perpetually self-renew without differentiating and to generate multiple types of lineage-restricted progenitors. http://purl.obolibrary.org/obo/CL_0000048 multipotent stem cell http://purl.obolibrary.org/obo/CL_0000034 stem cell A stem cell that can give rise to mulitple lineages of cells. http://purl.obolibrary.org/obo/CL_0000055 blast cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A precursor cell with a limited number of potential fates. http://purl.obolibrary.org/obo/CL_0000056 myoblast http://www.ebi.ac.uk/efo/EFO_0000324 cell type An embryonic cell that becomes a cell of muscle fiber. http://purl.obolibrary.org/obo/CL_0000057 fibroblast http://www.ebi.ac.uk/efo/EFO_0000324 cell type A large, flat, oval cell found in connective tissue and responsible for the formation of fibers. http://purl.obolibrary.org/obo/CL_0000062 osteoblast http://www.ebi.ac.uk/efo/EFO_0000324 cell type A bone-forming cell which secretes an extracellular matrix. Hydroxyapatite crystals are then deposited into the matrix to form bone. http://purl.obolibrary.org/obo/CL_0000065 ependymal cell http://purl.obolibrary.org/obo/CL_0000066 epithelial cell A neurectoderm derived cell that lines the neural lumen. [ JB:jb GOC:tfm PMID:9550134 ] http://purl.obolibrary.org/obo/CL_0000066 epithelial cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type Cell that cover the surface of the body and line its cavities. http://purl.obolibrary.org/obo/CL_0000071 blood vessel endothelial cell http://purl.obolibrary.org/obo/CL_0000115 endothelial cell The endothelial cells that line the vasculature. http://purl.obolibrary.org/obo/CL_0000077 mesothelial cell http://purl.obolibrary.org/obo/CL_0000066 epithelial cell A flattened epithelial cell of mesenchymal origin that lines the serous cavity. http://purl.obolibrary.org/obo/CL_0000080 circulating cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A cell which moves among different tissues of the body, via blood, lymph, or other medium. http://purl.obolibrary.org/obo/CL_0000081 blood cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A cell found predominately in the blood. http://purl.obolibrary.org/obo/CL_0000083 exocrine pancreas cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type Cells of the pancreas that secrete digestive enzymes, the archetypal secretory cell upon which much of the early work on the sequence of events in the secretory process was done. http://purl.obolibrary.org/obo/CL_0000094 granulocyte http://purl.obolibrary.org/obo/CL_0000766 myeloid leukocyte A polymorphonuclear white blood cell with granule-containing cytoplasm. http://purl.obolibrary.org/obo/CL_0000099 interneuron http://purl.obolibrary.org/obo/CL_0000540 neuron Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions. http://purl.obolibrary.org/obo/CL_0000100 motor neuron http://purl.obolibrary.org/obo/CL_0000540 neuron Neurons which activate muscle cells (MSH). http://purl.obolibrary.org/obo/CL_0000101 sensory neuron http://purl.obolibrary.org/obo/CL_0000540 neuron Any neuron having a sensory function; an afferent neuron conveying sensory impulses. http://purl.obolibrary.org/obo/CL_0000115 endothelial cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm. http://purl.obolibrary.org/obo/CL_0000125 glial cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type MERGED DEFINITION:nTARGET DEFINITION: The delicate network of branched cells and fibers that supports the tissue of the central nervous system.n--------------------nSOURCE DEFINITION: The cells of the supportive tissue of the central nervous system (neuroglia). These non-neural cells are of three kinds: astrocytes, oligodendrocytes (collectively termed macroglia) and microglia. http://purl.obolibrary.org/obo/CL_0000127 astrocyte http://purl.obolibrary.org/obo/CL_0000125 glial cell cells) are irregularly shaped with many long processes, including those with "end feet" which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier. They regulate the extracellular ionic and chemical environment, and http://purl.obolibrary.org/obo/CL_0000128 oligodendrocyte http://www.ebi.ac.uk/efo/EFO_0000324 cell type A class of large neuroglial (macroglial) cells in the central nervous system. Oligodendroglia may be called interfascicular, perivascular, or perineuronal (not the same as satellite cells, perineuronal of ganglia) according to their location. They form the insulating myelin sheath of axons in the central nervous system (MSH). http://purl.obolibrary.org/obo/CL_0000129 microglial cell http://purl.obolibrary.org/obo/CL_0000878 central nervous system macrophage MERGED DEFINITION:nTARGET DEFINITION: The small, non-neural, interstitial cells of mesodermal origin that form part of the supporting structure of the central nervous system. They are of various forms and may have slender branched processes. They are migratory and act as phagocytes to waste products of nerve tissue. n--------------------nSOURCE DEFINITION: One of the small interstitial phagocytic cells of the microglia. http://purl.obolibrary.org/obo/CL_0000136 fat cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of tryglycerides. http://purl.obolibrary.org/obo/CL_0000138 chondrocyte http://www.ebi.ac.uk/efo/EFO_0000324 cell type Polymorphic cell that form cartilage. http://purl.obolibrary.org/obo/CL_0000148 melanocyte http://www.ebi.ac.uk/efo/EFO_0000324 cell type An epidermal cell that produces melanin. http://purl.obolibrary.org/obo/CL_0000151 secretory cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A cell that specializes in controlled release of one or more substances. http://purl.obolibrary.org/obo/CL_0000160 goblet cell http://purl.obolibrary.org/obo/CL_0000151 secretory cell A cell of the epithelial lining that produce and secrete mucins. http://purl.obolibrary.org/obo/CL_0000162 parietal cell http://purl.obolibrary.org/obo/CL_0000151 secretory cell A large, oval stomach epithelial cell with a central nucleus; source of gastric acid. Secretes HCl. http://purl.obolibrary.org/obo/CL_0000163 endocrine cell http://purl.obolibrary.org/obo/CL_0000151 secretory cell A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions. http://purl.obolibrary.org/obo/CL_0000165 neuroendocrine cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type Neuroendocrine cells are cells that receive neuronal input (neurotransmitters released by nerve cells) and, as a consequence of this input, release message molecules (hormones) to the blood. An example of a neuroendocrine cell is the cell of the adrenal medulla which releases adrenalin to the blood. The major center of neuroendocrine integration in the body is found in the hypothalamus and the pituitary gland. Here hypothalamic neurosecretory cells release factors to the blood. http://purl.obolibrary.org/obo/CL_0000168 beta cell http://purl.obolibrary.org/obo/UBERON_0000016 endocrine pancreas A cell that composes the bulk of the islets of Langerhans and secretes insulin. http://purl.obolibrary.org/obo/CL_0000169 type B pancreatic cell http://www.ebi.ac.uk/efo/EFO_0002966 pancreatic cell A cell that secretes insulin and is located towards the center of the islets of Langerhans. http://purl.obolibrary.org/obo/CL_0000171 pancreatic A cell http://purl.obolibrary.org/obo/CL_0000066 epithelial cell A type of enteocrine cell found in the periphery of the islets of Langerhans that secretes glucagon. http://purl.obolibrary.org/obo/CL_0000173 pancreatic D cell http://www.ebi.ac.uk/efo/EFO_0002966 pancreatic cell A D cell located in the pancreas. Peripherally placed within the islets like type A cells; contains somatostatin. http://purl.obolibrary.org/obo/CL_0000178 Leydig cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A Leydig cell is a testosterone-secreting cell in the interstitial area, between the seminiferous tubules, in the testis. http://purl.obolibrary.org/obo/CL_0000182 hepatocyte http://www.ebi.ac.uk/efo/EFO_0000324 cell type The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. http://purl.obolibrary.org/obo/CL_0000185 myoepithelial cell http://purl.obolibrary.org/obo/CL_0000066 epithelial cell Contractile cells resembling smooth muscle cells that are present in glands, notably the mammary gland, and aid in secretion. This cell has long weaving dendritic processes containing myofilament. [ GOC:tfm ISBN:0721662544 ] http://purl.obolibrary.org/obo/CL_0000187 muscle cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type Mature contractile cells, commonly known as myocytes, that form one of three kinds of muscle. The three types of muscle cells are skeletal (muscle fibers), cardiac (myocytes, cardiac), and smooth (myocytes, smooth muscle). They are derived from embryonic (precursor) muscle cells called myoblasts (MSH). http://purl.obolibrary.org/obo/CL_0000192 smooth muscle cell http://purl.obolibrary.org/obo/CL_0000187 muscle cell Non-striated, elongated, spindle-shaped cells found lining the digestive tract, uterus, and blood vessels. They are derived from specialized myoblasts (myoblasts, smooth muscle) (MSH). http://purl.obolibrary.org/obo/CL_0000202 cochlear hair cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A mechanoreceptor cell located in the organ of Corti that is sensitive to auditory stimuli and in the vestibular apparatus that is sensitive to movement of the head. In each case the accessory sensory structures are arranged so that appropriate stimuli cause movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system. http://purl.obolibrary.org/obo/CL_0000211 electrically active cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A cell whose function is determined by the generation or the reception of an electric signal. http://purl.obolibrary.org/obo/CL_0000216 Sertoli cell http://purl.obolibrary.org/obo/CL_0000151 secretory cell A supporting cell projecting inward from the basement membrane of seminiferous tubules. They surround and nourish the developing male germ cells and secrete androgen binding protein. Their tight junctions with the spermatogonia and spermatocytes provide a blood-testis barrier. http://purl.obolibrary.org/obo/CL_0000218 Schwann cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A neuroglial cell of the peripheral nervous system which forms the insulating myelin sheaths of peripheral axons. http://purl.obolibrary.org/obo/CL_0000222 mesodermal cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A cell of the middle germ layer of the embryo. http://purl.obolibrary.org/obo/CL_0000232 erythrocyte http://purl.obolibrary.org/obo/CL_0000764 erythroid lineage cell A red blood cell. In mammals, mature erythrocytes are non-nucleated, biconcave disks containing hemoglobin whose function is to transport oxygen. http://purl.obolibrary.org/obo/CL_0000233 platelet http://purl.obolibrary.org/obo/CL_0000763 myeloid cell A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation. http://purl.obolibrary.org/obo/CL_0000235 macrophage http://purl.obolibrary.org/obo/CL_0000766 myeloid leukocyte A mononuclear phagocyte which differentiates from monocytes, is typically resident in a particular tissue, and capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells (Cell Ontology). http://purl.obolibrary.org/obo/CL_0000236 B cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity. http://purl.obolibrary.org/obo/CL_0000286 hyphal cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A cell of a filament of a fungal mycelium. http://purl.obolibrary.org/obo/CL_0000333 neural crest cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A cell of the strip of specialized ectoderm flanking each side of the embryonal neural plate, which after the closure of the neural tube, forms a column of isolated cells along the dorsal aspect of the neural tube. Most of the cranial and all of the spinal sensory ganglion cells arise by differentiation of neural crest cells. http://purl.obolibrary.org/obo/CL_0000337 neuroblast (sensu Vertebrata) http://purl.obolibrary.org/obo/CL_0000047 neuronal stem cell An embryonic cell that develops into a nerve cell or neuron. http://purl.obolibrary.org/obo/CL_0000346 hair follicle dermal papilla cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A specialized mesenchymal cell that resides in the dermal papilla located at the bottom of hair follicles. This cell plays a pivotal roles in hair formation, growth, and cycling. http://purl.obolibrary.org/obo/CL_0000349 extraembryonic cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A cell which is part of an extraembryonic structure associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis. http://purl.obolibrary.org/obo/CL_0000351 trophoblast cell http://purl.obolibrary.org/obo/CL_0000349 extraembryonic cell A cell lining the outside of the blastocyst. After binding to the endometrium, trophoblast cells develop into two distinct layers, an inner layer of mononuclear cytotrophoblast cells and an outer layer of continuous multinuclear cytoplasm, the syncytiotrophoblast cells, which form the early fetal-maternal interface. http://purl.obolibrary.org/obo/CL_0000352 epiblast cell http://purl.obolibrary.org/obo/CL_0002322 embryonic stem cell A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation. http://purl.obolibrary.org/obo/CL_0000362 epidermal cell http://purl.obolibrary.org/obo/CL_0000066 epithelial cell An epithelial cell of the integument (the outer layer of an organism). http://purl.obolibrary.org/obo/CL_0000371 protoplast http://www.ebi.ac.uk/efo/EFO_0000324 cell type The cell protoplasm after removal of the cell wall. http://purl.obolibrary.org/obo/CL_0000387 hemocyte http://www.ebi.ac.uk/efo/EFO_0000324 cell type A blood cell especially of an invertebrate animal. http://purl.obolibrary.org/obo/CL_0000415 diploid cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A cell whose nucleus has two haploid genomes. http://purl.obolibrary.org/obo/CL_0000421 coelomocyte http://www.ebi.ac.uk/efo/EFO_0000324 cell type A free floating cell, including amebocytes and eleocytes, in the coelom of certain animals, especially annelids. http://purl.obolibrary.org/obo/CL_0000442 follicular dendritic cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A cell with extensive dendritic processes found in the B cell areas (primary follicles and germinal centers) of lymphoid tissue. They are unrelated to the dendritic cell associated with T cells. Follicular dendritic cells have Fc receptors and C3b receptors, but unlike other dendritic cells, they do not process or present antigen in a way that allows recognition by T cells. Instead, they hold antigen in the form of immune complexes on their surfaces for long periods and can present antigen to B cells during an immune response. http://purl.obolibrary.org/obo/CL_0000451 dendritic cell http://purl.obolibrary.org/obo/CL_0000738 leukocyte A special type of cell that is a key regulator of the immune system, acting as a professional antigen-presenting cell, APC, capable of activating naive T cells and stimulating the growth and differentiation of B cells. Dendritic cells are found, for example, in the lymph nodes and spleen. As an APC, a dendritic cell can retain antigen for long periods on its surface, present the antigen to a T or B cell and so influence their behavior. http://purl.obolibrary.org/obo/CL_0000499 stromal cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere. http://purl.obolibrary.org/obo/CL_0000501 granulosa cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A supporting cell for the developing female gamete in the ovary of mammals. They develop from the coelomic epithelial cells of the gonadal ridge. Granulosa cells form a single layer around the mammalian oocyte in the primordial ovarian follicle and advance to form a multilayered cumulus oophorus surrounding the ovum in the Graafian follicle. The major functions of granulosa cells include the production of steroids and LH receptors. http://purl.obolibrary.org/obo/CL_0000510 paneth cell http://purl.obolibrary.org/obo/CL_0000151 secretory cell An epithelial cell found in the basal part of the intestinal glands (crypts of Lieberkuhn) including the appendix. Paneth cells synthesize and secrete lysozyme and cryptdins. Numerous in the deeper parts of the intestinal crypts, particularly in the duodenum, rich in zinc, contain large acidophilic granules, with irregular apical microvilli and prominent membrane-bound vacuoles containing matrix. http://purl.obolibrary.org/obo/CL_0000514 smooth muscle myoblast http://purl.obolibrary.org/obo/CL_0000187 muscle cell A precursor cell destined to differentiate into smooth muscle myocytes. http://purl.obolibrary.org/obo/CL_0000515 skeletal muscle myoblast http://purl.obolibrary.org/obo/CL_0000056 myoblast A myoblast that differentiates into skeletal muscle fibers. http://purl.obolibrary.org/obo/CL_0000525 syncytiotrophoblast cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A cell from the outer syncytial layer of the trophoblast of an early mammalian embryo. It It secretes hCG in order to maintain progesterone secretion and sustain a pregnancy. http://purl.obolibrary.org/obo/CL_0000540 neuron http://www.ebi.ac.uk/efo/EFO_0000324 cell type The basic cellular units of nervous tissue. Neurons are polarized cells with defined regions consisting of the cell body, an axon, and dendrites, although some types of neurons lack axons or dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. http://purl.obolibrary.org/obo/CL_0000547 proerythroblast http://purl.obolibrary.org/obo/CL_0000764 erythroid lineage cell An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. http://purl.obolibrary.org/obo/CL_0000549 basophilic erythroblast http://purl.obolibrary.org/obo/CL_0000765 erythroblast A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. http://purl.obolibrary.org/obo/CL_0000553 megakaryocyte progenitor cell http://purl.obolibrary.org/obo/CL_0000839 myeloid lineage restricted progenitor cell The earliest cytologically identifiable precursor in the thrombocytic series. http://purl.obolibrary.org/obo/CL_0000556 megakaryocyte http://purl.obolibrary.org/obo/CL_0000763 myeloid cell A large cell that has a lobulated nucleus, is found especially in the bone marrow, and is the source of blood platelets. http://purl.obolibrary.org/obo/CL_0000557 granulocyte monocyte progenitor cell http://purl.obolibrary.org/obo/CL_0002032 hematopoietic oligopotent progenitor cell A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata-1, Gata2 but do express C/EBPa, and Pu.1. http://purl.obolibrary.org/obo/CL_0000558 reticulocyte http://purl.obolibrary.org/obo/CL_0000764 erythroid lineage cell An immature erythrocyte showing a basophilic reticulum under vital staining. http://purl.obolibrary.org/obo/CL_0000576 monocyte http://purl.obolibrary.org/obo/CL_0000766 myeloid leukocyte A mononuclear phagocytic leukocyte, 13 to 25 mm in diameter, with an ovoid or kidney-shaped nucleus, containing lacy, linear chromatin and abundant gray-blue cytoplasm filled with fine reddish and azurophilic granules. Formed in the bone marrow from promonocytes, monocytes are transported to tissues such as the lung and liver, where they develop into macrophages. http://purl.obolibrary.org/obo/CL_0000579 border follicle cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A follicle cell that migrates from the anterior pole of the egg chamber, between the nurse cells, to the