Term IRI Term label Parent term IRI Parent term label Alternative term Definition http://purl.obolibrary.org/obo/BCGO_9000207 Ptf1a{tm1(tTAoff)Macd} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Ptf1a{tm1(tTAoff)Macd} A mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{tTA} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). Mice heterozygous for the tTA replacement of the Ptf1a gene are viable, fertile, of normal size, and do not display any behavioral abnormalities. The replacement places the expression of tTAoff (Gossen & Bujard, PNAS 89:5547, 1992) under the control of the regulatory sequences of the endogenous Ptf1a gene. This mouse was initially designed to be mated to a mouse (see BCBC #M461) bearing a bicistronic Ptf1a-lacZ transgene driven by the tetracycline-regulatory element (TRE: 7 copies of tetO with the CMV minimal promoter). For offspring homozygous for the tTA allele of Ptf1a and hemi- or homozygous for the transgene, the production of PTF1a is due solely to tTA-activation of the transgene, which is repressed by administration of tetracycline/doxycycline. This strategy allows embryonic developmental arrest at desired stages or cessation of gene function in adult mice for the pancreas (similar to that for Pdx1 described in Holland et al., PNAS 99:12236, 2002) and also for the cerebellum, retina, dorsal spinal cord and possibly hypothalamus. This transgenic mouse may be useful in studies of pancreatic endocrine/exocrine development and function, diabetes, and certain defects of the CNS. This tissue-specific expresser of tTA can also be bred with strains bearing other TRE-transgenes for organ-specific conditional expression analyses. Nearly all of the Ptf1a transcription unit has been replaced by a tTAoff coding sequence with accessory translational and RNA-processing signals, as follows, from 5' to 3': the Ptf1a gene transcriptional start and 49-bp of its 5'UTR; the Xenopus laevis beta-globin 5'UTR with Kozak initiator codon; the tTA coding sequence; and a 990-bp rabbit beta-globin gene fragment encoding the last 14-bp of its second exon, the 573-bp second intron, and the 364-bp last exon including a 98-bp 3'UTR with the polyA addition signal and addition site, and 39-bp of 3' beta-globin gene flanking sequence. The Ptf1a locus was modified by recombination-mediated cassette exchange using the cassette exchange allele in Ptf1a-LCA ES cells (Burlison et al., submitted). 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_0000300 textual entity http://purl.obolibrary.org/obo/IAO_0000030 information content entity text A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. http://purl.obolibrary.org/obo/IAO_0000312 publication about an investigation http://purl.obolibrary.org/obo/IAO_0000311 publication scientific publication A publication that is about an investigation http://purl.obolibrary.org/obo/IAO_0000577 centrally registered identifier symbol http://purl.obolibrary.org/obo/IAO_0000028 symbol CRID symbol A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. http://purl.obolibrary.org/obo/IAO_0000578 centrally registered identifier http://purl.obolibrary.org/obo/IAO_0000030 information content entity CRID An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. http://purl.obolibrary.org/obo/IAO_0000579 centrally registered identifier registry http://purl.obolibrary.org/obo/IAO_0000100 data set CRID registry A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process. http://purl.obolibrary.org/obo/OBI_0000018 material supplier role http://purl.obolibrary.org/obo/OBI_0000947 service provider role supplier a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. http://purl.obolibrary.org/obo/OBI_0000025 reference substance role http://purl.obolibrary.org/obo/BFO_0000023 role reference substance a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference. http://purl.obolibrary.org/obo/OBI_0000068 reporting party role http://purl.obolibrary.org/obo/OBI_0000202 investigation agent role submitter a study personnel role played by a party who reports the outcome of a study component http://purl.obolibrary.org/obo/OBI_0000070 assay http://purl.obolibrary.org/obo/OBI_0000011 planned process scientific observation A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. http://purl.obolibrary.org/obo/OBI_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_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_0000116 worker role http://purl.obolibrary.org/obo/OBI_0000202 investigation agent role worker a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline http://purl.obolibrary.org/obo/OBI_0000162 complete nutrient role http://purl.obolibrary.org/obo/OBI_0000204 nutrient role complete nutrient A nutrient role that inheres in a material entity and is realized in the use of that material entity by an organism to provide all needed nourishment. http://purl.obolibrary.org/obo/OBI_0000198 biological replicate role http://purl.obolibrary.org/obo/OBI_0000220 reference subject role biological replicate a reference participant role realized by equivalent treatment of participants http://purl.obolibrary.org/obo/OBI_0000202 investigation agent role http://purl.obolibrary.org/obo/BFO_0000023 role investigator A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing. http://purl.obolibrary.org/obo/OBI_0000204 nutrient role http://purl.obolibrary.org/obo/BFO_0000023 role nutrient a role that inheres in a material entity and is realized in the use of that material entity by an organism when it is used in that organism's metabolism and provides nourishment. http://purl.obolibrary.org/obo/OBI_0000220 reference subject role http://purl.obolibrary.org/obo/OBI_0000097 participant under investigation role reference participant a reference subject role which inheres in an organism or entity of organismal origin so that the characteristics or responses of the participant playing the reference participant role are used for comparison or reference http://purl.obolibrary.org/obo/OBI_0000248 feed role http://purl.obolibrary.org/obo/OBI_0000162 complete nutrient role feed a role that inheres in a material entity and is realized in the use of that material entity by lab animal to provide all needed nourishment. http://purl.obolibrary.org/obo/OBI_0000249 technical replicate role http://purl.obolibrary.org/obo/OBI_0000220 reference subject role technical replicate technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay http://purl.obolibrary.org/obo/OBI_0000291 transcription factor binding site identification http://purl.obolibrary.org/obo/OBI_0001146 binding assay TF binding a planned process with objective to find DNA region specifically recognized by proteins that function as transcription factors http://purl.obolibrary.org/obo/OBI_0000392 information processor function http://purl.obolibrary.org/obo/BFO_0000034 function data processor function An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process. http://purl.obolibrary.org/obo/OBI_0000398 image creation device http://purl.obolibrary.org/obo/OBI_0000832 measurement device image acquisition device An image creation device is a device which captures a digitized image of an object http://purl.obolibrary.org/obo/OBI_0000415 polymerase chain reaction http://purl.obolibrary.org/obo/OBI_0600058 enzymatic amplification PCR PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified. http://purl.obolibrary.org/obo/OBI_0000423 extract http://purl.obolibrary.org/obo/OBI_0000047 processed material extracted material an extract is a material entity which results from an extraction process http://purl.obolibrary.org/obo/OBI_0000424 transcription profiling assay http://purl.obolibrary.org/obo/OBI_0000443 analyte assay gene expression profiling An assay which aims to provide information about gene expression and transcription activity using ribonucleic acids collected from a material entity using a range of techniques and instrument such as DNA sequencers, DNA microarrays, Northern Blot http://purl.obolibrary.org/obo/OBI_0000435 genotyping assay http://purl.obolibrary.org/obo/OBI_0000443 analyte assay genotype profiling, SNP genotyping an assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions. http://purl.obolibrary.org/obo/OBI_0000456 material transformation objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification artifact creation objective an objective specifiction that creates an specific output object from input materials. http://purl.obolibrary.org/obo/OBI_0000552 reverse transcribed polymerase chain reaction http://purl.obolibrary.org/obo/OBI_0600058 enzymatic amplification reverse transcription polymerase chain reaction reverse transcribe pcr is a process which allow amplification of cDNA during a pcr reaction while the cDNA results from a retrotranscription of messenger RNA isolated from a material entity. http://purl.obolibrary.org/obo/OBI_0000648 clustered data set http://purl.obolibrary.org/obo/IAO_0000100 data set data set with assigned