anterior of the oocyte where they participate in formation of the micropyle. About 6-10 border cells per egg chamber migrate as a tightly associated cluster. http://purl.obolibrary.org/obo/CL_0000584 enterocyte http://purl.obolibrary.org/obo/CL_0002563 intestinal epithelial cell An epithelial cell that has its apical plasma membrane folded into microvilli to provide ample surface for the absorption of nutrients from the intestinal lumen. http://purl.obolibrary.org/obo/CL_0000586 germ cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type The reproductive cell in multicellular organisms. http://purl.obolibrary.org/obo/CL_0000598 pyramidal cell http://purl.obolibrary.org/obo/CL_0000540 neuron A projection neuron in the cerebral cortex and the hippocampus. Pyramidal cells have a pyramid-shaped soma with the apex and an apical dendrite pointed toward the pial surface and other dendrites and an axon emerging from the base. The axons may have local collaterals but also project outside their cortical region. http://purl.obolibrary.org/obo/CL_0000599 conidium http://www.ebi.ac.uk/efo/EFO_0000324 cell type An asexual, nonmotile spore formed by higher fungi; conidia are usually made from the side or tip of specialized sporogenous cells and do not form by progressive cleavage of the cytoplasm. http://purl.obolibrary.org/obo/CL_0000617 GABAergic neuron http://purl.obolibrary.org/obo/CL_0000540 neuron A neuron that uses GABA as a vesicular neurotransmitter http://purl.obolibrary.org/obo/CL_0000622 acinar cell http://purl.obolibrary.org/obo/CL_0000151 secretory cell A secretory cell that is grouped together with other cells of the same type to form grape shaped clusters known as acini (singular acinus). http://purl.obolibrary.org/obo/CL_0000628 photosynthetic cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A cell that can perform photosynthesis, in which carbohydrates are synthesized from carbon dioxide and water, using light as the energy source. http://purl.obolibrary.org/obo/CL_0000632 hepatic stellate cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A cell that is found in the perisinusoidal space of the liver that is capable of multiple roles including storage of retinol, presentation of antigen to T cells (including CD1d-restricted NKT cells), and upon activation, production of extracellular matrix components that can contribute to liver fibrosis. This activated state has a myofibroblast-like phenotype, though it's not clear in the literature if this is terminally differentiated. This cell type comprises approximately 8-15% of total cells in the liver. http://purl.obolibrary.org/obo/CL_0000646 basal cell http://purl.obolibrary.org/obo/CL_0000034 stem cell Undifferentiated; mitotic stem cell for other epithelial cell types; rounded or elliptical with little cytoplasm and few organelles; contain cytokeratin intermediate filament. http://purl.obolibrary.org/obo/CL_0000669 pericyte http://www.ebi.ac.uk/efo/EFO_0000324 cell type An elongated, contractile cell found wrapped about precapillary arterioles outside the basement membrane. They are relatively undifferentiated and may become fibroblasts, macrophages, or smooth muscle cells. http://purl.obolibrary.org/obo/CL_0000670 primordial germ cell http://purl.obolibrary.org/obo/CL_0000586 germ cell A primordial germ cell is a diploid germ cell precursors that transiently exist in the embryo before they enter into close association with the somatic cells of the gonad and become irreversibly committed as germ cells. http://purl.obolibrary.org/obo/CL_0000700 dopaminergic neuron http://purl.obolibrary.org/obo/CL_0000540 neuron A neuron that releases dopamine as a neurotransmitter. http://purl.obolibrary.org/obo/CL_0000711 cumulus cell http://purl.obolibrary.org/obo/CL_0000501 granulosa cell Cumulus cell is a specialized granulosa cell that surrounds and nourishes the oocyte. This cell-type surrounds the fully-grown oocyte to form a cumulus-oocyte complex (abbr. COC). The terms cumulus oophorus cells, cumulus granulosa cells, cumulus oophorous granulosa cells, granulosa-cumulus cells are used to make a distinction between this cell and the other functionally different subpopulation of granulosa cells at the wall of the Graafian follicle. http://purl.obolibrary.org/obo/CL_0000723 somatic stem cell http://purl.obolibrary.org/obo/CL_0002371 somatic cell A stem cell that can give rise to cell types of the body other than those of the germ-line. http://purl.obolibrary.org/obo/CL_0000738 leukocyte http://www.ebi.ac.uk/efo/EFO_0000324 cell type Any of the blood cells that are colorless, lack hemoglobin, contain a nucleus, and include the lymphocytes, monocytes, neutrophils, eosinophils, and basophils. http://purl.obolibrary.org/obo/CL_0000746 cardiac muscle cell http://purl.obolibrary.org/obo/CL_0000187 muscle cell A striated muscle cell found in the heart. They develop from cardiac myoblasts. http://purl.obolibrary.org/obo/CL_0000763 myeloid cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type Any of the immature blood cells that develop in the bone marrow, such as those involved in hematopoiesis. http://purl.obolibrary.org/obo/CL_0000764 erythroid lineage cell http://purl.obolibrary.org/obo/CL_0000763 myeloid cell A immature or mature cell in the lineage leading to and including erythrocytes. http://purl.obolibrary.org/obo/CL_0000765 erythroblast http://purl.obolibrary.org/obo/CL_0000764 erythroid lineage cell A nucleated precursor of an erythrocyte. http://purl.obolibrary.org/obo/CL_0000767 basophil http://purl.obolibrary.org/obo/CL_0000094 granulocyte Granular leukocytes characterized by a relatively pale-staining, lobate nucleus and cytoplasm containing coarse dark-staining granules of variable size and stainable by basic dyes. http://purl.obolibrary.org/obo/CL_0000771 eosinophil http://purl.obolibrary.org/obo/CL_0000094 granulocyte Granular leukocytes with a nucleus that usually has two lobes connected by a slender thread of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and stainable by eosin. http://purl.obolibrary.org/obo/CL_0000775 neutrophil http://purl.obolibrary.org/obo/CL_0000094 granulocyte A fully differentiated basophil, a granular leukocyte with 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. http://purl.obolibrary.org/obo/CL_0000777 mesangial phagocyte http://purl.obolibrary.org/obo/CL_0000864 tissue-resident macrophage A tissue-resident macrophage of the renal glomerular mesangium. http://purl.obolibrary.org/obo/CL_0000784 plasmacytoid dendritic cell http://purl.obolibrary.org/obo/CL_0000451 dendritic cell A dendritic cell type of distinct morphology, localization, and surface marker expression from other dendritic cell types and associated with early stage immune responses, particularly the release of physiologically abundant amounts of type I interferons in response to infection. http://purl.obolibrary.org/obo/CL_0000785 mature B cell http://purl.obolibrary.org/obo/CL_0000236 B cell A B cell that is mature, having left the bone marrow. Initially, these cells are IgM-positive and IgD-positive, and they can be activated by antigen. http://purl.obolibrary.org/obo/CL_0000786 plasma cell http://purl.obolibrary.org/obo/CL_0000151 secretory cell A terminally differentiated cell of the B lymphocyte lineage that produces antibodies; 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. http://purl.obolibrary.org/obo/CL_0000816 immature B cell http://purl.obolibrary.org/obo/CL_0000817 precursor B cell An immature B cell is a precursor B cell that has the phenotype surface IgM-positive and surface IgD-negative, and have not undergone class immunoglobulin class switching or peripheral encounter with antigen and activation. http://purl.obolibrary.org/obo/CL_0000817 precursor B cell http://purl.obolibrary.org/obo/CL_0000236 B cell A precursor B cell is a B cell with the phenotype CD10-positive (P08473/NEP_HUMAN; PIRSF001194). http://purl.obolibrary.org/obo/CL_0000822 B-2 B cell http://purl.obolibrary.org/obo/CL_0000785 mature B cell A conventional B cell subject to antigenic stimulation and dependent on T cell help and with a distinct surface marker expression pattern from B-1 B cells. These cells are CD43-negative. http://purl.obolibrary.org/obo/CL_0000837 hematopoietic multipotent progenitor cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A progenitor cell of any hematopoietic lineage, potentially multipotent. http://purl.obolibrary.org/obo/CL_0000839 myeloid lineage restricted progenitor cell http://purl.obolibrary.org/obo/CL_0002031 hematopoietic lineage restricted progenitor cell A progenitor cell of any myeloid lineage, potentially multipotent. http://purl.obolibrary.org/obo/CL_0000988 hematopoietic cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A blood cell. http://purl.obolibrary.org/obo/CL_0002079 pancreatic ductal cell http://www.ebi.ac.uk/efo/EFO_0002966 pancreatic cell Epithelial cell found in the ducts of the pancreas. This cell type contributes to the high luminal pH. http://purl.obolibrary.org/obo/CL_0002092 bone marrow cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells. [ GOC:tfm ISBN:0618947256 ] http://purl.obolibrary.org/obo/CL_0002144 capillary endothelial cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type An endothelial cell found in capillaries. http://purl.obolibrary.org/obo/CL_0002193 myelocyte http://purl.obolibrary.org/obo/CL_0002191 granulocytopoietic cell A cell type that is the first of the maturation stages of the granulocytic leukocytes normally found in the bone marrow. Granules are seen in the cytoplasm. The nuclear material of the myelocyte is denser than that of the myeloblast but lacks a definable membrane. The cell is flat and contains increasing numbers of granules as maturation progresses. http://purl.obolibrary.org/obo/CL_0002204 tuft cell http://purl.obolibrary.org/obo/CL_0000066 epithelial cell A cell type found in the gastrointestinal and respiratory tracts that is characterized by the presence of a tuft of blunt, squat microvilli (120-140 per cell). Function of this cell type is not known. http://purl.obolibrary.org/obo/CL_0002231 epithelial cell of prostate http://purl.obolibrary.org/obo/CL_0000066 epithelial cell An epithelial cell of the prostate. http://purl.obolibrary.org/obo/CL_0002248 pluripotent stem cell http://purl.obolibrary.org/obo/CL_0000723 somatic stem cell A pluripotent stem cell has the ability to form cells from all three germ layers (ectoderm, mesoderm, and endoderm). However, unlike totipotent stem cells, they cell can not generate all the cells of the whole organism such as placenta. http://purl.obolibrary.org/obo/CL_0002253 epithelial cell of large intestine http://purl.obolibrary.org/obo/CL_0002563 intestinal epithelial cell An epithelial cell of the large intestine. http://purl.obolibrary.org/obo/CL_0002275 pancreatic PP cell http://www.ebi.ac.uk/efo/EFO_0002966 pancreatic cell A PP cell located in the islets of the pancreas. http://purl.obolibrary.org/obo/CL_0002321 embryonic cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A cell of the embryo. http://purl.obolibrary.org/obo/CL_0002322 embryonic stem cell http://purl.obolibrary.org/obo/CL_0000034 stem cell Totipotent cell cultured from early embryo. Have the advantage that following modification in vitrothey can be used to produce chimeric embryos and thus transgenic animals. http://purl.obolibrary.org/obo/CL_0002327 mammary epithelial cell http://purl.obolibrary.org/obo/CL_0000066 epithelial cell An epithelial cell of the mammary gland. http://purl.obolibrary.org/obo/CL_0002334 preadipocyte http://www.ebi.ac.uk/efo/EFO_0000324 cell type A precursor to an adipocyte. http://purl.obolibrary.org/obo/CL_0002342 circulating endothelial cell http://purl.obolibrary.org/obo/CL_0000115 endothelial cell A circulating endothelial cell of the phenotype CD146-positive, CD105-positive, CD45-negative. This cell type is indicative of recent vascular damage. http://purl.obolibrary.org/obo/CL_0002351 progenitor cell of endocrine pancreas http://www.ebi.ac.uk/efo/EFO_0000324 cell type A multi-fate stem cell that is able to differentiate into the pancreas alpha, beta and delta endocrine cells. This cell type expresses neurogenin-3 and Isl-1. http://purl.obolibrary.org/obo/CL_0002353 fetal liver hematopoietic progenitor cell http://purl.obolibrary.org/obo/CL_0002352 gestational hematopoietic stem cell A hematopoietic stem cell that resides in the fetal liver. In mice, this cell type is first observed at E10.5. This cell type is MHC-positive, HSA-positive, AA4.1-positive, CD45-positive, Sca-1 positive, CD150-positive, CD48-negative and CD244-negative. http://purl.obolibrary.org/obo/CL_0002363 keratocyte http://purl.obolibrary.org/obo/CL_0000057 fibroblast A keratocyte is a specialized fibroblast residing in the stroma that has a flattened, dendritic cell located between the lamellae with a large flattened nucleus and lengthy processes which communicate with neighboring cells. This corneal layer, representing about 85-90% of corneal thickness, is built up from highly regular collagenous lamellae and extracellular matrix components. Keratocytes play the major role in keeping it transparent, healing its wounds, and synthesizing its components. This cell type secretes collagen I, V, VI, and keratin sulfate. http://purl.obolibrary.org/obo/CL_0002364 cortical thymic epithelial cell http://purl.obolibrary.org/obo/CL_0000066 epithelial cell An epithelial cell of the cortical portion of the thymus. Epithelial cells in this region are required for positive selection of CD8-positive T cells. [ PMID:18403190 GOC:tfm ] http://purl.obolibrary.org/obo/CL_0002365 medullary thymic epithelial cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type An epithelial cell of the medullary thymus. This cell type expresses a diverse range of tissue-specific antigens. This promiscuous gene expression is a cell-autonomous property of medullary epithelial cells and is maintained during the entire period of thymic T cell output. http://purl.obolibrary.org/obo/CL_0002368 respiratory epithelial cell http://purl.obolibrary.org/obo/CL_0000066 epithelial cell Epithelium of the respiratory portion of the bronchial tree. http://purl.obolibrary.org/obo/CL_0002371 somatic cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type One of the cells of the body that compose the tissues, organs, and parts of that individual other than the germ cells. http://purl.obolibrary.org/obo/CL_0002410 pancreatic stellate cell http://www.ebi.ac.uk/efo/EFO_0002966 pancreatic cell A cell that is found in the periacinar space of the exocrine pancreas and in perivascular and periductal regions of the pancreas, and has long cytoplasmic processes that encircle the base of the acinus. Expresses several intermediate filament proteins including vimentin and nestin. Shares many of the characteristics of hepatatic stellate cells, but not stellate cells of the central nervous system. Upon activation, this cell type undergoes morphological and gene expression changes that make the cell suggestive of being a type of myofibroblast. http://purl.obolibrary.org/obo/CL_0002451 mammary stem cell http://purl.obolibrary.org/obo/CL_0000034 stem cell A multi-fate stem cell that is the source of cells for growth of the mammary gland during puberty and gestation. This cell type gives rise to both the luminal and myoepithelial cell types of the gland, and have been shown to have the ability to regenerate the entire organ in mice. This cell type also plays an important role in carcinogenesis of the breast. This cell type is Lin-, CD24-positive, CD29-hi. [ PMID:16397499 GOC:tfm PMID:17851544 GOC:hjd PMID:15987436 ] http://purl.obolibrary.org/obo/CL_0002453 oligodendrocyte precursor cell http://purl.obolibrary.org/obo/CL_0000128 oligodendrocyte The cell type from which oligodendrocytes develop. This cell originates from multiple structures within the developing brain including the medial ganglion eminence and the lateral ganglionic eminence. These cells migrate throughout the central nervous system and persist into adulthood where they play an important role in remyelination of injured neurons. http://purl.obolibrary.org/obo/CL_0002540 mesenchymal stem cell of the bone marrow http://www.ebi.ac.uk/efo/EFO_0000586 mesenchymal stem cell A mesenchymal stem cell that is part of the bone marrow. [ GOC:tfm ] http://purl.obolibrary.org/obo/CL_0002551 fibroblast of dermis http://purl.obolibrary.org/obo/CL_0000057 fibroblast fibroblast that is part of dermis http://purl.obolibrary.org/obo/CL_0002553 lung fibroblast http://purl.obolibrary.org/obo/CL_0000057 fibroblast A fibroblast that is part of lung http://purl.obolibrary.org/obo/CL_0002563 intestinal epithelial cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type An epithelial cell of the intestine. [ GOC:tfm ] http://purl.obolibrary.org/obo/CL_0002601 uterine smooth muscle cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A smooth muscle cell of the uterus. http://purl.obolibrary.org/obo/CL_0002608 hippocampal neuron http://purl.obolibrary.org/obo/CL_0000540 neuron A neuron of the hippocampus. http://purl.obolibrary.org/obo/CL_0002617 adipocyte of breast http://purl.obolibrary.org/obo/CL_0000136 fat cell A fat cell that is part of the breast. http://purl.obolibrary.org/obo/CL_0002618 endothelial cell of umbilical vein http://purl.obolibrary.org/obo/CL_0000071 blood vessel endothelial cell An endothelial cell of the umbilical vein. [ GOC:tfm ] http://purl.obolibrary.org/obo/CL_0002619 adult endothelial progenitor cell http://www.ebi.ac.uk/efo/EFO_0000586 mesenchymal stem cell An adult angioblastic cell released from the bone marrow, capable of blood circulation and participation in angiogenesis by differentiating into blood vessel endothelial cells. Their existence is controversial. [ GOC:tfm PMID:20807818 PMID:9020076 ] http://purl.obolibrary.org/obo/CL_0002633 repiratory basal cell http://purl.obolibrary.org/obo/CL_0000646 basal cell A basal cell in the respiratory tract. [ PMID:20699479 GOC:tfm ] http://purl.obolibrary.org/obo/CL_0005019 pancreatic epsilon cell http://www.ebi.ac.uk/efo/EFO_0002966 pancreatic cell Ghrelin secreting cells found in the found in the exocrine pancreas. http://purl.obolibrary.org/obo/CL_0009004 retinal cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. http://purl.obolibrary.org/obo/CL_1000488 cholangiocyte http://purl.obolibrary.org/obo/CL_0000066 epithelial cell An epithelial cell that is part of the bile duct. Cholangiocytes contribute to bile secretion via net release of bicarbonate and water. They are cuboidal epithelium in the small interlobular bile ducts, but become columnar and mucus secreting in larger bile ducts approaching the porta hepatis and the extrahepatic ducts. [ PMID:18356246 PMID:16550043 GOC:tfm ] http://purl.obolibrary.org/obo/UBERON_0000016 endocrine pancreas http://purl.obolibrary.org/obo/CL_0000151 secretory cell The endocrine pancreas is made up of islet cells that produce insulin, glucagon and somatostatin[GO]. http://purl.obolibrary.org/obo/NCIT_C25621 Postal Code http://purl.obolibrary.org/obo/NGBO_6000161 personally identifiable information Any system designed to expedite the sorting and delivery of mail by assigning a series of alphanumeric codes to each delivery area. Also used to refer to any individual delivery area code. http://purl.obolibrary.org/obo/NCIT_C25690 Street Address http://www.w3.org/2006/vcard/ns#Address address The street name and building number where a person or organization can be found. http://purl.obolibrary.org/obo/NCIT_C25720 Zip Code http://purl.obolibrary.org/obo/NCIT_C25621 Postal Code A system designed to expedite the sorting and delivery of mail by assigning a series of numbers to each delivery area in the United States. Also used to refer to any individual delivery area code. 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/CL_0000002 immortal cell line cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite growth/propagation in vitro as part of a immortal cell line. http://purl.obolibrary.org/obo/CL_0000292 guard cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type One of a pair of cells flanking the stomatal pore and causing the opening and closing of the pore by changes in turgor. http://purl.obolibrary.org/obo/GENEPIO_0001562 reference genome identifier http://purl.obolibrary.org/obo/NGBO_6000244 reference genome datum Identifier for a reference genome (used to build or compare an assembly) that is used in the genome browsers and in the community http://purl.obolibrary.org/obo/GENEPIO_0001795 de-identified data http://purl.obolibrary.org/obo/IAO_0000027 data item A 'de-identified data' role between a user and given data entails that the user is authorized to see only those fields (including those that are encrypted) which do not contain information that could be use to identify particular individuals (whether patients or medical practitioners) or potentially organizations in the case where an investigation may implicate them. http://purl.obolibrary.org/obo/GENEPIO_0001888 Canada postal code http://purl.obolibrary.org/obo/NCIT_C25621 Postal Code A Canadian postal code is a postal code that pertains to a geographic region of Canada. http://edamontology.org/data_1093 Sequence accession http://purl.obolibrary.org/obo/GENEPIO_0001800 sequence identifier A persistent, unique identifier of a molecular sequence database entry. http://www.ebi.ac.uk/efo/EFO_0004950 date of birth http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum The point in time at which an individual was born. http://www.ebi.ac.uk/efo/EFO_0004953 date of diagnosis http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum The point at which a clinical diagnosis is made. http://semanticscience.org/resource/SIO_000811 URL http://purl.obolibrary.org/obo/IAO_0000577 centrally registered identifier symbol A Uniform Resource Locator or Universal Resource Locator (URL) is a specific character string that constitutes a reference to an Internet resource. http://purl.obolibrary.org/obo/GENO_0000815 sequence feature location http://purl.obolibrary.org/obo/BFO_0000031 generically dependent continuant The location of a sequence feature as defined by its start and end position on some reference coordinate system. http://www.ebi.ac.uk/efo/EFO_0005289 mural granulosa cell http://purl.obolibrary.org/obo/CL_0000501 granulosa cell The mural granulosa cells form during antral folliculogenesis, process in which a single antral cavity is formed, separating two functionally distinct granulosa cell populations. The mural granulosa cells line the wall of the follicle and are critical for steroidogenesis and ovulation. http://www.ebi.ac.uk/efo/EFO_0005495 NSM http://purl.obolibrary.org/obo/CL_0000165 neuroendocrine cell Neuron class of two pharyngeal neurosecretory-motor neurons. http://www.ebi.ac.uk/efo/EFO_0005497 pharyngeal muscle cell http://purl.obolibrary.org/obo/CL_0000187 muscle cell type of cells that make up muscle layers in the pharynx in worms such as C. elegans http://purl.obolibrary.org/obo/OMRSE_00000012 health care provider role http://purl.obolibrary.org/obo/OMRSE_00000010 human health care 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/OBIws_0000192 RNA sequence data http://purl.obolibrary.org/obo/OBI_0000973 sequence data A sequence data that is about the primary structure of RNA. http://purl.obolibrary.org/obo/ICO_0000146 eligibility of candidate participation http://purl.obolibrary.org/obo/BFO_0000017 realizable entity A realizable entity that represents the eligibility of a candidate according to a study protocol. 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/ICO_0000058 informed consented study period http://purl.obolibrary.org/obo/BFO_0000038 one-dimensional temporal region a one-dimensional temporal region that is a period of an informed consented study http://purl.obolibrary.org/obo/NGBO_0000037 SIFT score impact http://purl.obolibrary.org/obo/IAO_0000027 data item Data item which represents a normalized probability of observing the new amino acid at that position and ranges from 0 to 1. http://purl.obolibrary.org/obo/NGBO_0000038 DNA processed specimen http://purl.obolibrary.org/obo/OBI_0000953 processed specimen A processed specimen which is the output of preparing a DNA sample for further analysis. http://purl.obolibrary.org/obo/NGBO_0000055 PS1 criteria http://purl.obolibrary.org/obo/NGBO_0000063 ACMG strong variants classification Same amino acid change as a previously established pathogenic variant regardless of nucleotide change http://purl.obolibrary.org/obo/NGBO_0000056 PS2 criteria http://purl.obolibrary.org/obo/NGBO_0000063 ACMG strong variants classification De novo (both maternity and paternity confirmed) in a patient with the disease and no family history http://purl.obolibrary.org/obo/NGBO_0000057 PS4 criteria http://purl.obolibrary.org/obo/NGBO_0000063 ACMG strong variants classification The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls http://purl.obolibrary.org/obo/NGBO_0000058 PM1 criteria http://purl.obolibrary.org/obo/NGBO_0000065 ACMG moderate classification criteria Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation http://purl.obolibrary.org/obo/NGBO_0000059 PM2 criteria http://purl.obolibrary.org/obo/NGBO_0000065 ACMG moderate classification criteria Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or ExAC http://purl.obolibrary.org/obo/NGBO_0000060 PM6 criteria http://purl.obolibrary.org/obo/NGBO_0000065 ACMG moderate classification criteria Assumed de novo, but without confirmation of paternity and maternity http://purl.obolibrary.org/obo/NGBO_0000061 PM3 criteria http://purl.obolibrary.org/obo/NGBO_0000065 ACMG moderate classification criteria For recessive disorders, detected in trans with a pathogenic variant http://purl.obolibrary.org/obo/NGBO_0000062 PM4 criteria http://purl.obolibrary.org/obo/NGBO_0000065 ACMG moderate classification criteria Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants http://purl.obolibrary.org/obo/NGBO_0000063 ACMG strong variants classification http://purl.obolibrary.org/obo/NGBO_6000355 ACMG guidelines for classification of variants ACMG guidelines for classification of variants of strong variants classification http://purl.obolibrary.org/obo/NGBO_0000064 PS3 criteria http://purl.obolibrary.org/obo/NGBO_0000063 ACMG strong variants classification Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product http://purl.obolibrary.org/obo/NGBO_0000065 ACMG moderate classification criteria http://purl.obolibrary.org/obo/NGBO_6000355 ACMG guidelines for classification of variants ACMG guidelines for classification of variants of moderate classification http://purl.obolibrary.org/obo/NGBO_0000066 ACMG very strong classification criteria http://purl.obolibrary.org/obo/NGBO_6000355 ACMG guidelines for classification of variants ACMG guidelines for classification of variants of very strong classification http://purl.obolibrary.org/obo/NGBO_0000067 ACMG supporting classification criteria http://purl.obolibrary.org/obo/NGBO_6000355 ACMG guidelines for classification of variants ACMG guidelines for classification of variants of spporting classification http://purl.obolibrary.org/obo/NGBO_6000003 data file format http://purl.obolibrary.org/obo/IAO_0000030 information content entity Information content entity that is a standard way that information is encoded for storage in a computer file. http://purl.obolibrary.org/obo/NGBO_6000004 VCF format http://purl.obolibrary.org/obo/NGBO_6000003 data file format A file format which represent represent the format of a text file used in bioinformatics for storing gene sequence variations http://purl.obolibrary.org/obo/NGBO_6000005 SAM format http://purl.obolibrary.org/obo/NGBO_6000003 data file format A file format which represent a text-based format for storing biological sequences aligned to a reference sequence http://purl.obolibrary.org/obo/NGBO_6000006 FASTA format http://purl.obolibrary.org/obo/NGBO_6000003 data file format A file format which represent represent a text-based format for representing either nucleotide sequences or peptide sequences, in which base pairs or amino acids are represented using single-letter codes http://purl.obolibrary.org/obo/NGBO_6000007 FASTQ format http://purl.obolibrary.org/obo/NGBO_6000003 data file format A file format which represent text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores http://purl.obolibrary.org/obo/NGBO_6000009 unstained fixed tissue slide http://purl.obolibrary.org/obo/OMIABIS_0000052 fixed tissue slide specimen A fixed tissue slide specimen that is contain unstained tissue section(s) http://purl.obolibrary.org/obo/NGBO_6000012 2bit format http://purl.obolibrary.org/obo/NGBO_6000003 data file format A file format which represent a binary file format designed for storing a genome consists of multiple chromosomal sequences http://purl.obolibrary.org/obo/NGBO_6000014 bed graph format http://purl.obolibrary.org/obo/NGBO_6000003 data file format A file format which represent a data format allows display of continuous-valued data in track format http://purl.obolibrary.org/obo/NGBO_6000019 bed format http://purl.obolibrary.org/obo/NGBO_6000003 data file format A file format which represent represent format provides a flexible way to define the data lines that are displayed in an annotation track http://purl.obolibrary.org/obo/NGBO_6000021 BAM format http://purl.obolibrary.org/obo/NGBO_6000003 data file format A file format which represent binary format for storing sequence data. http://purl.obolibrary.org/obo/NGBO_6000029 shipping and receiving of samples SOP http://purl.obolibrary.org/obo/OBIB_0000070 standard operating procedure A standard operating procedure for shipping and receiving of sample http://purl.obolibrary.org/obo/NGBO_6000057 reference genome version number http://purl.obolibrary.org/obo/NGBO_6000244 reference genome datum A reference genome datum which represent reference genome edition http://purl.obolibrary.org/obo/NGBO_6000058 reference genome URI http://purl.obolibrary.org/obo/NGBO_6000244 reference genome datum A reference genome datum which represent a location where reference genome can be accessed online http://purl.obolibrary.org/obo/NGBO_6000081 information about local data storage http://purl.obolibrary.org/obo/NGBO_6000399 information about data storage location Information about data storage location information content entity which represent any physical hardware such as external hard drives, flash drives, and CD http://purl.obolibrary.org/obo/NGBO_6000083 information about cloud storage bucket http://purl.obolibrary.org/obo/NGBO_6000399 information about data storage location Information about data storage location information content entity which represent information about the basic containers that hold your data in cloud storage http://purl.obolibrary.org/obo/NGBO_6000089 name of specimen donor http://purl.obolibrary.org/obo/IAO_0020015 personal name A personal name that designates the human being donated specimen http://purl.obolibrary.org/obo/NGBO_6000092 material transfer agreement http://purl.obolibrary.org/obo/IAO_0000310 document A document which represent a contract that governs the transfer of tangible research materials between two organizations, when the recipient intends to use it for his or her own research purposes. http://purl.obolibrary.org/obo/NGBO_6000093 data transfer agreement http://purl.obolibrary.org/obo/IAO_0000310 document A document information content entity established between organisations that governs the transfer of one or more data sets from the owner/provider to a third party http://purl.obolibrary.org/obo/NGBO_6000098 specimen collection kit http://purl.obolibrary.org/obo/NGBO_6000236 assay kit An assay kit processed material comprises a sterile device for collecting a sample, a collection and dispersing device for depositing and holding the sample, a device for transferring the sample, and a container for storing the sample to be tested. There may also be a labeling system for identifying the sample and for diluting the sample http://purl.obolibrary.org/obo/NGBO_6000099 insulated shipping container http://purl.obolibrary.org/obo/OBI_0000967 container A container which used to ship temperature sensitive products such as foods, pharmaceuticals, organs, blood, biologic materials, and chemicals. They are used as part of a cold chain to help maintain product freshness and efficacy. http://purl.obolibrary.org/obo/NGBO_6000103 standard operating procedure actual use duration http://purl.obolibrary.org/obo/BFO_0000038 one-dimensional temporal region A one-dimensional temporal region that is a period of an duration of standard operation procedure http://purl.obolibrary.org/obo/NGBO_6000105 adapter ligation process http://purl.obolibrary.org/obo/OBI_0000094 material processing A material processing process which attaches synthetic oligonucleotides of a known sequence to one or both ends of cDNA fragments http://purl.obolibrary.org/obo/NGBO_6000106 specimen derivative http://purl.obolibrary.org/obo/OBI_0100051 specimen A specimen which is a recognizable part or product taken from specimen http://purl.obolibrary.org/obo/NGBO_6000122 bioinformatics analysis http://purl.obolibrary.org/obo/OBI_0200000 data transformation A data transformation which involeves curation, processing and analysis of complex biological data http://purl.obolibrary.org/obo/NGBO_6000123 gene expression level analysis http://purl.obolibrary.org/obo/NGBO_6000122 bioinformatics analysis A gene expression level analysis is a bioinformatics analysis that compares the RNA expression levels of multiple genes (profiling) and/or multiple samples (screening) http://purl.obolibrary.org/obo/NGBO_6000124 variant calling assay http://purl.obolibrary.org/obo/NGBO_6000122 bioinformatics analysis Variant calling is the process by which we identify variants from sequence data. http://purl.obolibrary.org/obo/NGBO_6000125 variant classification assay http://purl.obolibrary.org/obo/NGBO_6000261 genetic variantion analysis A genetic variation analysis which assign a formal classification to a detected genetic variant. http://purl.obolibrary.org/obo/NGBO_6000128 sequence clustring http://purl.obolibrary.org/obo/OBI_0200187 sequence analysis data transformation A bioinformatics analysis which attempt to group biological sequences that are somehow related http://purl.obolibrary.org/obo/NGBO_6000140 axt file format http://purl.obolibrary.org/obo/NGBO_6000003 data file format A file format which represent alignment files are produced from Blastz, an alignment tool available from Webb Miller's lab at Penn State University. The axtNet and axtChain alignments are produced by processing the alignment files with additional utilities written by Jim Kent at UCSC http://purl.obolibrary.org/obo/NGBO_6000148 paraffin embedding and Fixation quality check report http://purl.obolibrary.org/obo/NGBO_6000257 quality assesment report required quality check list for the procedure of paraffin embedding and/or fixation. http://purl.obolibrary.org/obo/NGBO_6000150 remnant specimen http://purl.obolibrary.org/obo/OBI_0100051 specimen a specimen which represent remaining portion of a specimen obtained for clinical purposes that is no longer needed for its original purpose and that would otherwise be discarded http://purl.obolibrary.org/obo/NGBO_6000157 specimen with potentially infectious materials http://purl.obolibrary.org/obo/OBI_0100051 specimen A specimen that derives from an organism and might contain infectious materials. http://purl.obolibrary.org/obo/NGBO_6000160 training manual http://purl.obolibrary.org/obo/IAO_0000310 document A training manual is a book or booklet of instructions, designed to improve the quality of a performed task. http://purl.obolibrary.org/obo/NGBO_6000161 personally identifiable information http://purl.obolibrary.org/obo/IAO_0000027 data item A data item infromation content entity that represent any data that could potentially identify a specific individual. Any information that can be used to distinguish one person from another and can be used for de-anonymizing anonymous data can be considered PII. http://purl.obolibrary.org/obo/NGBO_6000166 protein sequencing http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay A sequencing assay which involves the determination of the arrangement of the amino acid sequence of a protein. http://purl.obolibrary.org/obo/NGBO_6000175 biological database http://purl.obolibrary.org/obo/NGBO_6000248 database A database which represent libraries of life sciences information, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. http://purl.obolibrary.org/obo/NGBO_6000179 alignment http://purl.obolibrary.org/obo/NGBO_6000122 bioinformatics analysis A bioinformatics analysis data transformation which two or more things are positioned in a straight line or parallel to each other http://purl.obolibrary.org/obo/NGBO_6000181 database index http://purl.obolibrary.org/obo/OBI_0200000 data transformation A bioinformatics analysis that produces data structure that improves the speed of data retrieval operations on a database table at the cost of additional writes and storage space to maintain the index data structure http://purl.obolibrary.org/obo/NGBO_6000182 genome indexing http://purl.obolibrary.org/obo/NGBO_6000122 bioinformatics analysis A bioinformatics analysis which referes to the process of compressing to reduze the size of genome file http://purl.obolibrary.org/obo/NGBO_6000185 Allele-specific expression data http://purl.obolibrary.org/obo/OBI_0000101 measured expression level A measured expression level which refers to the characteristic of preferentially expressing a parental allele in the hybrid due to variations in regulatory sequences from the parental genomes. http://purl.obolibrary.org/obo/NGBO_6000186 microarray CNV genotypes data http://purl.obolibrary.org/obo/OBI_0000101 measured expression level A measured expression level measurement datum which represent copy number variation (CNV) obtained by microarray http://purl.obolibrary.org/obo/NGBO_6000190 microRNA expression data http://purl.obolibrary.org/obo/OBI_0000101 measured expression level A measured expression level measurement datum which refers to represent small non-coding RNAs of 19-24 nucleotides in length that downregulate gene expression during various crucial cell processes such as apoptosis, differentiation and development. http://purl.obolibrary.org/obo/NGBO_6000193 gene expression profile data http://purl.obolibrary.org/obo/OBI_0000101 measured expression level A measured expression level which refers to activity (the expression) of