discovered class labels A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels. http://purl.obolibrary.org/obo/OBI_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_0000674 center value http://purl.obolibrary.org/obo/IAO_0000027 data item median A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data. http://purl.obolibrary.org/obo/OBI_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_0000693 MeDIP-seq assay http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay Methylated DNA immunoprecipitation sequencing assay is an assay which aims at identifying methylated sites in genomic DNA and determining methylation pattern that affect gene transcription by relying on immunoprecipitation of methylated genomic DNA, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods. http://purl.obolibrary.org/obo/OBI_0000695 chain termination sequencing http://purl.obolibrary.org/obo/OBI_0000734 DNA sequencing by synthesis dye terminator sequencing is a DNA sequencing which rely on the use of dideoxynucleotides used in 4 distinct sequencing reaction on the same DNA sample. The dideoxynucleotides, once incorporated in the complementary DNA strand being synthesized by the DNA polymerase prevent any further chain elongation. The newly generated sequences are resolved on a polyacrylamide gel using electrophoresis and labels (either fluorochrome or radioactivity) are used to determine the nucleotide present at a given position http://purl.obolibrary.org/obo/OBI_0000697 Helicos sequencing http://purl.obolibrary.org/obo/OBI_0000734 DNA sequencing by synthesis true single molecule sequencing is a DNA sequencing which allows sequence identification of billions of DNA molecules immobilized to a surface by using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not requires amplification step and is typically able to produce reads of 25 base pair length. 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_0000716 ChIP-seq assay http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay chromatin immunoprecipitation sequencing assay an assay which aims at identifying protein binding sites in genomic DNA and determining how protein may regulate gene transcription by relying on immunoprecipitation of DNA bound protein, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods. http://purl.obolibrary.org/obo/OBI_0000722 paired-end library http://purl.obolibrary.org/obo/OBI_0000047 processed material paired-end tag (PET) library is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs http://purl.obolibrary.org/obo/OBI_0000724 Solexa sequencing http://purl.obolibrary.org/obo/OBI_0000734 DNA sequencing by synthesis reversible terminator sequencing is a DNA sequencing which allows sequence identification by relying on use of DNA polymerase and reversible terminator. The methods requires immobilization of genomic DNA fragment onto a surface and a specific clonal amplification step known as bridge PCR. Reliance on reversible terminator allow cycles of DNA chain extension by DNA polymerase and imaging without the need of electrophoretic separation of newly synthesized DNA fragment as with Sanger sequencing. http://purl.obolibrary.org/obo/OBI_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_0000750 study design independent variable http://purl.obolibrary.org/obo/IAO_0000033 directive information entity independent variable a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled http://purl.obolibrary.org/obo/OBI_0000751 study design dependent variable http://purl.obolibrary.org/obo/IAO_0000033 directive information entity dependent variable dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies. http://purl.obolibrary.org/obo/OBI_0000785 study design controlled variable http://purl.obolibrary.org/obo/IAO_0000033 directive information entity controlled variable Controlled variable specification is a part of a study design. They are the entities that could vary, but are kept constant to prevent their influence on the effect of the independent variable on the dependent. http://purl.obolibrary.org/obo/OBI_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/OBI_0000070 assay quantitative real time polymerase chain reaction A laboratory technique based on the PCR, which is used to amplify and simultaneously quantify 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_0000919 animal euthanization http://purl.obolibrary.org/obo/OBI_0600006 killing animal sacrifice A process in which is the end of life of animal is brought about in accordance with local regulations on treatment of animal subjects and using a method which causes minimal pain and distress to the animal subject http://purl.obolibrary.org/obo/OBI_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_0001007 image creation http://purl.obolibrary.org/obo/OBI_0000011 planned process image acquisition A planned process that captures an image of an object. http://purl.obolibrary.org/obo/OBI_0001031 array image creation http://purl.obolibrary.org/obo/OBI_0001007 image creation array image acquisition An image creation process that generate an image from the array. http://purl.obolibrary.org/obo/OBI_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_0001185 selectively maintained organism http://purl.obolibrary.org/obo/OBI_0100026 organism strain An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms http://purl.obolibrary.org/obo/OBI_0001248 ChIP-chip assay http://purl.obolibrary.org/obo/OBI_0001956 assay using chromatin immunoprecipitation ChIP-on-chip assay an assay that aims to investigate the interactions between protein and DNA relying on chromatin immunoprecipitation ('ChIP') combined with microarray technology ('chip'). Specially, it allows the identification of protein binding sites on a genome-wide basis. 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 assay in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and or to quantitate transcript abundance http://purl.obolibrary.org/obo/OBI_0001307 tiling microarray http://purl.obolibrary.org/obo/OBI_0400148 DNA microarray genome tiling array a DNA microarray which has short fragments of nucleic acid immobilized on a substrate. These are designed to cover the whole genome of the target species. Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions. http://purl.obolibrary.org/obo/OBI_0001393 comparative genomic hybridization by array assay http://purl.obolibrary.org/obo/OBI_0000435 genotyping assay array CGH An assay in which changes in DNA sequence copy number are analysed using a microarray. For example the analysis of LOH in tumor cells vs a non diseased sample or the comparison of clinical isolated of disease causing bacteria. http://purl.obolibrary.org/obo/OBI_0001403 ChIP-chip design http://purl.obolibrary.org/obo/OBI_0001425 protein binding site identification design ChIP-on-chip design A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and DNA microarray (chip) assays. http://purl.obolibrary.org/obo/OBI_0001508 sampling time measurement datum http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum time point A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point. http://purl.obolibrary.org/obo/OBI_0001617 PubMed ID http://purl.obolibrary.org/obo/IAO_0000577 centrally registered identifier symbol PubMed Identifier A CRID symbol that is sufficient to look up a citation from the PubMed, a literature database of life sciences and biomedical information. http://purl.obolibrary.org/obo/OBI_0001674 cap analysis of gene expression http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay CAGE An assay which aims at monitoring 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_0001848 chromatin interaction analysis by paired-end tag sequencing http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay ChIA-PET assay An assay that incorporates chromatin immunoprecipitation (ChIP)-based enrichment, chromatin proximity ligation, Paired-End Tags, and high-throughput sequencing to determine de novo long-range chromatin interactions genome-wide. http://purl.obolibrary.org/obo/OBI_0001849 structural analysis by paired-end tag sequencing http://purl.obolibrary.org/obo/OBI_0000626 DNA sequencing 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 http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay RNA-PET assay An assay that incorporates Paired-End Tags and sequencing technology to determine transcripts, gene structures, and gene expressions. http://purl.obolibrary.org/obo/OBI_0001853 DNase I hypersensitive sites sequencing assay http://purl.obolibrary.org/obo/OBI_0000626 DNA sequencing DNase-seq assay An assay to identify 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_0001857 RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay RIP-seq assay An assay that combines immunoprecipitation of an RNA-binding protein and RNA-seq to identify mRNAs associated with selected RNA binding proteins (RBPs). http://purl.obolibrary.org/obo/OBI_0001858 cross-linking immunoprecipitation high-throughput