thousands of genes at once, to create a global picture of cellular function. http://purl.obolibrary.org/obo/NGBO_6000195 whole exome sequence data http://purl.obolibrary.org/obo/OBI_0001573 DNA sequence data A mesurement datum that represent all of the protein-coding regions of genes in a genome (known as the exome) http://purl.obolibrary.org/obo/NGBO_6000198 single molecule real time sequencing data http://purl.obolibrary.org/obo/OBI_0001573 DNA sequence data A single molecule real time sequencing data is DNA sequence data generated from parallelized single molecule DNA sequencing method. http://purl.obolibrary.org/obo/NGBO_6000199 whole genome sequence data http://purl.obolibrary.org/obo/OBI_0001573 DNA sequence data A DNA sequence data which represent the the complete DNA sequence of an organism's genome at a single time http://purl.obolibrary.org/obo/NGBO_6000200 metagenomics sequence data http://purl.obolibrary.org/obo/OBI_0001573 DNA sequence data DNA sequence data which represent genomic DNA obtained from environmental samples http://purl.obolibrary.org/obo/NGBO_6000201 whole transcriptome sequence data http://purl.obolibrary.org/obo/OBIws_0000192 RNA sequence data RNA sequence data which represent the complete complement of transcripts in a sample, at a given time http://purl.obolibrary.org/obo/NGBO_6000204 16s RNA sequence data http://purl.obolibrary.org/obo/OBIws_0000192 RNA sequence data RNA sequence data which is about the 16s gene of one or more organisms. http://purl.obolibrary.org/obo/NGBO_6000207 variant prioritisation http://purl.obolibrary.org/obo/NGBO_6000261 genetic variantion analysis A genetic variation analysis which involves identifying biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes. http://purl.obolibrary.org/obo/NGBO_6000212 genetic variants filtration assay http://purl.obolibrary.org/obo/NGBO_6000261 genetic variantion analysis An assay which attempt to select highly confident variants and remove the ones that are falsely called http://purl.obolibrary.org/obo/NGBO_6000216 global sequence alignment http://purl.obolibrary.org/obo/OBI_0002567 sequence alignment A sequence alignment which align every residue in every sequence http://purl.obolibrary.org/obo/NGBO_6000217 local sequence alignment http://purl.obolibrary.org/obo/OBI_0002567 sequence alignment A sequence alignment which align dissimilar sequences that are suspected to contain regions of similarity or similar sequence motifs within their larger sequence context http://purl.obolibrary.org/obo/NGBO_6000218 multiple sequence alignment http://purl.obolibrary.org/obo/OBI_0002567 sequence alignment A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. http://purl.obolibrary.org/obo/NGBO_6000219 pairwise sequence alignment http://purl.obolibrary.org/obo/OBI_0002567 sequence alignment A sequence alignment bioinformatics analysis which identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences (protein or nucleic acid) http://purl.obolibrary.org/obo/NGBO_6000225 sequence similarity search http://purl.obolibrary.org/obo/NGBO_6000122 bioinformatics analysis A bioinformatics analysis which attempt to searching sequence databases by using alignment to a query sequence http://purl.obolibrary.org/obo/NGBO_6000227 command line flag http://purl.obolibrary.org/obo/IAO_0000028 symbol A symbol that is used to specify options for command line programs. http://purl.obolibrary.org/obo/NGBO_6000229 functional annotation http://purl.obolibrary.org/obo/OBI_0001944 sequence annotation Functional annotation is a bioinformatics analysis consists of attaching biological information to genomic elements such as: biochemical function, biological function, involved regulation and interactions and expression http://purl.obolibrary.org/obo/NGBO_6000232 data validation http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process which ensure data have undergone data cleansing to ensure they have data quality, that is, that they are both correct and useful. http://purl.obolibrary.org/obo/NGBO_6000233 format validation http://purl.obolibrary.org/obo/NGBO_6000232 data validation A data validation process that checks that the data is in a specified format (template), e.g., dates have to be in the format DD/ MM/YYYY is correct http://purl.obolibrary.org/obo/NGBO_6000235 sequence data quality validation http://purl.obolibrary.org/obo/NGBO_6000232 data validation A data validating whech validate sequencing quality scores and measure the probability that a base is called incorrectly. http://purl.obolibrary.org/obo/NGBO_6000236 assay kit http://purl.obolibrary.org/obo/OBI_0000047 processed material A processed material which contain a set of articles or equipment needed for a specific purpose. http://purl.obolibrary.org/obo/NGBO_6000237 DNA library http://purl.obolibrary.org/obo/OBI_0000047 processed material A process material which contains DNA fragments that represent the entire genome of an organism. http://purl.obolibrary.org/obo/NGBO_6000238 DNA extraction assay kit http://purl.obolibrary.org/obo/NGBO_6000236 assay kit An assay kit used for the technique of isolating DNA in a biological sample http://purl.obolibrary.org/obo/NGBO_6000244 reference genome datum http://purl.obolibrary.org/obo/IAO_0000027 data item A data item which represent datum related to reference genome used as a standard for comparison in basic research and clinical settings http://purl.obolibrary.org/obo/NGBO_6000246 data file URL http://purl.obolibrary.org/obo/NGBO_6000385 data storage datum A URL at which the data file file is stored. http://purl.obolibrary.org/obo/NGBO_6000248 database http://purl.obolibrary.org/obo/IAO_0000030 information content entity A database is an information content entity that describe a structured set of data held in a computer, especially one that is accessible in various ways. http://purl.obolibrary.org/obo/NGBO_6000255 library construction kit http://purl.obolibrary.org/obo/NGBO_6000236 assay kit An assay kit processed material that include a set of articles or equipment needed for library construction http://purl.obolibrary.org/obo/NGBO_6000257 quality assesment report http://purl.obolibrary.org/obo/IAO_0000088 report A report that represent the process of data collection and analysis through which the degree of conformity to predetermined standards and criteria are exemplified http://purl.obolibrary.org/obo/NGBO_6000258 sample derivative from specimen creation process http://purl.obolibrary.org/obo/OBI_0000094 material processing A material processing that has as its input a specimen and as its output a sample derivative. http://purl.obolibrary.org/obo/NGBO_6000259 compressed file http://purl.obolibrary.org/obo/IAO_0000027 data item A data item that represent sort of archive that contains one or more files that have been reduced in size through file compression process http://purl.obolibrary.org/obo/NGBO_6000261 genetic variantion analysis http://purl.obolibrary.org/obo/NGBO_6000122 bioinformatics analysis A bioinformatics analysis which analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model. http://purl.obolibrary.org/obo/NGBO_6000264 validation of known variant assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay which represent the process of targeting detected known disease causing genetic variant for validation purposes http://purl.obolibrary.org/obo/NGBO_6000265 allele specific PCR http://purl.obolibrary.org/obo/NGBO_6000264 validation of known variant assay A validation of known variant assay which permits the direct detection of any point mutation in human DNA by analyzing the PCR products in an ethidium bromide-stained agarose or polyacrylamide gel http://purl.obolibrary.org/obo/NGBO_6000269 copy number variation http://purl.obolibrary.org/obo/IAO_0000027 data item A molecular quality that represent the number of copies of a particular gene varies from one individual to the next (germline mutation) http://purl.obolibrary.org/obo/NGBO_6000270 copy number alteration http://purl.obolibrary.org/obo/IAO_0000027 data item A molecular quality that describe changes in copy number that have arisen in somatic tissues. http://purl.obolibrary.org/obo/NGBO_6000271 secure file transfer process http://purl.obolibrary.org/obo/OBI_0000011 planned process Secure file transfer is a planned process that represent data sharing via a secure, reliable delivery method. It is used to safeguard proprietary and personal data in transit and at rest. Most secure file sharing methods use standard protocols, including: Secure File Transfer Protocol (SFTP) http://purl.obolibrary.org/obo/NGBO_6000272 secure file transfer protocol http://purl.obolibrary.org/obo/NGBO_6000273 data transfer protocol A data transfer protocol is a network protocol that provides file access, file transfer, and file management over any reliable data stream http://purl.obolibrary.org/obo/NGBO_6000273 data transfer protocol http://purl.obolibrary.org/obo/OBI_0000272 protocol A protocol plan specification which describes the process of data transfer between two entities http://purl.obolibrary.org/obo/NGBO_6000274 hypertext transfer protocol secure http://purl.obolibrary.org/obo/NGBO_6000273 data transfer protocol A data transfer protocol, and extension of the Hypertext Transfer Protocol (HTTP). It is used for secure communication over a computer network, and is widely used on the Internet http://purl.obolibrary.org/obo/NGBO_6000276 library preparation protocol http://purl.obolibrary.org/obo/OBI_0000272 protocol A protocol plan specification which describes the process of generating a collection of DNA fragments for sequencing http://purl.obolibrary.org/obo/NGBO_6000278 result acceptance or rejection protocol http://purl.obolibrary.org/obo/OBI_0000272 protocol Protocol for acceptence or rejcetion must be based on metrics and quality control parameters established during test optimization and utilized during validation http://purl.obolibrary.org/obo/NGBO_6000279 specimen acceptance or rejection protocol http://purl.obolibrary.org/obo/OBI_0000272 protocol A protocol which describe the criteria for acceptance or rejection of a specimen http://purl.obolibrary.org/obo/NGBO_6000281 sequencing quality scores http://purl.obolibrary.org/obo/IAO_0000028 symbol Sequencing quality scores measure the probability that a base is called incorrectly. http://purl.obolibrary.org/obo/NGBO_6000282 HUGO gene nomenclature committee gene name http://purl.obolibrary.org/obo/NGBO_6000175 biological database A biological database that contains genes nomenclature created by the HUGO Gene Nomenclature Committee (HGNC) that sets the standards for human gene nomenclature. http://purl.obolibrary.org/obo/NGBO_6000283 aliquot http://purl.obolibrary.org/obo/OBI_0000953 processed specimen A specimen that is divided into separate parts which are typically stored in separate containers as individual samples http://purl.obolibrary.org/obo/NGBO_6000286 specimen tracking protocol http://purl.obolibrary.org/obo/OBI_0000272 protocol A protocol that ensure that biospecimens can be tracked accurately from the collection site through biospecimen arrival and subsequent http://purl.obolibrary.org/obo/NGBO_6000288 storage unit identifier http://semanticscience.org/resource/SIO_000115 identifier Each freezer, refrigerator, room temperature stor- age cabinet, or other unit appropriate to the collec- tions should have a unique identifier. http://purl.obolibrary.org/obo/NGBO_6000289 Availability of other specimen from the same donor http://purl.obolibrary.org/obo/IAO_0000027 data item A data item which represent the availability of other specimen from the same donor http://purl.obolibrary.org/obo/NGBO_6000290 specimen shipment identifier http://semanticscience.org/resource/SIO_000115 identifier An identifier which denotes number assigned by a shipper of specimen. http://purl.obolibrary.org/obo/NGBO_6000292 standard operating procedure version number http://purl.obolibrary.org/obo/IAO_0000129 version number A version number denotes standard operating procedure http://purl.obolibrary.org/obo/NGBO_6000293 standard operating procedure title http://semanticscience.org/resource/SIO_000116 name A unique SOP name which captures the essence of the practice described. http://purl.obolibrary.org/obo/NGBO_6000294 specimen shipping temperature http://purl.obolibrary.org/obo/PATO_0000146 temperature A temperature which represent specimen temperature during shipment. http://purl.obolibrary.org/obo/NGBO_6000296 refrigerated specimen temperature http://purl.obolibrary.org/obo/NGBO_6000294 specimen shipping temperature A specimen shipping tempruture which represent a Refrigerated temperature (2 to 8°C) - wet ice or gel packs (conditioned at –15°C, designed for refrigerated temperatures, or phase change material rated for refrigerated transport). http://purl.obolibrary.org/obo/NGBO_6000298 specimen destruction assay http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process with the objective to destroy an entire collection or specific specimen. http://purl.obolibrary.org/obo/NGBO_6000299 specimen culling http://purl.obolibrary.org/obo/OBI_0000011 planned process A specimen culling is the process of reviewing and eliminating specimens in a collection or an entire collection either by destruction or transfer to a new custodian http://purl.obolibrary.org/obo/NGBO_6000302 clinical variant interpretation http://purl.obolibrary.org/obo/IAO_0000027 data item A data item representing a variant’s significance in relation to a disease or phenotype. http://purl.obolibrary.org/obo/NGBO_6000303 pathogenic variant http://purl.obolibrary.org/obo/NGBO_6000302 clinical variant interpretation A clinical variant interpretation that represents a sequence variant that is previously reported and is a recognized cause of the disorder. http://purl.obolibrary.org/obo/NGBO_6000304 likely pathogenic variant http://purl.obolibrary.org/obo/NGBO_6000302 clinical variant interpretation A clinical variant interpretation that represents a sequence variant that is previously unreported and is of the type which is expected to cause the disorder. http://purl.obolibrary.org/obo/NGBO_6000305 variant of unknown significance http://purl.obolibrary.org/obo/NGBO_6000302 clinical variant interpretation A clinical variant interpretation that represents a sequence variant that is previously unreported and is of the type which may or may not be causative of the disorder. http://purl.obolibrary.org/obo/NGBO_6000306 likely benign variant http://purl.obolibrary.org/obo/NGBO_6000302 clinical variant interpretation A clinical variant interpretation that represents a sequence variant that is previously unreported and is probably not causative of disease http://purl.obolibrary.org/obo/NGBO_6000307 benign variant http://purl.obolibrary.org/obo/NGBO_6000302 clinical variant interpretation A clinical variant interpretation that represents a sequence variant previously classified or reported as a recognized neutral variant http://purl.obolibrary.org/obo/NGBO_6000318 expression quantitative trait loci http://purl.obolibrary.org/obo/GENO_0000902 genomic feature location A genomic feature location which represent the expression quantitative trait loci are genomic loci that explain all or a fraction of variation in expression levels of mRNAs http://purl.obolibrary.org/obo/NGBO_6000319 messenger RNA sequence data http://purl.obolibrary.org/obo/OBIws_0000192 RNA sequence data RNA sequence data that represent the sequence of single-stranded RNA molecule that is complementary to one of the DNA strands of a gene. The mRNA is an RNA version of the gene that leaves the cell nucleus and moves to the cytoplasm where proteins are made. http://purl.obolibrary.org/obo/NGBO_6000320 measurement datum availability statement http://purl.obolibrary.org/obo/IAO_0000027 data item A data item which indicates availability of specimen associated data http://purl.obolibrary.org/obo/NGBO_6000323 target region enrichment assay http://purl.obolibrary.org/obo/OBI_0000094 material processing A material processing which capture specific regions of interest after library preparation for next generation sequencing. http://purl.obolibrary.org/obo/NGBO_6000352 raw sequence file editing http://purl.obolibrary.org/obo/OBI_0200000 data transformation A bioinformatics analysis which involves any edit or change to a molecular sequence file. http://purl.obolibrary.org/obo/NGBO_6000353 omics data generation assay http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay An assay which generate OMICS data through a wet bench process such as sequencing techniques. http://purl.obolibrary.org/obo/NGBO_6000354 interpretation of clinical variant protocol http://purl.obolibrary.org/obo/OBI_0000272 protocol A protocol that describe the process of assigning a formal classification to the detected variant http://purl.obolibrary.org/obo/NGBO_6000355 ACMG guidelines for classification of variants http://purl.obolibrary.org/obo/NGBO_6000354 interpretation of clinical variant protocol A protocol which describes the guidance for the interpretation of sequence variants suggested by The American College of Medical Genetics and Genomics (ACMG). http://purl.obolibrary.org/obo/NGBO_6000359 Burrows-Wheeler Aligner algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm An algorithm which perform mapping of low-divergent sequences against a large reference genome, such as the human genome. http://purl.obolibrary.org/obo/NGBO_6000360 adapter ligation protocol http://purl.obolibrary.org/obo/OBI_0000272 protocol A protocol which describes the process of attaching synthetic oligonucleotides with known sequences to both or either ends of complementary DNA (cDNA) fragments as a prepration for sequencing http://purl.obolibrary.org/obo/NGBO_6000362 validation of known variant protocol http://purl.obolibrary.org/obo/OBI_0000272 protocol A protocol which describe the process of validation of known variant http://purl.obolibrary.org/obo/NGBO_6000364 allele specific PCR protocol http://purl.obolibrary.org/obo/OBI_0000272 protocol A protocol which describes the process of Allele-specific polymerase chain reaction (PCR) http://purl.obolibrary.org/obo/NGBO_6000365 data anonymization protocol http://purl.obolibrary.org/obo/OBI_0000272 protocol A protocol plan specification which describes the process of reducing the likelihood that the data can identify an individual. http://purl.obolibrary.org/obo/NGBO_6000377 BWA assembly process http://purl.obolibrary.org/obo/NGBO_6000122 bioinformatics analysis Bioinformatics analysis which performs gapped alignment for single-end reads, supports paired-end mapping, generates mapping quality, and gives multiple hits if required http://purl.obolibrary.org/obo/NGBO_6000382 bioinformatics analysis software http://purl.obolibrary.org/obo/IAO_0000010 software A software designed to extract meaningful information from the mass of molecular biology data http://purl.obolibrary.org/obo/NGBO_6000385 data storage datum http://purl.obolibrary.org/obo/IAO_0000027 data item A data item that represent information on data storage. http://purl.obolibrary.org/obo/NGBO_6000394 ligation objective http://purl.obolibrary.org/obo/OBI_0000686 material combination objective An objective specification to determine attaching synthetic oligonucleotides with known sequences to both or either ends of complementary DNA (cDNA) fragments http://purl.obolibrary.org/obo/NGBO_6000395 target enrichment protocol http://purl.obolibrary.org/obo/OBI_0000272 protocol A protocol which describes the workflow to capture specific regions of interest after library preparation for NGS and has many advantages over whole genome sequencing (WGS). http://purl.obolibrary.org/obo/NGBO_6000397 target sequence information http://purl.obolibrary.org/obo/IAO_0000104 plan specification A data item that which represent information about subset of genes or specific regions of interest of the genome. http://purl.obolibrary.org/obo/NGBO_6000399 information about data storage location http://purl.obolibrary.org/obo/NGBO_6000385 data storage datum An information content entity that is about the location of data storage http://purl.obolibrary.org/obo/NGBO_6000400 in-bead tagmentation library prepration http://purl.obolibrary.org/obo/OBI_0000711 library preparation A library preparation material processing which uses bead-linked transposomes for a more uniform tagmentation reaction compared to in-solution tagmentation reactions http://purl.obolibrary.org/obo/NGBO_6000402 name of data generation assay executor http://purl.obolibrary.org/obo/IAO_0020015 personal name A personal name that designates the person who executed the sequencing run. http://purl.obolibrary.org/obo/NGBO_6000405 assay kit version http://purl.obolibrary.org/obo/IAO_0000129 version number A version number of assay kit. http://purl.obolibrary.org/obo/NGBO_6000406 name of bioinformatics analysis executor http://purl.obolibrary.org/obo/IAO_0020015 personal name A personal name that designates the person who executed the bioinformatics analysis. http://purl.obolibrary.org/obo/NGBO_6000407 output data file http://purl.obolibrary.org/obo/NGBO_6000472 data file A data file which contain the output of data transformation process http://purl.obolibrary.org/obo/NGBO_6000408 input data file http://purl.obolibrary.org/obo/NGBO_6000472 data file A data file which contain the input for data transformation process http://purl.obolibrary.org/obo/NGBO_6000409 information about software http://purl.obolibrary.org/obo/IAO_0000030 information content entity Information content entity about bioinformatics software http://purl.obolibrary.org/obo/NGBO_6000410 bioinformatics software name http://purl.obolibrary.org/obo/NGBO_6000409 information about software Information about software includes software name http://purl.obolibrary.org/obo/NGBO_6000411 software version number http://purl.obolibrary.org/obo/NGBO_6000409 information about software Information about software includes information on software version number. http://purl.obolibrary.org/obo/NGBO_6000412 software parameter value http://purl.obolibrary.org/obo/NGBO_6000409 information about software Information about software includes information on software parameter value. http://purl.obolibrary.org/obo/NGBO_6000413 bioinformatics software parameter name http://purl.obolibrary.org/obo/NGBO_6000409 information about software Information about software includes information on software parameter name. http://purl.obolibrary.org/obo/NGBO_6000414 bioinformatics analysis execution date http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum of the bioinformatics analysis execution date. http://purl.obolibrary.org/obo/NGBO_6000415 software description http://purl.obolibrary.org/obo/NGBO_6000409 information about software Information about software includes software description. http://purl.obolibrary.org/obo/NGBO_6000416 software Documentation URI http://purl.obolibrary.org/obo/NGBO_6000409 information about software Information about software includes software documentation URI http://purl.obolibrary.org/obo/NGBO_6000417 software run identifier http://semanticscience.org/resource/SIO_000115 identifier An identifier which denotes the bioinformatics analysis ID. http://purl.obolibrary.org/obo/NGBO_6000418 data file description http://semanticscience.org/resource/SIO_000136 description A description of the file that contain raw data generated by a measurement device. http://purl.obolibrary.org/obo/NGBO_6000419 assay execution note http://purl.obolibrary.org/obo/IAO_0000314 document part A document part of relevant notes or instructions regarding data generation assay execution http://purl.obolibrary.org/obo/NGBO_6000439 detected gene mutation http://purl.obolibrary.org/obo/OBI_0001909 conclusion based on data A conclusion based on data about a permanent change in the DNA sequence that makes up a gene http://purl.obolibrary.org/obo/NGBO_6000472 data file http://purl.obolibrary.org/obo/IAO_0000030 information content entity Any data file as generated by some acquisition computer or console. http://purl.obolibrary.org/obo/NGBO_6000473 amino acid substitution http://purl.obolibrary.org/obo/IAO_0000027 data item A data item which represents the substitution of one or more amino acids. http://purl.obolibrary.org/obo/NGBO_6000474 data transfer agreement document act http://purl.obolibrary.org/obo/OBI_0302908 document editing A planned process of making the decision of the data transfer. http://purl.obolibrary.org/obo/NGBO_6000475 probe ID http://semanticscience.org/resource/SIO_000115 identifier An Identifier of an oligonucleotide probe. http://purl.obolibrary.org/obo/NGBO_6000476 oligonucleotide probe http://purl.obolibrary.org/obo/SO_0000001 region A region of short stretches of single-stranded DNA or RNA used to detect the presence of complementary nucleic acid sequences (target sequences) by hybridization. http://purl.obolibrary.org/obo/NGBO_6000477 expression quantitative trait loci data http://purl.obolibrary.org/obo/IAO_0000027 data item A data item that describe expression quantitative trait loci. http://purl.obolibrary.org/obo/NGBO_6000627 target enrichment kit http://purl.obolibrary.org/obo/NGBO_6000236 assay kit An assay kit used for the technique of target enrichment http://purl.obolibrary.org/obo/NGBO_6000685 bioinformatics pipeline http://purl.obolibrary.org/obo/OBI_0001943 software pipeline A software pipeline that is composed of a wide array of software algorithms to process biological raw data. http://purl.obolibrary.org/obo/NGBO_6000689 user information http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity about user authentication information. 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/IDO_0000619 immunosuppressive disposition http://purl.obolibrary.org/obo/BFO_0000016 disposition A disposition whose realization negatively regulates an immune response. http://purl.obolibrary.org/obo/OGMS_0000045 disorder http://purl.obolibrary.org/obo/BFO_0000040 material entity A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease. http://www.ebi.ac.uk/efo/EFO_0000187 Kaposi's sarcoma cell http://www.ebi.ac.uk/efo/EFO_0005934 disease cell type A multicentric, malignant neoplastic vascular proliferation characterized by bluish-red cutaneous nodules, usually on the legs, toes, or feet, that slowly increase in size and number and spread to more proximal sites. The tumors have endothelium-lined channels and vascular spaces mixed with aggregates of spindle-shaped cells; they may remain confined to skin and subcutaneous tissue, but widespread visceral involvement may occur. http://www.ebi.ac.uk/efo/EFO_0000572 lymphoblast http://www.ebi.ac.uk/efo/EFO_0000324 cell type Often referred to as a blast cell. Unlike other usages of the suffix -blast a lymphoblast is a further differentiation of a lymphocyte, T- or B-, occasioned by an antigenic stimulus. The lymphoblast usually develops by enlargement of a lymphocyte, active re-entry to the S phase of the cell cycle, mitogenesis and production of much m-RNA and ribosomes. http://www.ebi.ac.uk/efo/EFO_0000700 integumental cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type Cell coming from the intergument, organ that constitutes the external surface of the body. The intergument consists of the epidermis, dermis, and skin appendages. http://www.ebi.ac.uk/efo/EFO_0002451 HUVEC cell http://purl.obolibrary.org/obo/CL_0000115 endothelial cell A convenient source of human endothelial cells are those that line the large vein in the umbilical cord which is usually discarded together with the placenta after childbirth. The cells can be removed as a fairly pure suspension by mild enzymatic treatment of the vein followed by some mechanical distraction and will grow relatively easily in culture, retaining their differentiated characteristics for several passages. http://www.ebi.ac.uk/efo/EFO_0002968 embryonic stem cell derived neuronal stem cell http://purl.obolibrary.org/obo/CL_0000034 stem cell neural stem cells experimentally derived from ES cells http://www.ebi.ac.uk/efo/EFO_0003036 clear cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A cell with empty-appearing cytoplasm when viewed with a light microscope. http://www.ebi.ac.uk/efo/EFO_0003076 thyrocyte http://purl.obolibrary.org/obo/CL_0000066 epithelial cell An epithelial cell lining the thyroid follicle. http://www.ebi.ac.uk/efo/EFO_0004038 mouse embryonic stem cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type mouse embryonic stem cell http://www.ebi.ac.uk/efo/EFO_0004040 mouse embryonic fibroblast cell http://purl.obolibrary.org/obo/CL_0000057 fibroblast Mouse embryonic fibroblast cell http://www.ebi.ac.uk/efo/EFO_0004905 induced pluripotent stem cell http://purl.obolibrary.org/obo/CL_0002248 pluripotent stem cell Induced pluripotent stem cells (iPS cells or iPSCs) are a type of pluripotent stem cell artificially derived from a non-pluripotent cell. Various methods exist to revert cells to pluripotency such as reprogramming mediated through a mature metaphase II oocyte as in somatic cell nuclear transfer. http://www.ebi.ac.uk/efo/EFO_0004987 embryonal carcinoma cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type A cell which bears embryonal carcinoma. http://www.ebi.ac.uk/efo/EFO_0005023 adipose tissue derived mesenchymal stem cell http://www.ebi.ac.uk/efo/EFO_0000586 mesenchymal stem cell A adult mesenchymal stem cell derived from adipose tisssue http://www.ebi.ac.uk/efo/EFO_0005024 placental pericyte http://purl.obolibrary.org/obo/CL_0000669 pericyte A pericyte derived from the placenta. 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://www.ebi.ac.uk/efo/EFO_0009498 MSiPS http://www.ebi.ac.uk/efo/EFO_0004905 induced pluripotent stem cell Induced pluripotent stem cell line from a Caucasian male with type 2 diabetes, same donor as of MSLCL cell line. http://www.ebi.ac.uk/efo/EFO_0009501 CWRU1 http://www.ebi.ac.uk/efo/EFO_0004905 induced pluripotent stem cell Induced pluripotent stem cells derived from MSC658 fibroblasts. http://purl.obolibrary.org/obo/ngbo.owl/NGBO_6000284 peripheral blood mononuclear cell isolation http://purl.obolibrary.org/obo/OBI_0001483 cell collecting A cell collecting process used to isolate PBMCs, including T cells, from whole blood using density gradient centrifugation (e.g., Ficoll-Paque). http://purl.obolibrary.org/obo/CL_2000018 endothelial cell of coronary artery http://purl.obolibrary.org/obo/CL_0000071 blood vessel endothelial cell Any endothelial cell of artery that is part of a coronary artery. [ GOC:TermGenie ] http://purl.obolibrary.org/obo/CL_2000058 calvarial osteoblast http://purl.obolibrary.org/obo/CL_0000062 osteoblast Any osteoblast that is part of a skull. [ GOC:TermGenie ] http://purl.obolibrary.org/obo/CL_2000074 splenocyte http://purl.obolibrary.org/obo/CL_0000738 leukocyte Any leukocyte that is part of a spleen. [ GOC:TermGenie ] http://purl.obolibrary.org/obo/ICO_0000126 storage duration of signed informed consent form http://purl.obolibrary.org/obo/BFO_0000038 one-dimensional temporal region a termporal interval that represents a period of time during which a signed informed consent form is stored. http://purl.obolibrary.org/obo/NCIT_C42775 E-mail Address http://purl.obolibrary.org/obo/NGBO_6000161 personally identifiable information A text string identifier for a location to which e-mail can be delivered. 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/ICO_0000089 actual duration of study subject participation http://purl.obolibrary.org/obo/ICO_0000088 participation duration Total length of time of subject's participation in a clinical study; from the time of enrollment to the completion of follow-up. 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_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_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_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_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_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/ICO_0000127 planned duration of study subject participation http://purl.obolibrary.org/obo/ICO_0000088 participation duration a participation time that is the total length of time of subject's participation in a research study; from the time of enrollment to the completion of follow-up. 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_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/NCIT_C40978 Telephone Number http://purl.obolibrary.org/obo/NGBO_6000161 personally identifiable information A sequence of decimal digits (0-9) that is used for identifying a destination telephone line or other device in a telephone network. 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_9606 Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_314146 Euarchontoglires man http://purl.obolibrary.org/obo/OMIABIS_0001040 specimen meeting specification http://purl.obolibrary.org/obo/OBI_0100051 specimen adherance to specification http://purl.obolibrary.org/obo/OMIABIS_0001079 specimen donor http://purl.obolibrary.org/obo/NCBITaxon_9606 Homo sapiens sample donor 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/BTO_0000152 infected cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://purl.obolibrary.org/obo/BTO_0004298 corneal epithelial cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://purl.obolibrary.org/obo/BTO_0004578 vascular smooth muscle cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://www.ebi.ac.uk/efo/EFO_0005934 disease cell type http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://purl.obolibrary.org/obo/CL_0000112 columnar neuron http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://purl.obolibrary.org/obo/CL_0000384 ligament cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://purl.obolibrary.org/obo/CL_0000398 polygonal cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://purl.obolibrary.org/obo/CL_0000477 follicle cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://purl.obolibrary.org/obo/CL_0000520 prokaryotic cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://purl.obolibrary.org/obo/CL_0000521 fungal cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://purl.obolibrary.org/obo/CL_0002031 hematopoietic lineage restricted progenitor cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://purl.obolibrary.org/obo/CL_0002032 hematopoietic oligopotent progenitor cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://purl.obolibrary.org/obo/CL_0002319 neural cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://purl.obolibrary.org/obo/CL_1000497 kidney cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://www.ebi.ac.uk/efo/EFO_1000343 lympoid tissue http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://www.ebi.ac.uk/efo/EFO_1000615 utering smooth muscle cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://www.ebi.ac.uk/efo/EFO_1001464 glial brain cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://www.ebi.ac.uk/efo/EFO_1001468 mantle cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://www.ebi.ac.uk/efo/EFO_1001470 merkel cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://www.ebi.ac.uk/efo/EFO_0002966 pancreatic cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://www.ebi.ac.uk/efo/EFO_0002433 cumulus-oocyte complex http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://www.ebi.ac.uk/efo/EFO_0002439 mesophyll cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://www.ebi.ac.uk/efo/EFO_0002540 nestin positive islet-derived progenitor cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://www.ebi.ac.uk/efo/EFO_0002661 dendritic cell-derived intermediate cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://www.ebi.ac.uk/efo/EFO_0002662 dendritic cell-derived osteoclast http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://www.ebi.ac.uk/efo/EFO_0002665 monocyte-derived intermediate cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://www.ebi.ac.uk/efo/EFO_0002666 monocyte-derived osteoclast http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://www.ebi.ac.uk/efo/EFO_0002955 reproductive system cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://www.ebi.ac.uk/efo/EFO_0002956 musculo-skeletal system cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://www.ebi.ac.uk/efo/EFO_0002962 animal reproductive system cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://www.ebi.ac.uk/efo/EFO_0002963 nervous system cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://www.ebi.ac.uk/efo/EFO_0003970 mouse erythroleukemia cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://www.ebi.ac.uk/efo/EFO_0004039 mouse neural progenitor cell http://www.ebi.ac.uk/efo/EFO_0000324 cell type http://purl.obolibrary.org/obo/BTO_0000583 bone marrow cancer cell http://www.ebi.ac.uk/efo/EFO_0005934 disease cell type http://purl.obolibrary.org/obo/BTO_0001615 colorectal cancer cell http://www.ebi.ac.uk/efo/EFO_0005934 disease cell type http://purl.obolibrary.org/obo/CL_0002059 CD8alpha-positive thymic conventional dendritic cell http://purl.obolibrary.org/obo/CL_0000941 thymic conventional dendritic cell http://purl.obolibrary.org/obo/CL_0002460 CD8alpha-negative thymic conventional dendritic cell http://purl.obolibrary.org/obo/CL_0000941 thymic conventional dendritic cell http://purl.obolibrary.org/obo/BFO_0000003 occurrent http://purl.obolibrary.org/obo/BFO_0000001 entity 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_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://semanticscience.org/resource/SIO_000026 object quality http://purl.obolibrary.org/obo/BFO_0000019 quality 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/CARO_0000007 immaterial anatomical entity http://purl.obolibrary.org/obo/BFO_0000141 immaterial entity http://semanticscience.org/resource/SIO_000115 identifier http://semanticscience.org/resource/SIO_000179 label http://semanticscience.org/resource/SIO_000078 language entity http://purl.obolibrary.org/obo/IAO_0000030 information content entity http://www.w3.org/2006/vcard/ns#Address address http://purl.obolibrary.org/obo/IAO_0000300 textual entity http://semanticscience.org/resource/SIO_001041 study design http://purl.obolibrary.org/obo/IAO_0000310 document http://purl.obolibrary.org/obo/GENEPIO_0001800 sequence identifier http://purl.obolibrary.org/obo/IAO_0000577 centrally registered identifier symbol http://purl.obolibrary.org/obo/OMIABIS_0000094 sample collection or study contact role http://purl.obolibrary.org/obo/OMIABIS_0000012 contact role http://semanticscience.org/resource/SIO_000079 visual language entity http://semanticscience.org/resource/SIO_000078 language entity http://semanticscience.org/resource/SIO_000136 description