sequencing assay http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay HITS-CLIP An assay that employs UV-crosslinking between RNA and the protein, followed by immunoprecipitation with antibodies for the protein, fragmentation, and high-throughput used for screening for RNA sequences that interact with a particular RNA-binding protein. http://purl.obolibrary.org/obo/OBI_0001859 formaldehyde-assisted isolation of regulatory elements assay http://purl.obolibrary.org/obo/OBI_0000626 DNA sequencing FAIRE-seq assay An assay to determine the sequences of those DNA regions in the genome associated with regulatory activity. http://purl.obolibrary.org/obo/OBI_0001861 methylation-sensitive restriction enzyme sequencing assay http://purl.obolibrary.org/obo/OBI_0001266 DNA methylation profiling by high throughput sequencing assay MRE-seq assay An assay that identifies unmethylated CpGs by use of methylation sensitive restriction enzymes to fragment DNA. http://purl.obolibrary.org/obo/OBI_0001862 reduced representation bisulfite sequencing assay http://purl.obolibrary.org/obo/OBI_0000748 bisulfite sequencing reduced representation bisulfite-seq A bisulfite sequencing assay that identifies genomic methylation patterns by using a bisulfite based protocol that enriches CG-rich parts of the genome. http://purl.obolibrary.org/obo/OBI_0001863 shotgun bisulfite-seq assay http://purl.obolibrary.org/obo/OBI_0000748 bisulfite sequencing whole-genome shotgun bisulfite sequencing A bisulfite sequencing assay that identifies methylated cytosines across the genome using high throughput sequencing. http://purl.obolibrary.org/obo/OBI_0001864 RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay RAMPAGE An 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_0001905 secondary cultured cell population http://purl.obolibrary.org/obo/OBI_0100060 cultured cell population secondary cell culture sample A cultured cell population that is derived through one or more passages in culture. http://purl.obolibrary.org/obo/OBI_0001914 multiplex ligation-mediated amplification http://purl.obolibrary.org/obo/OBI_0000415 polymerase chain reaction Multiplex ligation-dependent probe amplification A polymerase chain reaction that amplifies multiple targets with a single primer pair mediated by hybridization of a primer with its target sequence using ligation. http://purl.obolibrary.org/obo/OBI_0001919 Carbon-copy chromosome conformation capture assay http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay 5C assay An assay that is used to analyze the organization of chromosomes at the genome-wide scale. http://purl.obolibrary.org/obo/OBI_0001920 DNA replication timing by sequencing assay http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay Repli-seq assay An assay in which timing of DNA replication is quantified as a function of genome position based on genome-wide sequencing. http://purl.obolibrary.org/obo/OBI_0001922 microRNA profiling by high throughput sequencing assay http://purl.obolibrary.org/obo/OBI_0001926 microRNA profiling assay microRNA-seq assay A RNA-seq assay in which high throughput sequencing technology is used to analyse the microRNA component of the transcriptome. http://purl.obolibrary.org/obo/OBI_0001924 micrococcal nuclease digestion followed by high throughput sequencing assay http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay MNase-seq assay An assay to identify nucleosome positioning by genome wide sequencing of regions senstative to digestion by micrococal nuclease http://purl.obolibrary.org/obo/OBI_0001925 chromatin immunoprecipitation with exonuclease sequencing assay http://purl.obolibrary.org/obo/OBI_0000716 ChIP-seq assay ChIP-exo assay A ChIP-seq assay to identify protein binding sites using an exonuclease to provide greater binding resolution of immunoprecipitation assay by genome wide sequencing. 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 in which aims to quantify the microRNA species within a biological sample. http://purl.obolibrary.org/obo/OBI_0001960 taxonomic diversity assessment by targeted gene survey http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay targeted gene survey DNA barcoding is an assay which aims to provide information about taxonomic information and community diversity by mean of sequencing specific genomic regions used as marker of identity or diversity. http://purl.obolibrary.org/obo/OBI_0001964 decision-theoretic analysis objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification decision analysis objective An objective specification which what includes a description of two or more alternative actions to take in a particular situation and a metric that enables comparisons of the two actions. The objective specified is achieved in a planned process which includes a data transformation, the output of which is an identification of the 'best' choice according to the metric. http://purl.obolibrary.org/obo/OBI_0002014 DNA methylation profiling by ChIP-chip assay http://purl.obolibrary.org/obo/OBI_0002020 epigenetic modification assay DNA methylation ChIP-chip A ChIP-chip assay that identifies sites of DNA methylation. http://purl.obolibrary.org/obo/OBI_0002015 transcription profiling by MPSS assay http://purl.obolibrary.org/obo/OBI_0000424 transcription profiling assay expression MPSS An assay in which the transcriptome of a biological sample is analysed using Massive Parallel Signature Sequencing (MPSS). http://purl.obolibrary.org/obo/OBI_0002016 histone modification identification by ChIP-chip assay http://purl.obolibrary.org/obo/OBI_0002020 epigenetic modification assay histone modification ChIP-chip A ChIP-chip assay to identify regions containing specific histones and their modifications. http://purl.obolibrary.org/obo/OBI_0002017 histone modification identification by ChIP-Seq assay http://purl.obolibrary.org/obo/OBI_0000716 ChIP-seq assay histone modification ChIP-Seq A ChIP-seq assay to identify regions containing specific histones and their modifications. http://purl.obolibrary.org/obo/OBI_0002018 transcription factor binding site identification by ChIP-chip assay http://purl.obolibrary.org/obo/OBI_0001248 ChIP-chip assay TF Binding ChIP-chip A ChIP-chip assay to identify binding sites for transcription factors. http://purl.obolibrary.org/obo/OBI_0002019 transcription factor binding site identification by ChIP-Seq assay http://purl.obolibrary.org/obo/OBI_0000716 ChIP-seq assay TF Binding ChIP-Seq A ChIP-seq assay to identify binding sites for transcription factors. 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_0002033 translation-associated transcript leader sequencing 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 http://purl.obolibrary.org/obo/OBI_0001271 RNA-seq assay TL-seq An RNA-seq assay combining 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 to sequence 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 A RNA-seq assay to identify the sequences that act as transcriptional enhancers in a direct, quantitative, and genome-wide manner from sheared genomic DNA. http://purl.obolibrary.org/obo/OBI_0002042 carbon-copy chromosome conformation capture assay followed by sequencing assay http://purl.obolibrary.org/obo/OBI_0001919 Carbon-copy chromosome conformation capture assay Carbon-copy chromosome conformation capture assay followed by sequencing A carbon-copy chromosome conformation capture assay to analyze the organization of chromosomes in an unbiased, genome-wide manner using high throughput sequening following carbon-copy chromosome conformation capture. http://purl.obolibrary.org/obo/OBI_0002043 individual-nucleotide resolution cross-linking and immunoprecipitation sequencing assay http://purl.obolibrary.org/obo/OBI_0001858 cross-linking immunoprecipitation high-throughput sequencing assay iCLIP assay A cross-linking immunoprecipitation high-throughput sequencing assay to identify protein-RNA interactions by using UV light to covalently bind proteins and RNA molecules, allowing for a very stringent purification of the linked protein-RNA complexes. http://purl.obolibrary.org/obo/OBI_0002044 RNA Bind-n-Seq assay http://purl.obolibrary.org/obo/OBI_0001271 RNA-seq assay RNBS assay A 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 for quantitatively profiling RNA polyadenylation at the transcriptome level. http://purl.obolibrary.org/obo/OBI_0100060 cultured cell population http://purl.obolibrary.org/obo/OBI_0000047 processed material cell culture sample A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history. http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://purl.obolibrary.org/obo/OBI_0000011 planned process data processing A planned process that produces output data from input data. http://purl.obolibrary.org/obo/OBI_0200089 multiple testing correction method http://purl.obolibrary.org/obo/OBI_0000668 error correction data transformation multiple testing procedure A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate http://purl.obolibrary.org/obo/OBI_0200175 class discovery data transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation unsupervised classification data transformation A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery. http://purl.obolibrary.org/obo/OBI_0200178 class discovery objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective unsupervised classification objective A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic. http://purl.obolibrary.org/obo/OBI_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_0400112 liquid handler http://purl.obolibrary.org/obo/OBI_0000968 device liquid_handling_instrument a device that is used for automated liquid transfer and handling. http://purl.obolibrary.org/obo/OBI_0400116 thermal cycler http://purl.obolibrary.org/obo/OBI_0001034 environmental control device thermocycler An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. http://purl.obolibrary.org/obo/OBI_0400118 vortexer http://purl.obolibrary.org/obo/OBI_0001033 perturbation device vortex_mixer A vortexer is an instrument that mixes small vials of liquid by creating a rotation of the liquid around its own center. It consists of an electric motor with the drive shaft oriented vertically and attached to a cupped rubber piece mounted slightly off-center. As the motor runs the rubber piece oscillates rapidly in a circular motion. When a test tube or other appropriate container is pressed into the rubber cup (or touched to its edge) the motion is transmitted to the liquid inside and a vortex is created. http://purl.obolibrary.org/obo/OBI_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_0500000 study design http://purl.obolibrary.org/obo/IAO_0000104 plan specification experimental design A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. http://purl.obolibrary.org/obo/OBI_0500006 parallel group design http://purl.obolibrary.org/obo/OBI_0500000 study design independent measure design A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design. Subjects of a treatment group receive a unique combination of independent variable values making up a treatment http://purl.obolibrary.org/obo/OBI_0600002 tumor grading http://purl.obolibrary.org/obo/OBI_0000070 assay grading of tumor Determination of the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus. http://purl.obolibrary.org/obo/OBI_0600006 killing http://purl.obolibrary.org/obo/OBI_0000094 material processing sacrifice A protocol application in which an organism is intentionally put to death http://purl.obolibrary.org/obo/OBI_0600016 pooling specimens http://purl.obolibrary.org/obo/OBI_0000652 material combination sample pooling physical combination of several instances of like material http://purl.obolibrary.org/obo/OBI_0600018 material portioning http://purl.obolibrary.org/obo/OBI_0600014 material component separation apportioning a material processing in which the input substance is partitioned into a number of portions that are similar in composition. http://purl.obolibrary.org/obo/OBI_0600020 histology http://purl.obolibrary.org/obo/OBI_0000070 assay histopathology the visual examination of cells or tissue (or images of them) with an assessment regarding a quality of the cells or tissue. Parts are: staining, imaging, judgement 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_0600043 genetic transformation http://purl.obolibrary.org/obo/OBI_0000094 material processing genetic modification the introduction. alteration or integration of genetic material into a cell or organism http://purl.obolibrary.org/obo/OBI_0600064 recombinant vector cloning http://purl.obolibrary.org/obo/OBI_0000274 adding a material entity into a target molecular cloning a planned process with the objective to insert genetic material into a cloning vector for future replication of the inserted material http://purl.obolibrary.org/obo/OBI_1000029 phage display library http://purl.obolibrary.org/obo/OBI_0000731 recombinant vector display library a phage display library is a collection of materials in which a mixture of genes or gene fragments is expressed and can be individually selected and amplified. http://purl.obolibrary.org/obo/OBI_1000036 cell lysate http://purl.obolibrary.org/obo/OBI_0000047 processed material lysed material a cell lysate is a material entity which is output of a cell lysis process http://purl.obolibrary.org/obo/OBI_1000207 assay bead http://purl.obolibrary.org/obo/OBI_0000047 processed material bead A globular or round particle of defined physicochemical properties and size which can be exploited as either the primary substance for detection or as a secondary solid platform for the attachment of bioactive molecules. http://purl.obolibrary.org/obo/BCGO_9001221 Gt(ROSA)26Sor{tm1(Ccnd1T286A)Stang} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Gt(ROSA)26Sor{tm1(Ccnd1T286A)Stang} A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{(Ccnd1T286A)} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This strain expresses both mutant cyclin D1{T286A} and a cherry reporter under the regulation of a tetracycline-responsive bi-directional minimal CMV promoter (TRE-Tight; tetO). The cyclin D1-T286A mutant cannot be phosphorylated by GSK-3beta and is resistant to polyubiquitination. Therefore, cyclin D1-T286A remains nuclear throughout the cell cycle and has an extended half-life relative to wild-type cyclin D1. This strain represents an effective tool for generating inducible tissue-specific cyclin D1{T286A} mutants with a cherry reporter. http://purl.obolibrary.org/obo/BCGO_0000012 Tg(Ins1-EGFP/GH1)14Hara mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Tg(Ins1-EGFP/GH1)14Hara A mouse strain containing a transgene in which EGFP (transgene) is driven by the Ins1 promoter (NCBI Gene ID: 16333). Hemizygous mice show expression of EGFP in beta lineage cells of the pancreas. http://purl.obolibrary.org/obo/BCGO_0000013 C57BL/6 mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain black 6 A mouse strain that is a laboratory mouse generated from long inbreeding with nearly identical genotype. C57BL/6 mouse has a dark brown, nearly black coat, and an easily irritable temperament. It has a good reproductive performance and is the most widely used "genetic background" for genetically modified mice for use as models of human disease. http://purl.obolibrary.org/obo/BCGO_0000016 Sox17{(GFPCre)Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Sox17{(GFPCre)Mgn} A mouse strain in which part or all of the targeted gene, SRY-box containing gene 17 (NCBI Gene ID: 20671) is replaced to create Sox17{GFPCre} using the Loxed Cassette Acceptor allele Sox17{tm1(LCA)}). Using an RMCE strategy, we inserted a GFP-Cre (Green fluorescent protein-Cre-recombinase) fusion protein into a Sox17 LCA allele thereby replacing Sox17 coding sequences. The Sox17{GFPCre} mice may be used to track Sox17-expressing cells and their early progeny, or to conditionally inactivate genes in Sox17-expressing cells. http://purl.obolibrary.org/obo/BCGO_0000017 Pdx1{(CFP)Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain RES1301 mouse strain A mouse strain in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{tm1.2(CFP)} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). This mouse contains a cyan fluorescent protein (CFP, Cerulean), tagged with 3 copies of an SV40 NLS knocked into the endogenous Pdx1 gene. This mouse strain enables pre-pancreatic endoderm to be easily identified in the developing mouse embryo and the isolation of Pdx1(+) cells by FACS. http://purl.obolibrary.org/obo/BCGO_0000018 Ptf1a{tm1Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain ptf1aYFP mouse strain A mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create ptf1a{tm1.1(YFP)} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}).

Ptf1a{YFP} mice may be used to visualize yellow fluorescent protein (YFP) expression from the ptf1a allele. Ptf1a is expressedin pancreatic buds beginning at E9.5 andplays a vital role in the growth and lineage specification of pancreatic multipotent progenitor cells (MPCs). Ptf1a is also expressed in the neuronal precursors of the cerebellum, spinal cord, and retina where it also performs fate determining roles.