http://semanticscience.org/resource/SIO_000078 language entity http://semanticscience.org/resource/SIO_000651 textual entity http://semanticscience.org/resource/SIO_000079 visual language entity http://semanticscience.org/resource/SIO_001383 gene symbol http://semanticscience.org/resource/SIO_000120 scientific name http://semanticscience.org/resource/SIO_000179 label http://semanticscience.org/resource/SIO_000651 textual entity http://semanticscience.org/resource/SIO_000942 numeric label http://semanticscience.org/resource/SIO_000179 label http://semanticscience.org/resource/SIO_000116 name http://semanticscience.org/resource/SIO_000179 label http://semanticscience.org/resource/SIO_010053 evolutionary lineage http://semanticscience.org/resource/SIO_001196 history http://semanticscience.org/resource/SIO_010060 family history http://semanticscience.org/resource/SIO_001196 history http://semanticscience.org/resource/SIO_010673 medical history http://semanticscience.org/resource/SIO_001196 history http://www.ebi.ac.uk/efo/EFO_0000586 mesenchymal stem cell http://purl.obolibrary.org/obo/CL_0000034 stem cell http://purl.obolibrary.org/obo/CL_0001008 Kit and Sca1-positive hematopoietic stem cell http://purl.obolibrary.org/obo/CL_0000037 hematopoietic stem cell http://purl.obolibrary.org/obo/CL_0001024 CD34-positive, CD38-negative hematopoietic stem cell http://purl.obolibrary.org/obo/CL_0000037 hematopoietic stem cell http://purl.obolibrary.org/obo/CL_0002246 peripheral blood stem cell http://purl.obolibrary.org/obo/CL_0000037 hematopoietic stem cell http://purl.obolibrary.org/obo/CL_0002352 gestational hematopoietic stem cell http://purl.obolibrary.org/obo/CL_0000037 hematopoietic stem cell http://purl.obolibrary.org/obo/CL_0002000 Kit-positive erythroid progenitor cell http://purl.obolibrary.org/obo/CL_0000038 erythroid progenitor cell http://purl.obolibrary.org/obo/CL_0002003 CD34-positive, GlyA-negative erythroid progenitor cell http://purl.obolibrary.org/obo/CL_0000038 erythroid progenitor cell http://www.ebi.ac.uk/efo/EFO_0002534 fetal blood cell http://purl.obolibrary.org/obo/CL_0000081 blood cell http://purl.obolibrary.org/obo/CL_0000390 blood cell (sensu Nematoda and Protostomia) http://purl.obolibrary.org/obo/CL_0000081 blood cell http://purl.obolibrary.org/obo/CL_0002318 periperhal blood mesothelial cell http://purl.obolibrary.org/obo/CL_0000081 blood cell http://purl.obolibrary.org/obo/CL_0000588 odontoclast http://purl.obolibrary.org/obo/CL_0000092 osteoclast http://purl.obolibrary.org/obo/CL_0000778 mononuclear osteoclast http://purl.obolibrary.org/obo/CL_0000092 osteoclast http://purl.obolibrary.org/obo/CL_0000779 multinuclear osteoclast http://purl.obolibrary.org/obo/CL_0000092 osteoclast http://purl.obolibrary.org/obo/CL_0000484 connective tissue type mast cell http://purl.obolibrary.org/obo/CL_0000097 mast cell http://purl.obolibrary.org/obo/CL_0000485 mucosal type mast cell http://purl.obolibrary.org/obo/CL_0000097 mast cell http://www.ebi.ac.uk/efo/EFO_0002572 large adipocyte http://purl.obolibrary.org/obo/CL_0000136 fat cell http://www.ebi.ac.uk/efo/EFO_0002573 small adipocyte http://purl.obolibrary.org/obo/CL_0000136 fat cell http://purl.obolibrary.org/obo/CL_0002598 bronchial smooth muscle cell http://purl.obolibrary.org/obo/CL_0000192 smooth muscle cell http://purl.obolibrary.org/obo/CL_0000562 nucleate erythrocyte http://purl.obolibrary.org/obo/CL_0000232 erythrocyte http://purl.obolibrary.org/obo/CL_0000595 enucleate erythrocyte http://purl.obolibrary.org/obo/CL_0000232 erythrocyte http://purl.obolibrary.org/obo/CL_0000861 elicited macrophage http://purl.obolibrary.org/obo/CL_0000235 macrophage http://purl.obolibrary.org/obo/CL_0000864 tissue-resident macrophage http://purl.obolibrary.org/obo/CL_0000235 macrophage http://purl.obolibrary.org/obo/CL_0000818 transitional stage B cell http://purl.obolibrary.org/obo/CL_0000236 B cell http://purl.obolibrary.org/obo/CL_0000990 conventional dendritic cell http://purl.obolibrary.org/obo/CL_0000451 dendritic cell http://purl.obolibrary.org/obo/CL_0001014 CD1a-positive Langerhans cell http://purl.obolibrary.org/obo/CL_0000453 Langerhans cell http://purl.obolibrary.org/obo/CL_0001015 CD8_alpha-low Langerhans cell http://purl.obolibrary.org/obo/CL_0000453 Langerhans cell http://purl.obolibrary.org/obo/CL_0002457 epidermal Langerhans cell http://purl.obolibrary.org/obo/CL_0000453 Langerhans cell http://purl.obolibrary.org/obo/CL_0000679 glutamatergic neuron http://purl.obolibrary.org/obo/CL_0000540 neuron http://purl.obolibrary.org/obo/CL_0002004 CD34-negative, GlyA-negative proerythroblast http://purl.obolibrary.org/obo/CL_0000547 proerythroblast http://purl.obolibrary.org/obo/CL_0002012 Kit-low proerythroblast http://purl.obolibrary.org/obo/CL_0000547 proerythroblast http://purl.obolibrary.org/obo/CL_0002013 GlyA-positive basophillic erythroblast http://purl.obolibrary.org/obo/CL_0000549 basophilic erythroblast http://purl.obolibrary.org/obo/CL_0002014 Kit-negative, Ly-76 high basophilic erythroblast http://purl.obolibrary.org/obo/CL_0000549 basophilic erythroblast http://purl.obolibrary.org/obo/CL_0002015 Kit-negative, Ly-76 high polychromatophilic erythroblast http://purl.obolibrary.org/obo/CL_0000550 polychromatophilic erythroblast http://purl.obolibrary.org/obo/CL_0002016 CD71-low, GlyA-positive polychromatic erythroblast http://purl.obolibrary.org/obo/CL_0000550 polychromatophilic erythroblast http://purl.obolibrary.org/obo/CL_0002017 Kit-negative, Ly-76 high orthochromatophilic erythroblasts http://purl.obolibrary.org/obo/CL_0000552 orthochromatic erythroblast http://purl.obolibrary.org/obo/CL_0002018 CD71-negative, GlyA-positive orthochromatic erythroblast http://purl.obolibrary.org/obo/CL_0000552 orthochromatic erythroblast http://purl.obolibrary.org/obo/CL_0002023 CD34-positive, CD41-positive, CD42-positive megakaryocyte progenitor cell http://purl.obolibrary.org/obo/CL_0000553 megakaryocyte progenitor cell http://purl.obolibrary.org/obo/CL_0002024 Kit-positive megakaryocyte progenitor cell http://purl.obolibrary.org/obo/CL_0000553 megakaryocyte progenitor cell http://purl.obolibrary.org/obo/CL_0002025 CD34-positive, CD41-positive, CD42-negative megakaryocyte progenitor cell http://purl.obolibrary.org/obo/CL_0000553 megakaryocyte progenitor cell http://purl.obolibrary.org/obo/CL_0002026 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell http://purl.obolibrary.org/obo/CL_0000556 megakaryocyte http://purl.obolibrary.org/obo/CL_0002027 CD9-positive, CD41-positive megakaryocyte cell http://purl.obolibrary.org/obo/CL_0000556 megakaryocyte http://purl.obolibrary.org/obo/CL_0002001 CD34-positive, CD38-positive granulocyte monocyte progenitor http://purl.obolibrary.org/obo/CL_0000557 granulocyte monocyte progenitor cell http://purl.obolibrary.org/obo/CL_0002002 Kit-positive granulocyte monocyte progenitor http://purl.obolibrary.org/obo/CL_0000557 granulocyte monocyte progenitor cell http://purl.obolibrary.org/obo/CL_0002421 nucleated reticulocyte http://purl.obolibrary.org/obo/CL_0000558 reticulocyte http://purl.obolibrary.org/obo/CL_0002422 enucleated reticulocyte http://purl.obolibrary.org/obo/CL_0000558 reticulocyte http://purl.obolibrary.org/obo/CL_0000860 classical monocyte http://purl.obolibrary.org/obo/CL_0000576 monocyte http://purl.obolibrary.org/obo/CL_0000875 non-classical monocyte http://purl.obolibrary.org/obo/CL_0000576 monocyte http://purl.obolibrary.org/obo/CL_0001022 CD115-positive monocyte http://purl.obolibrary.org/obo/CL_0000576 monocyte http://purl.obolibrary.org/obo/CL_0002393 intermediate monocyte http://purl.obolibrary.org/obo/CL_0000576 monocyte http://purl.obolibrary.org/obo/CL_0000015 male germ cell http://purl.obolibrary.org/obo/CL_0000586 germ cell http://purl.obolibrary.org/obo/CL_0002021 GlyA-positive erythrocyte http://purl.obolibrary.org/obo/CL_0000595 enucleate erythrocyte http://purl.obolibrary.org/obo/CL_0002022 Ly-76 high positive erythrocyte http://purl.obolibrary.org/obo/CL_0000595 enucleate erythrocyte http://purl.obolibrary.org/obo/CL_0002155 echinocyte http://purl.obolibrary.org/obo/CL_0000595 enucleate erythrocyte http://purl.obolibrary.org/obo/CL_0002357 fetal derived definitive erythrocyte http://purl.obolibrary.org/obo/CL_0000595 enucleate erythrocyte http://purl.obolibrary.org/obo/CL_0002007 Kit-low, CD34-positive eosinophil progenitor cell http://purl.obolibrary.org/obo/CL_0000611 eosinophil progenitor cell http://purl.obolibrary.org/obo/CL_0002008 CD34-positive, CD38-positive eosinophil progenitor cell http://purl.obolibrary.org/obo/CL_0000611 eosinophil progenitor cell http://purl.obolibrary.org/obo/CL_0002030 Fc-epsilon RIalpha-high basophil progenitor cell http://purl.obolibrary.org/obo/CL_0000613 basophil progenitor cell http://purl.obolibrary.org/obo/CL_0000766 myeloid leukocyte http://purl.obolibrary.org/obo/CL_0000738 leukocyte http://purl.obolibrary.org/obo/CL_0002087 nongranular leukocyte http://purl.obolibrary.org/obo/CL_0000738 leukocyte http://purl.obolibrary.org/obo/CL_0000762 nucleated thrombocyte http://purl.obolibrary.org/obo/CL_0000763 myeloid cell http://purl.obolibrary.org/obo/CL_0002417 primitive erythroid lineage cell http://purl.obolibrary.org/obo/CL_0000764 erythroid lineage cell http://purl.obolibrary.org/obo/CL_0000550 polychromatophilic erythroblast http://purl.obolibrary.org/obo/CL_0000765 erythroblast http://purl.obolibrary.org/obo/CL_0000552 orthochromatic erythroblast http://purl.obolibrary.org/obo/CL_0000765 erythroblast http://purl.obolibrary.org/obo/CL_0000092 osteoclast http://purl.obolibrary.org/obo/CL_0000766 myeloid leukocyte http://purl.obolibrary.org/obo/CL_0000097 mast cell http://purl.obolibrary.org/obo/CL_0000766 myeloid leukocyte http://purl.obolibrary.org/obo/CL_0000647 multinucleated giant cell http://purl.obolibrary.org/obo/CL_0000766 myeloid leukocyte http://purl.obolibrary.org/obo/CL_0000889 myeloid suppressor cell http://purl.obolibrary.org/obo/CL_0000766 myeloid leukocyte http://purl.obolibrary.org/obo/CL_0002150 epitheloid cell http://purl.obolibrary.org/obo/CL_0000766 myeloid leukocyte http://purl.obolibrary.org/obo/CL_0000043 mature basophil http://purl.obolibrary.org/obo/CL_0000767 basophil http://purl.obolibrary.org/obo/CL_0000768 immature basophil http://purl.obolibrary.org/obo/CL_0000767 basophil http://purl.obolibrary.org/obo/CL_0000614 basophilic myelocyte http://purl.obolibrary.org/obo/CL_0000768 immature basophil http://purl.obolibrary.org/obo/CL_0000769 basophilic metamyelocyte http://purl.obolibrary.org/obo/CL_0002192 metamyelocyte http://purl.obolibrary.org/obo/CL_0000770 band form basophil http://purl.obolibrary.org/obo/CL_0000768 immature basophil http://purl.obolibrary.org/obo/CL_0000041 mature eosinophil http://purl.obolibrary.org/obo/CL_0000771 eosinophil http://purl.obolibrary.org/obo/CL_0000772 immature eosinophil http://purl.obolibrary.org/obo/CL_0000771 eosinophil http://purl.obolibrary.org/obo/CL_0000612 eosinophilic myelocyte http://purl.obolibrary.org/obo/CL_0002193 myelocyte http://purl.obolibrary.org/obo/CL_0000773 eosinophilic metamyelocyte http://purl.obolibrary.org/obo/CL_0002192 metamyelocyte http://purl.obolibrary.org/obo/CL_0000774 band form eosinophil http://purl.obolibrary.org/obo/CL_0000772 immature eosinophil http://purl.obolibrary.org/obo/CL_0000096 mature neutrophil http://purl.obolibrary.org/obo/CL_0000775 neutrophil http://purl.obolibrary.org/obo/CL_0000776 immature neutrophil http://purl.obolibrary.org/obo/CL_0000775 neutrophil http://purl.obolibrary.org/obo/CL_0000560 band form neutrophil http://purl.obolibrary.org/obo/CL_0000776 immature neutrophil http://purl.obolibrary.org/obo/CL_0000580 neutrophilic myelocyte http://purl.obolibrary.org/obo/CL_0002193 myelocyte http://purl.obolibrary.org/obo/CL_0000582 neutrophilic metamyelocyte http://purl.obolibrary.org/obo/CL_0002192 metamyelocyte http://purl.obolibrary.org/obo/CL_0002394 CD141-positive myeloid dendritic cell http://purl.obolibrary.org/obo/CL_0000782 myeloid dendritic cell http://purl.obolibrary.org/obo/CL_0002399 CD1c-positive myeloid dendritic cell http://purl.obolibrary.org/obo/CL_0000782 myeloid dendritic cell http://purl.obolibrary.org/obo/CL_0002532 CD16-positive myeloid dendritic cell http://purl.obolibrary.org/obo/CL_0000782 myeloid dendritic cell http://purl.obolibrary.org/obo/CL_0000942 thymic plasmacytoid dendritic cell http://purl.obolibrary.org/obo/CL_0000784 plasmacytoid dendritic cell http://purl.obolibrary.org/obo/CL_0000989 CD11c-low plasmacytoid dendritic cell http://purl.obolibrary.org/obo/CL_0000784 plasmacytoid dendritic cell http://purl.obolibrary.org/obo/CL_0000991 CD11c-negative plasmacytoid dendritic cell http://purl.obolibrary.org/obo/CL_0000784 plasmacytoid dendritic cell http://purl.obolibrary.org/obo/CL_0000787 memory B cell http://purl.obolibrary.org/obo/CL_0000785 mature B cell http://purl.obolibrary.org/obo/CL_0000788 naive B cell http://purl.obolibrary.org/obo/CL_0000785 mature B cell http://purl.obolibrary.org/obo/CL_0000819 B-1 B cell http://purl.obolibrary.org/obo/CL_0000785 mature B cell http://purl.obolibrary.org/obo/CL_0000843 follicular B cell http://purl.obolibrary.org/obo/CL_0000785 mature B cell http://purl.obolibrary.org/obo/CL_0000844 germinal center B cell http://purl.obolibrary.org/obo/CL_0000785 mature B cell http://purl.obolibrary.org/obo/CL_0000845 marginal zone B cell http://purl.obolibrary.org/obo/CL_0000785 mature B cell http://purl.obolibrary.org/obo/CL_0000968 Be cell http://purl.obolibrary.org/obo/CL_0000785 mature B cell http://purl.obolibrary.org/obo/CL_0000969 regulatory B cell http://purl.obolibrary.org/obo/CL_0000785 mature B cell http://purl.obolibrary.org/obo/CL_0000980 plasmablast http://purl.obolibrary.org/obo/CL_0000785 mature B cell http://purl.obolibrary.org/obo/CL_0002056 Fraction F mature B cell http://purl.obolibrary.org/obo/CL_0000785 mature B cell http://purl.obolibrary.org/obo/CL_0002402 Peyer's patch B cell http://purl.obolibrary.org/obo/CL_0000785 mature B cell http://purl.obolibrary.org/obo/CL_0000974 long lived plasma cell http://purl.obolibrary.org/obo/CL_0000786 plasma cell http://purl.obolibrary.org/obo/CL_0000975 short lived plasma cell http://purl.obolibrary.org/obo/CL_0000786 plasma cell http://purl.obolibrary.org/obo/CL_0000967 Bm5 B cell http://purl.obolibrary.org/obo/CL_0000787 memory B cell http://purl.obolibrary.org/obo/CL_0000970 unswitched memory B cell http://purl.obolibrary.org/obo/CL_0000787 memory B cell http://purl.obolibrary.org/obo/CL_0000972 class switched memory B cell http://purl.obolibrary.org/obo/CL_0000787 memory B cell http://purl.obolibrary.org/obo/CL_0000981 double negative memory B cell http://purl.obolibrary.org/obo/CL_0000787 memory B cell http://purl.obolibrary.org/obo/CL_0002101 CD38-positive naive B cell http://purl.obolibrary.org/obo/CL_0000788 naive B cell http://purl.obolibrary.org/obo/CL_0002102 CD38-negative naive B cell http://purl.obolibrary.org/obo/CL_0000788 naive B cell http://purl.obolibrary.org/obo/CL_0000820 B-1a B cell http://purl.obolibrary.org/obo/CL_0000819 B-1 B cell http://purl.obolibrary.org/obo/CL_0000821 B-1b B cell http://purl.obolibrary.org/obo/CL_0000819 B-1 B cell http://purl.obolibrary.org/obo/CL_0002029 Fc-epsilon RIalpha-low mast cell progenitor http://purl.obolibrary.org/obo/CL_0000831 mast cell progenitor http://purl.obolibrary.org/obo/CL_0000042 neutrophilic myeloblast http://purl.obolibrary.org/obo/CL_0000835 myeloblast http://purl.obolibrary.org/obo/CL_0000829 basophilic myeloblast http://purl.obolibrary.org/obo/CL_0000835 myeloblast http://purl.obolibrary.org/obo/CL_0000832 eosinophilic myeloblast http://purl.obolibrary.org/obo/CL_0000835 myeloblast http://purl.obolibrary.org/obo/CL_0000564 neutrophilic promyelocyte http://purl.obolibrary.org/obo/CL_0000836 promyelocyte http://purl.obolibrary.org/obo/CL_0000830 basophilic promyelocyte http://purl.obolibrary.org/obo/CL_0000836 promyelocyte http://purl.obolibrary.org/obo/CL_0000833 eosinophilic promyelocyte http://purl.obolibrary.org/obo/CL_0000836 promyelocyte http://purl.obolibrary.org/obo/CL_0002151 late promyelocyte http://purl.obolibrary.org/obo/CL_0000836 promyelocyte http://purl.obolibrary.org/obo/CL_0002154 early promyelocyte http://purl.obolibrary.org/obo/CL_0000836 promyelocyte http://purl.obolibrary.org/obo/CL_0000936 early lymphoid progenitor http://purl.obolibrary.org/obo/CL_0000837 hematopoietic multipotent progenitor cell http://purl.obolibrary.org/obo/CL_0002035 Slamf1-negative multipotent progenitor cell http://purl.obolibrary.org/obo/CL_0000837 hematopoietic multipotent progenitor cell http://purl.obolibrary.org/obo/CL_0002036 Slamf1-positive multipotent progenitor cell http://purl.obolibrary.org/obo/CL_0000837 hematopoietic multipotent progenitor cell http://purl.obolibrary.org/obo/CL_0002043 CD34-positive, CD38-negative multipotent progenitor cell http://purl.obolibrary.org/obo/CL_0000837 hematopoietic multipotent progenitor cell http://purl.obolibrary.org/obo/CL_0000828 thromboblast http://purl.obolibrary.org/obo/CL_0000839 myeloid lineage restricted progenitor cell http://purl.obolibrary.org/obo/CL_0000831 mast cell progenitor http://purl.obolibrary.org/obo/CL_0000839 myeloid lineage restricted progenitor cell http://purl.obolibrary.org/obo/CL_0002028 basophil mast progenitor cell http://purl.obolibrary.org/obo/CL_0000839 myeloid lineage restricted progenitor cell http://purl.obolibrary.org/obo/CL_0002191 granulocytopoietic cell http://purl.obolibrary.org/obo/CL_0000839 myeloid lineage restricted progenitor cell http://purl.obolibrary.org/obo/CL_0002194 monopoietic cell http://purl.obolibrary.org/obo/CL_0000839 myeloid lineage restricted progenitor cell http://purl.obolibrary.org/obo/CL_0000961 Bm1 B cell http://purl.obolibrary.org/obo/CL_0000843 follicular B cell http://purl.obolibrary.org/obo/CL_0000962 Bm2 B cell http://purl.obolibrary.org/obo/CL_0000843 follicular B cell http://purl.obolibrary.org/obo/CL_0000963 Bm3-delta B cell http://purl.obolibrary.org/obo/CL_0000844 germinal center B cell http://purl.obolibrary.org/obo/CL_0000964 Bm2' B cell http://purl.obolibrary.org/obo/CL_0000844 germinal center B cell http://purl.obolibrary.org/obo/CL_0000965 Bm3 B cell http://purl.obolibrary.org/obo/CL_0000844 germinal center B cell http://purl.obolibrary.org/obo/CL_0000966 Bm4 B cell http://purl.obolibrary.org/obo/CL_0000844 germinal center B cell http://purl.obolibrary.org/obo/CL_0002057 CD14-positive, CD16-negative classical monocyte http://purl.obolibrary.org/obo/CL_0000860 classical monocyte http://purl.obolibrary.org/obo/CL_0002395 Gr1-high classical monocyte http://purl.obolibrary.org/obo/CL_0000860 classical monocyte http://purl.obolibrary.org/obo/CL_0000862 suppressor macrophage http://purl.obolibrary.org/obo/CL_0000861 elicited macrophage http://purl.obolibrary.org/obo/CL_0000863 inflammatory macrophage http://purl.obolibrary.org/obo/CL_0000861 elicited macrophage http://purl.obolibrary.org/obo/CL_0000890 alternatively activated macrophage http://purl.obolibrary.org/obo/CL_0000861 elicited macrophage http://purl.obolibrary.org/obo/CL_0000091 Kupffer cell http://purl.obolibrary.org/obo/CL_0000864 tissue-resident macrophage http://purl.obolibrary.org/obo/CL_0000581 peritoneal macrophage http://purl.obolibrary.org/obo/CL_0000864 tissue-resident macrophage http://purl.obolibrary.org/obo/CL_0000583 alveolar macrophage http://purl.obolibrary.org/obo/CL_0000864 tissue-resident macrophage http://purl.obolibrary.org/obo/CL_0000866 thymic macrophage http://purl.obolibrary.org/obo/CL_0000864 tissue-resident macrophage http://purl.obolibrary.org/obo/CL_0000867 secondary lymphoid organ macrophage http://purl.obolibrary.org/obo/CL_0000864 tissue-resident macrophage http://purl.obolibrary.org/obo/CL_0000878 central nervous system macrophage http://purl.obolibrary.org/obo/CL_0000864 tissue-resident macrophage http://purl.obolibrary.org/obo/CL_0002060 melanophage http://purl.obolibrary.org/obo/CL_0000864 tissue-resident macrophage http://purl.obolibrary.org/obo/CL_0002247 pleural macrophage http://purl.obolibrary.org/obo/CL_0000864 tissue-resident macrophage http://purl.obolibrary.org/obo/CL_0002476 bone marrow macrophage http://purl.obolibrary.org/obo/CL_0000864 tissue-resident macrophage http://purl.obolibrary.org/obo/CL_0002477 adipose macrophage http://purl.obolibrary.org/obo/CL_0000864 tissue-resident macrophage http://purl.obolibrary.org/obo/CL_0000882 thymic medullary macrophage http://purl.obolibrary.org/obo/CL_0000866 thymic macrophage http://purl.obolibrary.org/obo/CL_0000883 thymic cortical macrophage http://purl.obolibrary.org/obo/CL_0000866 thymic macrophage http://purl.obolibrary.org/obo/CL_0000868 lymph node macrophage http://purl.obolibrary.org/obo/CL_0000867 secondary lymphoid organ macrophage http://purl.obolibrary.org/obo/CL_0000871 splenic macrophage http://purl.obolibrary.org/obo/CL_0000867 secondary lymphoid organ macrophage http://purl.obolibrary.org/obo/CL_0000884 mucosa-associated lymphoid tissue macrophage http://purl.obolibrary.org/obo/CL_0000867 secondary lymphoid organ macrophage http://purl.obolibrary.org/obo/CL_0000887 lymph node subcapsular sinus macrophage http://purl.obolibrary.org/obo/CL_0000868 lymph node macrophage http://purl.obolibrary.org/obo/CL_0000888 lymph node tingible body macrophage http://purl.obolibrary.org/obo/CL_0000868 lymph node macrophage http://purl.obolibrary.org/obo/CL_0000872 splenic marginal zone macrophage http://purl.obolibrary.org/obo/CL_0000871 splenic macrophage http://purl.obolibrary.org/obo/CL_0000873 splenic metallophillic macrophage http://purl.obolibrary.org/obo/CL_0000871 splenic macrophage http://purl.obolibrary.org/obo/CL_0000874 splenic red pulp macrophage http://purl.obolibrary.org/obo/CL_0000871 splenic macrophage http://purl.obolibrary.org/obo/CL_0000876 splenic white pulp macrophage http://purl.obolibrary.org/obo/CL_0000871 splenic macrophage http://purl.obolibrary.org/obo/CL_0002058 Gr1-low non-classical monocyte http://purl.obolibrary.org/obo/CL_0000875 non-classical monocyte http://purl.obolibrary.org/obo/CL_0002396 CD14-low, CD16-positive monocyte http://purl.obolibrary.org/obo/CL_0000875 non-classical monocyte http://purl.obolibrary.org/obo/CL_0000879 meningeal macrophage http://purl.obolibrary.org/obo/CL_0000878 central nervous system macrophage http://purl.obolibrary.org/obo/CL_0000880 choroid-plexus macrophage http://purl.obolibrary.org/obo/CL_0000878 central nervous system macrophage http://purl.obolibrary.org/obo/CL_0000881 perivascular macrophage http://purl.obolibrary.org/obo/CL_0000878 central nervous system macrophage http://purl.obolibrary.org/obo/CL_0000869 tonsillar macrophage http://purl.obolibrary.org/obo/CL_0000884 mucosa-associated lymphoid tissue macrophage http://purl.obolibrary.org/obo/CL_0000885 gut-associated lymphoid tissue macrophage http://purl.obolibrary.org/obo/CL_0000884 mucosa-associated lymphoid tissue macrophage http://purl.obolibrary.org/obo/CL_0000886 nasal and broncial associated lymphoid tissue macrophage http://purl.obolibrary.org/obo/CL_0000884 mucosa-associated lymphoid tissue macrophage http://purl.obolibrary.org/obo/CL_0000865 gastrointestinal tract (lamina propria) macrophage http://purl.obolibrary.org/obo/CL_0000885 gut-associated lymphoid tissue macrophage http://purl.obolibrary.org/obo/CL_0000870 Peyer's patch macrophage http://purl.obolibrary.org/obo/CL_0000885 gut-associated lymphoid tissue macrophage http://purl.obolibrary.org/obo/CL_0002467 Gr1-high myeloid suppressor cell http://purl.obolibrary.org/obo/CL_0000889 myeloid suppressor cell http://purl.obolibrary.org/obo/CL_0002468 Gr1-low myeloid suppressor cell http://purl.obolibrary.org/obo/CL_0000889 myeloid suppressor cell http://purl.obolibrary.org/obo/CL_0000943 Be1 Cell http://purl.obolibrary.org/obo/CL_0000968 Be cell http://purl.obolibrary.org/obo/CL_0000944 Be2 cell http://purl.obolibrary.org/obo/CL_0000968 Be cell http://purl.obolibrary.org/obo/CL_0000971 IgM memory B cell http://purl.obolibrary.org/obo/CL_0000970 unswitched memory B cell http://purl.obolibrary.org/obo/CL_0002111 CD38-negative unswitched memory B cell http://purl.obolibrary.org/obo/CL_0000970 unswitched memory B cell http://purl.obolibrary.org/obo/CL_0002114 CD38-positive unswitched memory B cell http://purl.obolibrary.org/obo/CL_0000970 unswitched memory B cell http://purl.obolibrary.org/obo/CL_0000948 IgE memory B cell http://purl.obolibrary.org/obo/CL_0000972 class switched memory B cell http://purl.obolibrary.org/obo/CL_0000973 IgA memory B cell http://purl.obolibrary.org/obo/CL_0000972 class switched memory B cell http://purl.obolibrary.org/obo/CL_0000979 IgG memory B cell http://purl.obolibrary.org/obo/CL_0000972 class switched memory B cell http://purl.obolibrary.org/obo/CL_0002117 IgG-negative class switched memory B cell http://purl.obolibrary.org/obo/CL_0000972 class switched memory B cell http://purl.obolibrary.org/obo/CL_0000947 IgE plasma cell http://purl.obolibrary.org/obo/CL_0000974 long lived plasma cell http://purl.obolibrary.org/obo/CL_0000985 IgG plasma cell http://purl.obolibrary.org/obo/CL_0000974 long lived plasma cell http://purl.obolibrary.org/obo/CL_0000986 IgM plasma cell http://purl.obolibrary.org/obo/CL_0000974 long lived plasma cell http://purl.obolibrary.org/obo/CL_0000987 IgA plasma cell http://purl.obolibrary.org/obo/CL_0000974 long lived plasma cell http://purl.obolibrary.org/obo/CL_0000951 IgE short lived plasma cell http://purl.obolibrary.org/obo/CL_0000975 short lived plasma cell http://purl.obolibrary.org/obo/CL_0000976 IgA short lived plasma cell http://purl.obolibrary.org/obo/CL_0000975 short lived plasma cell http://purl.obolibrary.org/obo/CL_0000977 IgG short lived plasma cell http://purl.obolibrary.org/obo/CL_0000975 short lived plasma cell http://purl.obolibrary.org/obo/CL_0000978 IgM short lived plasma cell http://purl.obolibrary.org/obo/CL_0000975 short lived plasma cell http://purl.obolibrary.org/obo/CL_0002105 CD38-positive IgG memory B cell http://purl.obolibrary.org/obo/CL_0000979 IgG memory B cell http://purl.obolibrary.org/obo/CL_0002108 CD38-negative IgG memory B cell http://purl.obolibrary.org/obo/CL_0000979 IgG memory B cell http://purl.obolibrary.org/obo/CL_0000949 IgD plasmablast http://purl.obolibrary.org/obo/CL_0000980 plasmablast http://purl.obolibrary.org/obo/CL_0000950 IgE plasmablast http://purl.obolibrary.org/obo/CL_0000980 plasmablast http://purl.obolibrary.org/obo/CL_0000982 IgG plasmablast http://purl.obolibrary.org/obo/CL_0000980 plasmablast http://purl.obolibrary.org/obo/CL_0000983 IgM plasmablast http://purl.obolibrary.org/obo/CL_0000980 plasmablast http://purl.obolibrary.org/obo/CL_0000984 IgA plasmablast http://purl.obolibrary.org/obo/CL_0000980 plasmablast http://purl.obolibrary.org/obo/CL_0002103 IgG-positive double negative memory B cell http://purl.obolibrary.org/obo/CL_0000981 double negative memory B cell http://purl.obolibrary.org/obo/CL_0002104 IgG-negative double negative memory B cell http://purl.obolibrary.org/obo/CL_0000981 double negative memory B cell http://purl.obolibrary.org/obo/CL_0000992 immature CD11c-low plasmacytoid dendritic cell http://purl.obolibrary.org/obo/CL_0000989 CD11c-low plasmacytoid dendritic cell http://purl.obolibrary.org/obo/CL_0000993 mature CD11c-low plasmacytoid dendritic cell http://purl.obolibrary.org/obo/CL_0000989 CD11c-low plasmacytoid dendritic cell http://purl.obolibrary.org/obo/CL_0002455 CD8_alpha-negative plasmactyoid dendritic cell http://purl.obolibrary.org/obo/CL_0000989 CD11c-low plasmacytoid dendritic cell http://purl.obolibrary.org/obo/CL_0002456 CD8_alpha-positive plasmactyoid dendritic cell http://purl.obolibrary.org/obo/CL_0000989 CD11c-low plasmacytoid dendritic cell http://purl.obolibrary.org/obo/CL_0000941 thymic conventional dendritic cell http://purl.obolibrary.org/obo/CL_0000990 conventional dendritic cell http://purl.obolibrary.org/obo/CL_0000453 Langerhans cell http://purl.obolibrary.org/obo/CL_0000990 conventional dendritic cell http://purl.obolibrary.org/obo/CL_0000782 myeloid dendritic cell http://purl.obolibrary.org/obo/CL_0000990 conventional dendritic cell http://purl.obolibrary.org/obo/CL_0000840 immature conventional dendritic cell http://purl.obolibrary.org/obo/CL_0000990 conventional dendritic cell http://purl.obolibrary.org/obo/CL_0000841 mature conventional dendritic cell http://purl.obolibrary.org/obo/CL_0000990 conventional dendritic cell http://purl.obolibrary.org/obo/CL_0000998 CD8_alpha-negative CD11b-negative dendritic cell http://purl.obolibrary.org/obo/CL_0000990 conventional dendritic cell http://purl.obolibrary.org/obo/CL_0001000 CD8_alpha-positive CD11b-negative dendritic cell http://purl.obolibrary.org/obo/CL_0000990 conventional dendritic cell http://purl.obolibrary.org/obo/CL_0001006 dermal dendritic cell http://purl.obolibrary.org/obo/CL_0000990 conventional dendritic cell http://purl.obolibrary.org/obo/CL_0001007 interstitial dendritic cell http://purl.obolibrary.org/obo/CL_0000990 conventional dendritic cell http://purl.obolibrary.org/obo/CL_0002461 CD103-positive dendritic cell http://purl.obolibrary.org/obo/CL_0000990 conventional dendritic cell http://purl.obolibrary.org/obo/CL_0002462 adipose dendritic cell http://purl.obolibrary.org/obo/CL_0000990 conventional dendritic cell http://purl.obolibrary.org/obo/CL_0002465 CD11b-positive dendritic cell http://purl.obolibrary.org/obo/CL_0000990 conventional dendritic cell http://purl.obolibrary.org/obo/CL_0002507 langerin-positive lymph node dendritic cell http://purl.obolibrary.org/obo/CL_0000990 conventional dendritic cell http://purl.obolibrary.org/obo/CL_0002508 langerin-negative, CD103-negative lymph node dendritic cell http://purl.obolibrary.org/obo/CL_0000990 conventional dendritic cell http://purl.obolibrary.org/obo/CL_0000994 immature CD11c-negative plasmacytoid dendritic cell http://purl.obolibrary.org/obo/CL_0000991 CD11c-negative plasmacytoid dendritic cell http://purl.obolibrary.org/obo/CL_0000996 mature CD11c-negative plasmacytoid dendritic cell http://purl.obolibrary.org/obo/CL_0000991 CD11c-negative plasmacytoid dendritic cell http://purl.obolibrary.org/obo/CL_0001001 immature CD8_alpha-negative CD11b-negative dendritic cell http://purl.obolibrary.org/obo/CL_0000998 CD8_alpha-negative CD11b-negative dendritic cell http://purl.obolibrary.org/obo/CL_0001002 mature CD8_alpha-negative CD11b-negative dendritic cell http://purl.obolibrary.org/obo/CL_0000998 CD8_alpha-negative CD11b-negative dendritic cell http://purl.obolibrary.org/obo/CL_0001004 immature CD8_alpha-positive CD11b-negative dendritic cell http://purl.obolibrary.org/obo/CL_0001000 CD8_alpha-positive CD11b-negative dendritic cell http://purl.obolibrary.org/obo/CL_0001005 mature CD8_alpha-positive CD11b-negative dendritic cell http://purl.obolibrary.org/obo/CL_0001000 CD8_alpha-positive CD11b-negative dendritic cell http://purl.obolibrary.org/obo/CL_0001009 immature dermal dendritic cell http://purl.obolibrary.org/obo/CL_0001006 dermal dendritic cell http://purl.obolibrary.org/obo/CL_0001010 mature dermal dendritic cell http://purl.obolibrary.org/obo/CL_0001006 dermal dendritic cell http://purl.obolibrary.org/obo/CL_0002458 langerin-positive dermal dendritic cell http://purl.obolibrary.org/obo/CL_0001006 dermal dendritic cell http://purl.obolibrary.org/obo/CL_0002459 langerin-negative dermal dendritic cell http://purl.obolibrary.org/obo/CL_0001006 dermal dendritic cell http://purl.obolibrary.org/obo/CL_0002526 CD14-positive dermal dendritic cell http://purl.obolibrary.org/obo/CL_0001006 dermal dendritic cell http://purl.obolibrary.org/obo/CL_0002529 CD1a-positive dermal dendritic cell http://purl.obolibrary.org/obo/CL_0001006 dermal dendritic cell http://purl.obolibrary.org/obo/CL_0001011 immature interstitial dendritic cell http://purl.obolibrary.org/obo/CL_0001007 interstitial dendritic cell http://purl.obolibrary.org/obo/CL_0001013 mature interstitial dendritic cell http://purl.obolibrary.org/obo/CL_0001007 interstitial dendritic cell http://purl.obolibrary.org/obo/CL_0002044 Kit-positive, integrin beta7-high basophil mast progenitor cell http://purl.obolibrary.org/obo/CL_0002028 basophil mast progenitor cell http://purl.obolibrary.org/obo/CL_0000838 lymphoid lineage restricted progenitor cell http://purl.obolibrary.org/obo/CL_0002031 hematopoietic lineage restricted progenitor cell http://purl.obolibrary.org/obo/CL_0001019 CD115-positive monocyte OR common dendritic progenitor http://purl.obolibrary.org/obo/CL_0002031 hematopoietic lineage restricted progenitor cell http://purl.obolibrary.org/obo/CL_0001029 common dendritic progenitor http://purl.obolibrary.org/obo/CL_0002031 hematopoietic lineage restricted progenitor cell http://purl.obolibrary.org/obo/CL_0002010 pre-conventional dendritic cell http://purl.obolibrary.org/obo/CL_0002031 hematopoietic lineage restricted progenitor cell http://purl.obolibrary.org/obo/CL_0000049 common myeloid progenitor http://purl.obolibrary.org/obo/CL_0002032 hematopoietic oligopotent progenitor cell http://purl.obolibrary.org/obo/CL_0000050 megakaryocyte-erythroid progenitor cell http://purl.obolibrary.org/obo/CL_0002032 hematopoietic oligopotent progenitor cell http://purl.obolibrary.org/obo/CL_0000051 common lymphoid progenitor http://purl.obolibrary.org/obo/CL_0002032 hematopoietic oligopotent progenitor cell http://purl.obolibrary.org/obo/CL_0000995 CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor http://purl.obolibrary.org/obo/CL_0002032 hematopoietic oligopotent progenitor cell http://purl.obolibrary.org/obo/CL_0001012 CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor http://purl.obolibrary.org/obo/CL_0002032 hematopoietic oligopotent progenitor cell http://purl.obolibrary.org/obo/CL_0001030 CD117-positive common myeloid progenitor OR CD217-positive common lymphoid progenitor http://purl.obolibrary.org/obo/CL_0002032 hematopoietic oligopotent progenitor cell http://purl.obolibrary.org/obo/CL_0002009 macrophage dendritic cell progenitor http://purl.obolibrary.org/obo/CL_0002032 hematopoietic oligopotent progenitor cell http://purl.obolibrary.org/obo/CL_0002471 MHC-II-negative non-classical monocyte http://purl.obolibrary.org/obo/CL_0002058 Gr1-low non-classical monocyte http://purl.obolibrary.org/obo/CL_0002472 MHC-II-low non-classical monocyte http://purl.obolibrary.org/obo/CL_0002058 Gr1-low non-classical monocyte http://purl.obolibrary.org/obo/CL_0002473 MHC-II-high non-classical monocyte http://purl.obolibrary.org/obo/CL_0002058 Gr1-low non-classical monocyte http://purl.obolibrary.org/obo/CL_0002109 B220-positive CD38-positive naive B cell http://purl.obolibrary.org/obo/CL_0002101 CD38-positive naive B cell http://purl.obolibrary.org/obo/CL_0002110 B220-low CD38-positive naive B cell http://purl.obolibrary.org/obo/CL_0002101 CD38-positive naive B cell http://purl.obolibrary.org/obo/CL_0002106 IgD-positive CD38-positive IgG memory B cell http://purl.obolibrary.org/obo/CL_0002105 CD38-positive IgG memory B cell http://purl.obolibrary.org/obo/CL_0002107 IgD-negative CD38-positive IgG memory B cell http://purl.obolibrary.org/obo/CL_0002105 CD38-positive IgG memory B cell http://purl.obolibrary.org/obo/CL_0002112 B220-positive CD38-negative unswitched memory B cell http://purl.obolibrary.org/obo/CL_0002111 CD38-negative unswitched memory B cell http://purl.obolibrary.org/obo/CL_0002113 B220-low CD38-negative unswitched memory B cell http://purl.obolibrary.org/obo/CL_0002111 CD38-negative unswitched memory B cell http://purl.obolibrary.org/obo/CL_0002115 B220-positive CD38-positive unswitched memory B cell http://purl.obolibrary.org/obo/CL_0002114 CD38-positive unswitched memory B cell http://purl.obolibrary.org/obo/CL_0002116 B220-low CD38-positive unswitched memory B cell http://purl.obolibrary.org/obo/CL_0002114 CD38-positive unswitched memory B cell http://purl.obolibrary.org/obo/CL_0002118 CD38-negative IgG-negative class switched memory B cell http://purl.obolibrary.org/obo/CL_0002117 IgG-negative class switched memory B cell http://purl.obolibrary.org/obo/CL_0002119 CD38-positive IgG-negative class switched memory B cell http://purl.obolibrary.org/obo/CL_0002117 IgG-negative class switched memory B cell http://purl.obolibrary.org/obo/CL_0002120 CD24-positive CD38-negative IgG-negative class switched memory B cell http://purl.obolibrary.org/obo/CL_0002118 CD38-negative IgG-negative class switched memory B cell http://purl.obolibrary.org/obo/CL_0002121 CD24-negative CD38-negative IgG-negative class switched memory B cell http://purl.obolibrary.org/obo/CL_0002118 CD38-negative IgG-negative class switched memory B cell http://purl.obolibrary.org/obo/CL_0002122 B220-positive CD38-positive IgG-negative class switched memory B cell http://purl.obolibrary.org/obo/CL_0002119 CD38-positive IgG-negative class switched memory B cell http://purl.obolibrary.org/obo/CL_0002123 B220-low CD38-positive IgG-negative class switched memory B cell http://purl.obolibrary.org/obo/CL_0002119 CD38-positive IgG-negative class switched memory B cell http://purl.obolibrary.org/obo/CL_0000611 eosinophil progenitor cell http://purl.obolibrary.org/obo/CL_0002191 granulocytopoietic cell http://purl.obolibrary.org/obo/CL_0000613 basophil progenitor cell http://purl.obolibrary.org/obo/CL_0002191 granulocytopoietic cell http://purl.obolibrary.org/obo/CL_0000834 neutrophil progenitor cell http://purl.obolibrary.org/obo/CL_0002191 granulocytopoietic cell http://purl.obolibrary.org/obo/CL_0000835 myeloblast http://purl.obolibrary.org/obo/CL_0002191 granulocytopoietic cell http://purl.obolibrary.org/obo/CL_0000836 promyelocyte http://purl.obolibrary.org/obo/CL_0002191 granulocytopoietic cell http://purl.obolibrary.org/obo/CL_0002192 metamyelocyte http://purl.obolibrary.org/obo/CL_0002191 granulocytopoietic cell http://purl.obolibrary.org/obo/CL_0000040 monoblast http://purl.obolibrary.org/obo/CL_0002194 monopoietic cell http://purl.obolibrary.org/obo/CL_0000559 promonocyte http://purl.obolibrary.org/obo/CL_0002194 monopoietic cell http://purl.obolibrary.org/obo/CL_0002397 CD14-positive, CD16-positive monocyte http://purl.obolibrary.org/obo/CL_0002393 intermediate monocyte http://purl.obolibrary.org/obo/CL_0002398 Gr1-positive, CD43-positive monocyte http://purl.obolibrary.org/obo/CL_0002393 intermediate monocyte http://purl.obolibrary.org/obo/CL_0002469 MHC-II-negative classical monocyte http://purl.obolibrary.org/obo/CL_0002395 Gr1-high classical monocyte http://purl.obolibrary.org/obo/CL_0002470 MHC-II-positive classical monocyte http://purl.obolibrary.org/obo/CL_0002395 Gr1-high classical monocyte http://purl.obolibrary.org/obo/CL_0002355 primitive red