http://purl.obolibrary.org/obo/BCGO_0000019 B6.129S-Neurog3{tm1(EGFP)Khk}/Mmcd mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain ngn3-EGFP mouse strain A mouse strain in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Gene Replacement) to targeted mutation 1, Klaus H Kaestner (MGI ID: Neurog3{tm1(EGFP)Khk}). A targeted mutation at the Neurogenin 3 locus where EGFP replaces entire coding region of Neurogenin3. The basic phenotype is EGFP expression in developing endocrine cells of pancreas and in glandular regions of the stomach. http://purl.obolibrary.org/obo/BCGO_0000020 Insm1tm2Mgn mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain RES661 mouse strain A mouse strain contains a GFP-Cre fusion protein which replaces the Insm1 coding sequence. These mice express green fluorescent protein (GFP) under control of the Insm1 gene locus. Insm1 is expressed in pancreatic primordium starting at E9.5. Insm1 is also expressed in neural precursor cells and tumors of may be used for lineage tracing of Insm1-positive cells in both wild-type and Insm1-null mice. http://purl.obolibrary.org/obo/BCGO_0000028 129X1/SvJ mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain 129X1 A mouse strain that is a laboratory mouse generated from inbreeding. It has white-bellied, pink-eyed, light chinchilla (off-white) or albino or white-bellied, pink-eyed, light chinchilla (light tan). It has a good reproductive performance and is widely used in the production of targeted mutations due to the availability of multiple embryonic stem cell lines derived from them. http://purl.obolibrary.org/obo/BCGO_0000046 Sox17-expressing definitive endodermal cell http://purl.obolibrary.org/obo/CL_0000223 endodermal cell Sox17 expressing cell from the embryo body proper an endodermal cell that is part of the definitive endoderm and expresses a gene for SOX-17 http://purl.obolibrary.org/obo/BCGO_0000047 Sox17-expressing Epcam+ pancreatic epithelial cell http://purl.obolibrary.org/obo/CL_0000066 epithelial cell Sox17 expressing cell in ventral pancreatic bud an epithelial cell that is part of the ventral pancreatic bud, expresses a gene for SOX-17 and has Epcam in the plasma membrane. http://purl.obolibrary.org/obo/BCGO_0000048 Pdx1-expressing foregut endodermal cell http://purl.obolibrary.org/obo/CL_0000223 endodermal cell Pdx1-expressing endoderm cell an endodermal cell that is part of the foregut endoderm and expresses the gene for pancreas/duodenum homeobox protein 1 http://purl.obolibrary.org/obo/BCGO_0000049 Ptf1a-expressing multipotent pancreatic cell http://purl.obolibrary.org/obo/CL_0000055 non-terminally differentiated cell Ptf1a-expressing cell a non-terminally differentiated cell that is part of the pancreatic bud, participates in pancreas development and expresses the gene for pancreas transcription factor 1 subunit alpha. http://purl.obolibrary.org/obo/BCGO_0000050 Ptf1a-lacking pancreatic progenitor cell http://purl.obolibrary.org/obo/CL_0000055 non-terminally differentiated cell Ptf1a-null cell a non-terminally differentiated cell that is part of the pancreatic bud but lacks pancreas transcription factor 1 subunit alpha. http://purl.obolibrary.org/obo/BCGO_0000051 neurogenin-3-expressing endocrine progenitor cell http://www.ebi.ac.uk/efo/EFO_0002966 pancreatic cell Ngn3-expressing cell a non-terminally differentiated cell that participates in endocrine pancreas developement and expresses the gene for neurogenin-3. http://purl.obolibrary.org/obo/BCGO_0000052 neurogenin-3-lacking pancreatic progenitor cell http://www.ebi.ac.uk/efo/EFO_0002966 pancreatic cell Ngn3-null cell a non-terminally differentiated cell that is part of the pancreas, participates in pancreas development and lacks neurogenin-3. http://purl.obolibrary.org/obo/BCGO_0000053 Insm1-expressing endocrine progenitor cell http://www.ebi.ac.uk/efo/EFO_0002966 pancreatic cell Insm1 expressing pancreatic endocrine cell a non-terminally differentiated cell that participates in endocrine pancreas development and expresses a gene for insulinoma-associated protein 1 http://purl.obolibrary.org/obo/BCGO_0000054 Insm1-lacking endocrine progenitor cell http://purl.obolibrary.org/obo/CL_0000055 non-terminally differentiated cell Non-functional Insm1 expressing pancreatic endocrine cell a non-terminally differentiated cell that is part of the endocrine pancreas and lacks insulinoma-associated protein 1 http://purl.obolibrary.org/obo/BCGO_0000055 insulin-expressing immature beta cell http://purl.obolibrary.org/obo/CL_0000169 type B pancreatic cell insulin-expressing nascent beta cells a type B pancreatic cell that is immature and expresses a gene for insulin http://purl.obolibrary.org/obo/BCGO_0000056 insulin-expressing mature beta cell http://purl.obolibrary.org/obo/BCGO_0000014 functional beta cell like cell insulin-expressing mature beta cells a type B pancreatic cell that is mature and expresses a gene for insulin http://purl.obolibrary.org/obo/BCGO_0000086 long non-coding RNA http://purl.obolibrary.org/obo/SO_0000655 ncRNA lncRNA A ncRNA which is transcribed, non-protein coding, and longer than 200 nucleotides. http://purl.obolibrary.org/obo/BCGO_0000088 transcription factor binding site identification by SACO assay http://purl.obolibrary.org/obo/OBI_0001956 assay using chromatin immunoprecipitation TF Binding SACO An assay that uses chromatin immunoprecipitation combined with serial analysis of chromatin occupancy (SACO) to identify binding sites for transcription factors. http://purl.obolibrary.org/obo/BCGO_0000089 transcriptional profiling by MARIS assay http://purl.obolibrary.org/obo/OBI_0000424 transcription profiling assay MARIS An assay that aims to measure abundance of transcripts using high-quality RNA isolated from cells following intracellular antibody staining and fluorescence-activated cell sorting (FACS). http://purl.obolibrary.org/obo/BCGO_9000177 B6.CBA-{Tg(Gcg-cre)1Herr}/Mmnc mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain B6.CBA-{Tg(Gcg-cre)1Herr}/Mmnc A mouse strain containing a transgene in which Cre (transgene) is driven by the Gcg promoter (NCBI Gene ID: 14526).

A transgenic alteration consisting of a SacI fragment containing the glucagon promoter, inserted at SacI of pBS-beta globin-Cre, resulting in Cre expression in pancreatic lineage cells.

http://purl.obolibrary.org/obo/BCGO_9000178 B6.CBA-{Tg(Ipf1-EGFP)1Herr}/Mmnc mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain B6.CBA-{Tg(Ipf1-EGFP)1Herr}/Mmnc A mouse strain containing a transgene in which EGFP (transgene) is driven by the Ipf1 promoter (NCBI Gene ID: 18609). This strain allows Expression of EGFP in pancreatic precursor populations. http://purl.obolibrary.org/obo/BCGO_9000179 B6;D2-Tg(Ins-cre)23Herr mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain B6;D2-Tg(Ins-cre)23Herr A mouse strain containing a transgene in which Cre (transgene) is driven by the Ins1 promoter (NCBI Gene ID: 24505). This strain relies on the recombination of floxed DNA in insulin-producing beta cells. http://purl.obolibrary.org/obo/BCGO_9000180 B6;D2-Tg(NEUROG3-cre)1Herr mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain B6;D2-Tg(NEUROG3-cre)1Herr A mouse strain containing a transgene in which Cre (transgene) is driven by the Neurog3 promoter (NCBI Gene ID: 11925).

All islet endocrine cells inherit a recombination event, if a segment of DNA is loxP-flanked. Transgene encoding Cre recombinase under the control of a human Neurogenin3 promoter.

http://purl.obolibrary.org/obo/BCGO_9000181 BX129-Neurod1{tmAK71(lacZ)Jle/Mmcd} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain BX129-Neurod1{tmAK71(lacZ)Jle/Mmcd} A mouse strain containing a transgene in which LacZ-Neo (transgene) is driven by the Neurod1 promoter (NCBI Gene ID: 18012). Homozygous phenotype: Postnatal lethal due to neonatal diabetes Pancreas--5% insulin production, no islet formation Gut--no CCK or secretin production Inner ear defects resulting in deafness--no cochlear ganglia and poor vestibular ganglia formation Cerebellar defect resulting in ataxia-- >90% depletion of cerebellar granule cells Hippocampal defects--no dentate gyrus. http://purl.obolibrary.org/obo/BCGO_9000182 STOCK Ipf1{tm1Cvw} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain STOCK Ipf1{tm1Cvw} A mouse strain in which the targeted gene, insulin promoter factor 1, homeodomain transcription factor (NCBI Gene ID: 18609), has been modified (allele type: Global Null) to targeted mutation 1, Christopher V E Wright (MGI ID: Ipf1{tm1Cvw}). http://purl.obolibrary.org/obo/BCGO_9000183 STOCK Ipf1{tm2Cvw}/Mmnc mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain STOCK Ipf1{tm2Cvw}/Mmnc A mouse strain in which the targeted gene, insulin promoter factor 1, homeodomain transcription factor (NCBI Gene ID: 18609), has been modified (allele type: Gene Replacement) to insulin promoter factor 1, homeodomain transcription factor / targeted mutation 2, Christopher V E Wright (MGI ID: Ipf1{tm2Cvw}). The homozygous phenotype of these animals show growth retardation and dehydration with lack of gastric emptying; ie. a-pancreatic. Heterozygous phenotype includes expression of beta-galactosidase in developing stomach, bile duct and cystic ducts and early pancreatic buds. http://purl.obolibrary.org/obo/BCGO_9000184 STOCK Ptf1a{tm1(cre)Cvw} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain STOCK Ptf1a{tm1(cre)Cvw} A mouse strain in which the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213), has been modified (allele type: Gene Replacement) to targeted mutation 1.1, Christopher VE Wright (MGI ID: Ptf1a{tm1.1(cre)Cvw}).

Homozygous phenotype is altered pancreatic development with loss of exocrine acini.