blood cell http://purl.obolibrary.org/obo/CL_0002417 primitive erythroid lineage cell http://purl.obolibrary.org/obo/CL_0002356 primitive reticulocyte http://purl.obolibrary.org/obo/CL_0002417 primitive erythroid lineage cell http://purl.obolibrary.org/obo/CL_0002358 pyrenocyte http://purl.obolibrary.org/obo/CL_0002417 primitive erythroid lineage cell http://purl.obolibrary.org/obo/CL_0002361 primitive erythroid progenitor http://purl.obolibrary.org/obo/CL_0002417 primitive erythroid lineage cell http://purl.obolibrary.org/obo/CL_0002019 Ly-76 high reticulocyte http://purl.obolibrary.org/obo/CL_0002422 enucleated reticulocyte http://purl.obolibrary.org/obo/CL_0002020 GlyA-positive reticulocytes http://purl.obolibrary.org/obo/CL_0002422 enucleated reticulocyte http://purl.obolibrary.org/obo/CL_0000999 CD4-positive CD11b-positive dendritic cell http://purl.obolibrary.org/obo/CL_0002465 CD11b-positive dendritic cell http://purl.obolibrary.org/obo/CL_0002454 Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell http://purl.obolibrary.org/obo/CL_0002465 CD11b-positive dendritic cell http://purl.obolibrary.org/obo/CL_0002466 small intestine serosal dendritic cell http://purl.obolibrary.org/obo/CL_0002465 CD11b-positive dendritic cell http://purl.obolibrary.org/obo/CL_0002474 lymphoid MHC-II-negative classical monocyte http://purl.obolibrary.org/obo/CL_0002469 MHC-II-negative classical monocyte http://purl.obolibrary.org/obo/CL_0002475 lymphoid MHC-II-negative non-classical monocyte http://purl.obolibrary.org/obo/CL_0002471 MHC-II-negative non-classical monocyte http://purl.obolibrary.org/obo/CL_0002478 F4/80-negative adipose macrophage http://purl.obolibrary.org/obo/CL_0002477 adipose macrophage http://purl.obolibrary.org/obo/CL_0002479 F4/80-positive adipose macrophage http://purl.obolibrary.org/obo/CL_0002477 adipose macrophage http://purl.obolibrary.org/obo/CL_0002509 CD103-positive, langerin-positive lymph node dendritic cell http://purl.obolibrary.org/obo/CL_0002507 langerin-positive lymph node dendritic cell http://purl.obolibrary.org/obo/CL_0002510 CD103-negative, langerin-positive lymph node dendritic cell http://purl.obolibrary.org/obo/CL_0002507 langerin-positive lymph node dendritic cell http://purl.obolibrary.org/obo/CL_0002511 CD11b-low, CD103-negative, langerin-negative lymph node dendritic cell http://purl.obolibrary.org/obo/CL_0002508 langerin-negative, CD103-negative lymph node dendritic cell http://purl.obolibrary.org/obo/CL_0002512 CD11b-high, CD103-negative, langerin-negative lymph node dendritic cell http://purl.obolibrary.org/obo/CL_0002508 langerin-negative, CD103-negative lymph node dendritic cell 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_314146 Euarchontoglires http://purl.obolibrary.org/obo/NCBITaxon_40674 Mammalia http://semanticscience.org/resource/SIO_000119 brand name http://semanticscience.org/resource/SIO_000116 name http://semanticscience.org/resource/SIO_000120 scientific name http://semanticscience.org/resource/SIO_000116 name http://semanticscience.org/resource/SIO_000181 first name http://semanticscience.org/resource/SIO_000116 name http://semanticscience.org/resource/SIO_000182 last name http://semanticscience.org/resource/SIO_000116 name http://semanticscience.org/resource/SIO_000183 personal name http://semanticscience.org/resource/SIO_000116 name http://semanticscience.org/resource/SIO_000785 answer http://semanticscience.org/resource/SIO_000136 description http://semanticscience.org/resource/SIO_001166 annotation http://semanticscience.org/resource/SIO_000136 description http://semanticscience.org/resource/SIO_001196 history http://semanticscience.org/resource/SIO_000136 description http://www.ebi.ac.uk/efo/EFO_0005293 B-lymphoblast http://www.ebi.ac.uk/efo/EFO_0000572 lymphoblast http://semanticscience.org/resource/SIO_000184 legal name http://semanticscience.org/resource/SIO_000183 personal name http://semanticscience.org/resource/SIO_000653 version label http://semanticscience.org/resource/SIO_000115 identifier http://semanticscience.org/resource/SIO_000675 unique identifier http://semanticscience.org/resource/SIO_000115 identifier http://purl.obolibrary.org/obo/BFO_0000001 entity http://purl.obolibrary.org/obo/RO_0002234 has output http://purl.obolibrary.org/obo/RO_0000057 has_participant produces p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. 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 is 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 is 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_0001015 location of http://purl.obolibrary.org/obo/RO_0001025 located_in (type level) 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_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 is 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/BFO_0000062 preceded by http://purl.obolibrary.org/obo/RO_0002222 temporal relation preceded_by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. 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/RO_0002233 has input http://purl.obolibrary.org/obo/RO_0000057 has_participant consumes p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. http://purl.obolibrary.org/obo/RO_0004027 disease has inflammation site http://purl.obolibrary.org/obo/RO_0004026 disease has location A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity http://purl.obolibrary.org/obo/RO_0004028 realized in response to stimulus http://purl.obolibrary.org/obo/RO_0002410 causally related to A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. http://purl.obolibrary.org/obo/RO_0004029 disease has feature http://purl.obolibrary.org/obo/RO_0040035 disease relationship A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. http://purl.obolibrary.org/obo/RO_0004030 disease arises from structure http://purl.obolibrary.org/obo/RO_0004019 disease has basis in A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. http://purl.obolibrary.org/obo/BFO_0000184 history of http://purl.obolibrary.org/obo/BFO_0000066 occurs in [copied from inverse property 'has history'] b has_history c iff c history_of b [XXX-001 http://purl.obolibrary.org/obo/RO_0004020 disease has basis in dysfunction of http://purl.obolibrary.org/obo/RO_0004019 disease has basis in A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. http://purl.obolibrary.org/obo/RO_0004021 disease has basis in disruption of http://purl.obolibrary.org/obo/RO_0004019 disease has basis in A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. http://purl.obolibrary.org/obo/RO_0004022 disease has basis in feature http://purl.obolibrary.org/obo/RO_0004019 disease has basis in A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. http://purl.obolibrary.org/obo/RO_0004024 disease causes disruption of http://purl.obolibrary.org/obo/RO_0004023 causal relationship with disease as subject A relationship between a disease and a process where the disease process disrupts the execution of the process. http://purl.obolibrary.org/obo/BFO_0000063 followed by http://purl.obolibrary.org/obo/RO_0002222 temporal relation The assertion P 'followed by' P1 tells us something about Ps in general: that is, it tells us something about what happened later, given what we know about what happened earlier. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be preceded by some instance of P. Note that assertions using this property only are rather weak. Typically we will be interested in stronger relations, for example in the relation 'directly followed by'. 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 denotes is 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_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/NGBO_6000380 trace_from 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/NGBO_6000380 trace_from 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_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_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/RO_0002223 starts http://purl.obolibrary.org/obo/BFO_0000050 part of inverse of starts with http://purl.obolibrary.org/obo/OMIABIS_0000042 is contact information about http://purl.obolibrary.org/obo/IAO_0000136 is about a is contact information for b, if a is a information content entity, b is a human being or an organization and a identifies a physical location or electronic resource that allows to initiate communication with a. http://purl.obolibrary.org/obo/RO_0003302 causes or contributes to condition http://purl.obolibrary.org/obo/RO_0002410 causally related to A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition. http://purl.obolibrary.org/obo/RO_0002244 related via exposure to http://purl.obolibrary.org/obo/RO_0002410 causally related to Any relationship between an exposure event or process and any other entity. http://purl.obolibrary.org/obo/RO_0002245 over-expressed in http://purl.obolibrary.org/obo/RO_0002206 expressed in g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background. http://purl.obolibrary.org/obo/RO_0002246 under-expressed in http://purl.obolibrary.org/obo/RO_0002206 expressed in g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background. http://purl.obolibrary.org/obo/RO_0002302 is treated by substance http://purl.obolibrary.org/obo/RO_0002410 causally related to Inverse of 'is substance that treats' http://purl.obolibrary.org/obo/STATO_0000102 executes http://purl.obolibrary.org/obo/NGBO_6000380 trace_from relationship between a planned process and the plan specification that it carries out; it is defined as equivalent to the composed relationship (realizes o concretizes) http://www.ebi.ac.uk/swo/SWO_0000131 directly preceded by http://purl.obolibrary.org/obo/BFO_0000060 preceded by Entity A is 'directly preceded by' entity B if there are no intermediate entities temporally between the two entities. WIthin SWO this property is mainly used to describe versions of entities such as software. http://www.ebi.ac.uk/swo/SWO_0000132 directly followed by http://purl.obolibrary.org/obo/BFO_0000063 followed by 'directly followed by' is an object property which further specializes the parent 'followed by' property. In the assertion 'C directly followed by C1', says that Cs generally are immediately followed by C1s. http://purl.obolibrary.org/obo/RO_0003310 condition ameliorated by http://purl.obolibrary.org/obo/RO_0002410 causally related to A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity. http://purl.obolibrary.org/obo/RO_0003311 condition exacerbated by http://purl.obolibrary.org/obo/RO_0002410 causally related to A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity. http://purl.obolibrary.org/obo/RO_0002501 causal relation between processes http://purl.obolibrary.org/obo/RO_0002410 causally related to p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. http://purl.obolibrary.org/obo/RO_0002595 causal relation between material entity and a process http://purl.obolibrary.org/obo/RO_0002410 causally related to A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. http://purl.obolibrary.org/obo/RO_0002608 process has causal agent http://purl.obolibrary.org/obo/RO_0002410 causally related to Inverse of 'causal agent in process' http://purl.obolibrary.org/obo/RO_0002206 expressed in http://purl.obolibrary.org/obo/RO_0002330 genomically related to x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process http://purl.obolibrary.org/obo/RO_0002291 ubiquitously expressed in http://purl.obolibrary.org/obo/RO_0002206 expressed in x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x http://purl.obolibrary.org/obo/RO_0002292 expresses http://purl.obolibrary.org/obo/RO_0002330 genomically related to Inverse of 'expressed in' http://purl.obolibrary.org/obo/RO_0002293 ubiquitously expresses http://purl.obolibrary.org/obo/RO_0002292 expresses inverse of ubiquiotously expressed in http://purl.obolibrary.org/obo/RO_0009501 realized in response to http://purl.obolibrary.org/obo/RO_0002410 causally related to r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. http://purl.obolibrary.org/obo/RO_0004026 disease has location http://purl.obolibrary.org/obo/RO_0040035 disease relationship A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. http://purl.obolibrary.org/obo/RO_0002009 cell expresses http://purl.obolibrary.org/obo/RO_0002292 expresses A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g. http://purl.obolibrary.org/obo/RO_0002452 has symptom http://purl.obolibrary.org/obo/RO_0002200 has phenotype A relation that holds between a disease or an organism and a phenotype http://purl.obolibrary.org/obo/RO_0002607 is marker for http://purl.obolibrary.org/obo/RO_0002610 correlated with c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. http://purl.obolibrary.org/obo/OBI_0001950 has performer http://purl.obolibrary.org/obo/NGBO_6000380 trace_from http://semanticscience.org/resource/SIO_000673 has unique identifier http://semanticscience.org/resource/SIO_000671 has identifier http://semanticscience.org/resource/SIO_000674 is unique identifier for http://semanticscience.org/resource/SIO_000672 is identifier for 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/RO_0004019 disease has basis in http://purl.obolibrary.org/obo/RO_0004023 causal relationship with disease as subject http://purl.obolibrary.org/obo/RO_0004025 disease causes dysfunction of http://purl.obolibrary.org/obo/RO_0004023 causal relationship with disease as subject http://purl.obolibrary.org/obo/RO_0002506 causal relation between material entities http://purl.obolibrary.org/obo/RO_0002410 causally related to http://purl.obolibrary.org/obo/RO_0004000 condition has genetic basis in http://purl.obolibrary.org/obo/RO_0002410 causally related to http://purl.obolibrary.org/obo/RO_0004017 realizable has basis in http://purl.obolibrary.org/obo/RO_0002410 causally related to http://purl.obolibrary.org/obo/RO_0004018 is basis for realizable http://purl.obolibrary.org/obo/RO_0002410 causally related to http://purl.obolibrary.org/obo/RO_0004023 causal relationship with disease as subject http://purl.obolibrary.org/obo/RO_0040035 disease relationship http://semanticscience.org/resource/SIO_000255 has annotation http://semanticscience.org/resource/SIO_000008 has attribute http://semanticscience.org/resource/SIO_000671 has identifier http://semanticscience.org/resource/SIO_000008 has attribute http://semanticscience.org/resource/SIO_000008 has attribute http://semanticscience.org/resource/SIO_000001 is related to http://semanticscience.org/resource/SIO_000011 is attribute of http://semanticscience.org/resource/SIO_000001 is related to http://semanticscience.org/resource/SIO_000254 is annotation of http://semanticscience.org/resource/SIO_000011 is attribute of http://semanticscience.org/resource/SIO_000672 is identifier for http://semanticscience.org/resource/SIO_000011 is attribute of 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/RO_0000052 inheres in 'inheres in at all times' 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 is 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_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_0001025 located_in (type level) 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/IAO_0000136 is about is_about is a (currently) primitive relation that relates an information artifact to an entity. 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_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_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_0001688 has organization member Relating an organization to a legal person or organization. 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/RO_0002351 has member has member is a mereological relation between a collection and an item. http://purl.obolibrary.org/obo/IAO_0020012 designates x designates y, if for any given group of language users, x is an information content entity, is about y, and represents y in a linguistic context.. http://purl.obolibrary.org/obo/IAO_0020018 is designated by p1 is designated by p2, if p2 is an information content entity that represents p1 in a linguistic context. http://purl.obolibrary.org/obo/OBIB_0000037 has maximum capacity A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. http://purl.obolibrary.org/obo/OBIB_0000038 has actual load A relation that relates a container to a measurement datum that specifies the actual amount of material in the container. http://purl.obolibrary.org/obo/OMIABIS_0000009 administrates a administrates b if c owns b and some rights and obligations grounded in the owning relation regarding b are transferred from c to a. http://purl.obolibrary.org/obo/OMIABIS_0000048 is owned by a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b. http://purl.obolibrary.org/obo/RO_0002200 has phenotype A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). http://www.ebi.ac.uk/swo/SWO_0004002 has format specification Has format specification is a type of "is encoded in" relationship which specifically describes the relationship between data and a data format specification. http://purl.obolibrary.org/obo/RO_0002180 has component 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/RO_0002353 output of inverse of has output http://purl.obolibrary.org/obo/NGBO_6000380 trace_from A relation that is used to follow traceability of specimen activity http://purl.obolibrary.org/obo/NGBO_6000381 track_to A relation that is used to track specimen activity http://purl.obolibrary.org/obo/NGBO_6000690 userEmailId A data property that set user email ID http://purl.obolibrary.org/obo/NGBO_6000691 userID A data property that set user ID http://purl.obolibrary.org/obo/NGBO_6000692 userPassword A data property that set user password http://purl.obolibrary.org/obo/NGBO_6000693 userName A data property that set user name http://purl.obolibrary.org/obo/RO_0002330 genomically related to holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. http://purl.obolibrary.org/obo/RO_0002410 causally related to This relation groups causal relations between material entities and causal relations between processes http://purl.obolibrary.org/obo/RO_0002201 phenotype of inverse of has phenotype http://purl.obolibrary.org/obo/RO_0002610 correlated with A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. http://purl.obolibrary.org/obo/RO_0010001 generically depends on A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*. http://purl.obolibrary.org/obo/RO_0010002 is carrier of *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t* http://purl.obolibrary.org/obo/RO_0040035 disease relationship This relation groups relations between diseases and any other kind of entity. http://purl.obolibrary.org/obo/BFO_0000054 realized in realized_in http://purl.obolibrary.org/obo/RO_0001018 contained in contained_in http://purl.obolibrary.org/obo/BFO_0000060 preceded by http://purl.obolibrary.org/obo/BFO_0000055 realizes http://purl.obolibrary.org/obo/GEO_000000012 member of http://purl.obolibrary.org/obo/OMIABIS_0000008 owns http://purl.obolibrary.org/obo/BFO_0000156 has temporal occupant http://purl.obolibrary.org/obo/OMRSE_00000020 is-aggregate-of http://purl.obolibrary.org/obo/RO_0002222 temporal relation http://purl.obolibrary.org/obo/RO_0001019 contains http://www.bioassayontology.org/bao#BAO_0002008 has form http://purl.obolibrary.org/obo/RO_0002001 aligned with http://semanticscience.org/resource/SIO_000001 is related to