http://purl.obolibrary.org/obo/BCGO_9000185 STOCK Tg(Foxa3-cre)1Khk mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain STOCK Tg(Foxa3-cre)1Khk A mouse strain containing a transgene in which Cre (transgene) is driven by the Foxa3 promoter (NCBI Gene ID: 15377). http://purl.obolibrary.org/obo/BCGO_9000186 STOCK Tg(Ipf1-cre/Esr1)1Dam/Mmcd mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain STOCK Tg(Ipf1-cre/Esr1)1Dam/Mmcd A mouse strain containing a transgene in which Cre (transgene) is driven by the Ipf1 promoter (NCBI Gene ID: 18609). http://purl.obolibrary.org/obo/BCGO_9000189 STOCK-Tg(Ipf1-cre)89.1Dam/Mmcd mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain STOCK-Tg(Ipf1-cre)89.1Dam/Mmcd A mouse strain containing a transgene in which Cre (transgene) is driven by the Ipf1 promoter (NCBI Gene ID: 18609). http://purl.obolibrary.org/obo/BCGO_9000190 STOCK Tg(Neurog3-cre)1Dam/Mmcd mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain STOCK Tg(Neurog3-cre)1Dam/Mmcd A mouse strain containing a transgene in which Cre (transgene) is driven by the Neurog3 promoter (NCBI Gene ID: 11925). http://purl.obolibrary.org/obo/BCGO_9000191 Gck{tm3Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Gck{tm3Mgn} A mouse strain in which the targeted gene, Glucokinase (NCBI Gene ID: 103988), has been modified (allele type: Global Mutation) to targeted mutation 3 (MGI ID: Gck{tm3Mgn}). This line of mice provides a model for Persistant Hyperinsulinemic Hypoglycemia of Infancy, or PHHI-GK, a rare genetic disease of humans. A gk{A456V} mutation, originally identified in a human pedigree with PHHI-GK, was introduced into these mice by gene knock-in. These mice may be useful for studies of sustained hypoglycemia. The mutation has been bred into a C57BL/6J strain thereby facilitating direct comparisons to both wild type C57BL/6J animals and to animals with a gk{K414E} mutation. http://purl.obolibrary.org/obo/BCGO_9000192 Gck{tm2Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Gck{tm2Mgn} A mouse strain in which the targeted gene, Glucokinase (NCBI Gene ID: 103988), has been modified (allele type: Global Mutation) to targeted mutation 2 (MGI ID: Gck{tm2Mgn}). This line of mice contains a gk{K414E} point mutation that was introduced by gene knock-in. This point mutation wasidentified in aMODY-GK pedigree. These mice will be useful for studies of sustained hyperglycemia since they contain only a single mutation and are congenic with the C57BL/6J strain. http://purl.obolibrary.org/obo/BCGO_9000193 Gck{tm1.1Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Gck{tm1.1Mgn} A mouse strain in which the targeted gene, Glucokinase (NCBI Gene ID: 103988), has been modified (allele type: Conditional Null) to targeted mutation 1.1 (MGI ID: Gck{tm1.1Mgn}). Gk{lox} mice may be used to generate cell specific knock-outs of glucokinase, depending which cre-expressing transgenic mouse is used. In humans, glucokinase gene mutations cause maturity onset diabetes of the young (MODY-GK), a disease that is characterized by early onset and persistent hyperglycemia. Thus, these mice are useful in determining how diminished experssion of glucokinase in specific cells causes hyperglycemia. http://purl.obolibrary.org/obo/BCGO_9000194 pck{tm1.1Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain pck{tm1.1Mgn} A mouse strain in which the targeted gene, phosphoenolpyruvate carboxykinase 1 (NCBI Gene ID: 18534), has been modified (allele type: Conditional Null) to targeted mutation 1.1, Mark A Magnuson (MGI ID: Pck1{tm1.1Mgn} ). These mice may be used to study tissue-specific functions of phosphoenolpyruvate carboxykinase (Pck1). This enzyme is essential for gluconeogenesis and also is important for regulating anapleurosis/catapleurosis of TCA cycle intermediates. By generating mice that are homozygous for the pck{lox} allele and that contain a tissue-specific Cre transgene, Pck1 can be deleted from various sites. http://purl.obolibrary.org/obo/BCGO_9000195 Rik{tm1.3Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Rik{tm1.3Mgn} A mouse strain in which the targeted gene, Rictor (NCBI Gene ID: 78757), has been modified (allele type: Global Null) to targeted mutation 1.3 (MGI ID: 4921505C17Rik{tm2Mgn}). Rictor is an essential part of mTOR complex 2 (mTORC2). mTORC2 phosphorylates Ser473 of Akt/PKB. Eliminating this gene disrupts the function of mTORC2, thereby preventing growth factor mediated activation of Akt/PKB. Thus, these mice have utility for studying both the sites of expression and function of rictor. http://purl.obolibrary.org/obo/BCGO_9000196 Rik{tm1.1Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Rik{tm1.1Mgn} A mouse strain in which the targeted gene, Rictor (NCBI Gene ID: 78757), has been modified (allele type: Conditional Null) to targeted mutation 1.1 (MGI ID: 4921505C17Rik{tm1.1Mgn}). These mice carrya conditional allele for Rictor, a component mTOR complex 2 (mTORC2). Disruption of the Rictor gene attenuates phosphorylation ofSer473 of Akt/PKB, which is important for a normal response to growth factor stimulation acting through the PI3-kinase signaling pathway. http://purl.obolibrary.org/obo/BCGO_9000197 Pparg{tm1.1Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Pparg{tm1.1Mgn} A mouse strain in which the targeted gene, Peroxisome proliferator-activated receptor gamma (NCBI Gene ID: 19016), has been modified (allele type: Conditional Null) to targeted mutation 1.1Mgn (MGI ID: Pparg{tm1.1Mgn}). These mice carry a conditional allele for PPARgamma that can be used in combination with various cre-expressing transgenes. http://purl.obolibrary.org/obo/BCGO_9000198 B6.129X1-Abcc8{tm1.1Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain B6.129X1-Abcc8{tm1.1Mgn} A mouse strain in which the targeted gene, ATP-binding cassette, sub-family C (CFTR/MRP), member 8 (NCBI Gene ID: 20927), has been modified (allele type: Global Null) to targeted mutation 1.1Mgn (MGI ID: Sur1{neotm1.1Mgn}). These mice contain a global knock-out of the sulfonylurea receptor (Sur1), which is part of the ATP-dependent potassium channel. In humans, mutations in Sur1 cause persistent hyperinsulinemic hypoglycemia of infancy (PHHI). http://purl.obolibrary.org/obo/BCGO_9000199 Tg(Pdx1-Neurog3-ER)1Agb mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Tg(Pdx1-Neurog3-ER)1Agb A mouse strain containing a transgene in which Neurog3-ER (transgene) is driven by the Pdx1 promoter (NCBI Gene ID: 18609). The transgene is driven by the Pdx1 promoter whcih targets it in pancreas progenitor during development. These mice express a fusion protein between the pro-endocrine transcription factor Ngn3 and the tamoxifen responsive estrogen receptor. An IRES site allows GFP to be co-expressed with Ngn3-ER. The protein is active only upon tamoxifen injection. http://purl.obolibrary.org/obo/BCGO_9000203 Glucagon:rtta mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Glucagon:rtta A mouse strain containing a transgene in which rtTA (transgene) is driven by the Gcg promoter (NCBI Gene ID: 14562). These mice expresses the rtTA (tetracycline transactivator) in islet alpha cells upon treatment with doxicycline. http://purl.obolibrary.org/obo/BCGO_9000204 C57/CBAJ-Hprt{tm3(Ins2-HBEGF)Ugfm} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain C57/CBAJ-Hprt{tm3(Ins2-HBEGF)Ugfm} A mouse strain in which the targeted gene, hypoxanthine guanine phosphoribosyl transferase 1 (NCBI Gene ID: 15452), has been modified (allele type: Gene Replacement) to (MGI ID: ). C57/CBAJ-Hprt{tm3(Ins2-HBEGF)Ugfm} carries a transgene encoding the human diphtheria toxin receptor under the control of rat insulin II promoter, was inserted by homologous recombination at the Hprt locus of the X chromosome. It provides a model for depletion of 50% of beta cells using Diphtheria toxin. http://purl.obolibrary.org/obo/BCGO_9000205 B6-Nkx6-1{tm1Msan} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain B6-Nkx6-1{tm1Msan} A mouse strain in which the targeted gene, Nkx6.1 (NCBI Gene ID: 18096), has been modified (allele type: Global Null) to targeted mutation (MGI ID: Nkx6.1{tm1(DsRed2)}). An IRES-DsRed2 cassette was introduced into exon 1 of the Nkx6.1 genomic sequence. The insertion generates a null allele. DsRed2 expression is not detected in these mice. http://purl.obolibrary.org/obo/BCGO_9000206 Tg(RIP-Cre/ESR1){Ydor} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Tg(RIP-Cre/ESR1){Ydor} A mouse strain containing a transgene in which CreER (transgene) is driven by the Ins promoter (NCBI Gene ID: 16333). A transgenic mouse expression tamoxifen-inducible Cre recombinase under rat insulin promoter. Upon the injection of tamoxifen, loxP-flanked DNA sequences in beta cells will be deleted. http://purl.obolibrary.org/obo/BCGO_9000209 NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} Tg(Ins2-HBEGF){6832Ugfm}/Sz mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} Tg(Ins2-HBEGF){6832Ugfm}/Sz A mouse strain containing a transgene in which DTR (transgene) is driven by the RIP promoter (NCBI Gene ID: ). NOD-Prkdc{scid} IL2rg{null}Tg(Ins2-HBEGF){6832Ugfm} mice are deficient in mature lymphocytes and NK cells, survive beyond 16 months of age, and even after sublethal irradiation resist lymphoma development. They can be induced to become hypoglycemic when Diphtheria toxin is used. 100% of beta cells will be depleted upon administration of diphtheria toxin. http://purl.obolibrary.org/obo/BCGO_9000210 NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl}Hprt{tm3(Ins2-HBEGF)Ugfm}/Sz mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl}Hprt{tm3(Ins2-HBEGF)Ugfm}/Sz A mouse strain containing a transgene in which DTR (transgene) is driven by the RIP promoter (NCBI Gene ID: ). NOD-scid IL2rg{null}Hprt{tm3(Ins2-HBEGF)Ugfm} mice are deficient in mature lymphocytes and NK cells, survive beyond 16 months of age, and even after sublethal irradiation resist lymphoma development. They can be induced to become hypoglycemic when Diphtheria toxin is used. 50% of beta cells will be depleted after diphtheria toxin administration. http://purl.obolibrary.org/obo/BCGO_9000211 NOD.Cg-Rag1{tm1Mom} Ins2{Akita} Prf1{tm1Sdz}/Sz mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain NOD.Cg-Rag1{tm1Mom} Ins2{Akita} Prf1{tm1Sdz}/Sz A mouse strain in which the targeted gene, recombination activating gene 1 (NCBI Gene ID: 19373), has been modified (allele type: Global Null) to (MGI ID: ). The NOD-Rag1{null} Prf1{null} Ins2{Akita} mouse is the first immunodeficient, spontaneously hyperglycemic mouse strain described that is based on the Ins2{Akita} mutation. This strain is suitable as hosts for human islet and human beta stem and progenitor cell transplantation in the absence of the need for pharmacological induction of diabetes. This strain of mice also has low levels of innate immunity and can be engrafted with a human immune system for the study of human islet allograft rejection. http://purl.obolibrary.org/obo/BCGO_9000212 NOD.Cg-Rag1{tm1Mom} Il2rg{tm1Wjl}/Sz mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain NOD.Cg-Rag1{tm1Mom} Il2rg{tm1Wjl}/Sz A mouse strain in which the targeted gene, interleukin 2 receptor, gamma chain (NCBI Gene ID: 16186), has been modified (allele type: Global Null) to (MGI ID: Il2rg{tm1Wjl}). Backcrossing of the Rag1 null allele onto the NOD/Lt strain background (NOD-Rag1{null} mice) provided a radio-resistant and longer-lived model for human-cell engraftment. Mutations in X-chromosome-linked Il2rg gene cause X-linked severe combined immunodeficiency (XSCID). Immunodeficient NOD-Rag1{null} IL2rg {null}mice tolerated much higher levels of irradiation conditioning than did NOD-Prkdc{scid} IL2rg {null} mice. http://purl.obolibrary.org/obo/BCGO_9000214 NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} Tg(Ins1-EGFP/GH1){14Hara}/Sz mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} Tg(Ins1-EGFP/GH1){14Hara}/Sz A mouse strain in which the targeted gene, interleukin 2 receptor, gamma chain (NCBI Gene ID: 16186), has been modified (allele type: Global Null) to targeted mutation 1 (MGI ID: Il2rg{tm1Wjl}). NOD.Cg-Prkdc{scid}Il2rg{tm1Wjl}Tg(Ins1-EGFP/GH1){14Hara}/Sz is a immunodeficient mouse carries a GFP transgene under the control of mouse insulin promoter 1, which leads to expression of eGFP in the beta cells. http://purl.obolibrary.org/obo/BCGO_9000215 Neurog3{tm1Ggr} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Neurog3{tm1Ggr} A mouse strain in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Other) to targeted mutation 1 (MGI ID: Ngn3{EYFP/+}). A targeting construct was designed to insert an IRES-EYFP and a floxed puro downstream of the coding sequence. Crossing with mice expressing Cre in the germ line excised the puromycin resistance gene. Coding region for Ngn3 is kept intact consequentely homozygous mice express Ngn3 protein , do not develop diabetes and behave like wild-types. in these mice, Ngn3-positive progenitors express EYFP and can be purified by FACS. http://purl.obolibrary.org/obo/BCGO_9000216 Tg(tetO-Ptf1a,lacZ)Macd mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Tg(tetO-Ptf1a,lacZ)Macd A mouse strain containing a transgene in which bicistronic Ptf1a-lacZ (transgene) is driven by the TRE promoter (NCBI Gene ID: ). Mice hemi- or homozygous for the transgene are viable, fertile, normal size, and do not display any behavioral abnormalities. Expression of the bicistronic transgene is directed by a heptameric tetO repeat linked to the CMV minimal promoter (collectively the tetracycline-response element). The mice do not express lacZ until a tetracycline-gransactivator (tTA) protein is produced; thereafter Ptf1a and lacZ genes are highly expressed. This mouse was designed to be mated to an apancreatic targeted mutant with tTAoff in place of the Ptf1a coding sequence (see BCBC strain M321). The combined genetic alterations provide normal pancreatic development and function until doxycycline-administration render the mice conditionally null of Ptf1a. This approach allows embryonic developmental arrest at desired stages or cessation of gene function in adult mice for the pancreas, cerebellum, retina, dorsal spinal cord and possibly hypothalamus. This transgenic mouse may be useful in studies of pancreatic endocrine/exocrine development and function, diabetes, and and certain defects of the CNS. This transgenic can also be bred with other tTA strains for conditional mutation analysis. http://purl.obolibrary.org/obo/BCGO_9000218 Ptf1a{tm2(W298A)Macd} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Ptf1a{tm2(W298A)Macd} A mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{tm2(W298A)} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). This mouse strain has a 2-bp site-directed mutation in the endogenous Ptf1a locus that changes codon 298 from tryptophan to alanine. The mutation disrupts the ability of the PTF1a protein to bind RBPJ. Mice heterozygous for the mutation are viable, fertile, of normal size, and do not display any behavioral abnormalities. Mice homozygous for the mutation phenocopy the homozygous Ptf1a-null. Newborn homozygotes are apancreatic, devoid of the dI4 and dILA GABAergic dorsal interneurons, have an incomplete cerebellum, and die shortly after birth. http://purl.obolibrary.org/obo/BCGO_9000219 Rbpjl{tm1(lacZ)Macd} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Rbpjl{tm1(lacZ)Macd} A mouse strain in which the targeted gene, Recombination signal binding protein for immunoglobulin kappa J region-like (NCBI Gene ID: 19668), has been modified (allele type: Global Mutation) to Rbpjl{tm1Macd} (MGI ID: Rbpjl{tm1(lacZ)}). This mouse strain has the Rbpjl gene region spanning exons 7, 8, and 9 replaced with lacZ in-frame. A pgk-neo resistance cassette has been removed by Cre-loxP deletion from the founder. Mice heterozygous and homozygous for the lacZ replacement are viable, fertile, of normal size, and do not display any behavioral abnormalities. In mature mice, the pancreas is one-third smaller than normal, due to less acinar tissue. Expression of the lacZ, measured by bet-galactosidase histostaining is very low. http://purl.obolibrary.org/obo/BCGO_9000220 STOCK Pdx1{tm1Macd}/J mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain STOCK Pdx1{tm1Macd}/J A mouse strain in which the targeted gene, Pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609), has been modified (allele type: Gene Replacement) to targeted mutation 1 (MGI ID: Pdx1{tmd1Macd}). Mice homozygous for the targeted mutation fail to develop a pancreas. Heterozygous mice have normal pancreatic development, but have partially impaired glucose tolerance in adulthood. The substitution of the targeted Ipf1/Pdx1 gene with tTAoff inactivates the endogenous allele and places tTAoff expression under the control of the endogenous transcriptional regulatory sequences of the Pdx1 locus. Identical to the endogenous allele, mutant locus expression is detectable in the pancreas and adjacent duodenum but not in other visceral organs or salivary glands. This mutant may be useful to direct tetracycline-regulated expression of responder transgenes in studies of pancreatic endocrine/exocrine development and function and diabetes. This mutant can also be bred with other tetO/TRE strains for pancreas-specific applications. This mutant was originally designed to be mated with mice engineered with a heptameric tetracycline operator (tetO)-controlled bicistronic transgene coding for a normal PDX1 protein and with a beta-galactosidase or EGFP reporter (see BCBC mouse M561). The combined modifications allow normal pancreatic development and function until doxycycline-administration renders the mouse conditionally null of the Pdx1 gene. This configuration for conditional expression of Pdx1is most effective when the transgene locus is homozygous. This allows embryonic developmental arrest at desired stages or cessation of function in adult mice by tetracycline administration. http://purl.obolibrary.org/obo/BCGO_9000221 STOCK Tg(tetO-Pdx1,lacZ)958.1Macd mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain STOCK Tg(tetO-Pdx1,lacZ)958.1Macd A mouse strain containing a transgene in which bicistronic Pdx1-lacZ (transgene) is driven by the TRE promoter (NCBI Gene ID: ). Mice hemizygous and homozygous for the transgenic insert are viable, fertile, of normal size, and do not display any behavioral abnormalities. Expression of the bicistronic transgene is directed by a heptameric tetO repeat fused to a minimal promoter (collectively the tetracycline-response element, or TRE). Transgenic mice do not express lacZ until a tetracycline-transactivator (tTA) protein is introduced; thereafter Pdx1 and lacZ from the transgene are expressed. All cells expressing transgenic Pdx1 coexpress the reporter. Further, mRNA levels of the transgene and endogenous Pdx1 fluctuate in concert during development. This mouse was originally designed to be mated to an apancreatic targeted mutant with the coding sequence of the Pdx1 locus replaced with that for tTAoff (see BCBC #M541). The combined mutations allow normal pancreatic development and function until doxycycline treatments render the mouse conditionally null of the endogenous gene. For this configuration, rescue of pancreatic development is most effective when the transgene locus is homozygous. This allows embryonic developmental arrest at desired stages or cessation of function in adult mice by administration of tetracycline/doxycycline. This transgenic strain may be useful in studies of pancreatic development and endocrine/exocrine function and diabetes. This strain can also be bred with other tTA strains for regulating Pdx1 expression in other contexts. http://purl.obolibrary.org/obo/BCGO_9000222 Neurog3{tm2(EGFP)Ggr} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Neurog3{tm2(EGFP)Ggr} A mouse strain in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Other) to targeted mutation 2 (MGI ID: Neurog3{tm2(EGFP)Ggr). A targeting construct was designed to insert an IRES-EGFP and a floxed puro downstream of the coding sequence. Crossing with mice expressing Cre in the germ line excised the puromycin resistance gene. Homozygous mice express Ngn3 protein, do not develop diabetes and behave like wild-types. Ngn3-positive cells are labeled with EGFP and can be purified by FACS. http://purl.obolibrary.org/obo/BCGO_9000223 Tg(Neurog3-IRES-NLS-LacZ)1Ggr mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Tg(Neurog3-IRES-NLS-LacZ)1Ggr A mouse strain containing a transgene in which LacZ (transgene) is driven by the Neurog3 promoter (NCBI Gene ID: 11925). Transgenic mice where Ngn3-positive cell are labeled with beta-galactosidase. Due to the stability of beta-galactosidase protein, the early descendants of Ngn3-positve cells are also labeled. To generate the Ngn3 promoter::LacZ construct, a 6.86 kb XbaI-XhoI fragment (6696 bp of 5' genomic and untranslated region sequences and 176 bp of ngn3 coding region) of mouse ngn3 genomic DNA was cloned upstream of the IRES-NLS-LacZ-pA sequence in pBS-INL vector resulting in plasmid pngn3(6.8)-INL. The 10.6 kb Ngn3-IRES-NLS-LacZ insert was released by NotI digestion and microinjected into murine oocyte pronuclei, and transgenic line was generated and maintained by crossing into a CD1 outbred background. http://purl.obolibrary.org/obo/BCGO_9000224 Tg(Ins1-mRFP)2Ggr mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Tg(Ins1-mRFP)2Ggr A mouse strain containing a transgene in which mRFP (transgene) is driven by the Ins1 promoter (NCBI Gene ID: 1633). These transgenic mice express the monomeric red fluorescent protein under the control of Ins1 gene (BAC) regulatory elements. http://purl.obolibrary.org/obo/BCGO_9000225 Arx{tm1Pgr} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Arx{tm1Pgr} A mouse strain in which the targeted gene, Arx (NCBI Gene ID: 11878), has been modified (allele type: Gene Replacement) to targeted mutation 1 (MGI ID: Arx{tm1Pgr}). These mice were created by insertion of the LacZ gene (with nuclear localization signal) into the Arx locus by homologous recombination in embryonic stem cells. The Arx gene is localized on the X chromosome. Knockout mice die after birth with due to hypoglycemia. Therefore male mice die at day 2 past birth. The colony has to be propagated with female mice. Arx-deficient mice do not produce alpha cells in the islets of Langerhans. http://purl.obolibrary.org/obo/BCGO_9000228 Mafa{tm1.1Rwst} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Mafa{tm1.1Rwst} A mouse strain in which the targeted gene, v-maf musculoaponeurotic fibrosarcoma oncogene family, protein A (avian) (NCBI Gene ID: 378435), has been modified (allele type: Conditional Null) to targeted mutation 1.1 (MGI ID: Mafa{tm1.1(lox)}). Mafa is a basic leucine-zipper containing member of the large Maf transcription factor family.It is part of the RIPE3b1 activator complex and functions as a key activator of insulin and pdx-1 gene transcription. Mafa{lox} mice may be used to generate both global and cell-specific Mafa null mice, depending on which cre-expressing transgenic mouse is used. Removal of Mafa gene might have a profound effect on beta cell function; thus we can closely monitor the expression of islet hormones, transcription functions and the glucose sensing machinery immunohistochemically. The experiment will provide us with the information about the role of Mafa plays in vivo in islet beta cells and the developing pancreas, thus helping us to understand how transcription activator contribute to the pathogenesis and the treatment of diabetes. http://purl.obolibrary.org/obo/BCGO_9000229 Myt1{tm1.1Ggu} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Myt1{tm1.1Ggu} A mouse strain in which the targeted gene, Myt1 (myelin transcriptioin factor 1) (NCBI Gene ID: 1100535 ), has been modified (allele type: Conditional Null) to targeted mutation 1.1 (MGI ID: Myt1{tm1.1Ggu}). Two loxP sites flank exon 6 of Myt1b. The allele behaves as wild type allele without Cre-mediated deletion. Cre-mediated deletion creates null Myt1 allele. The homozygous null is neonatal lethal. Myt1 null pancreas has abnormal islet cell differentiation, ie. single cells produce multiple hormones. Pancreatic-specific Myt1 deletion results in glucose intolerance in males. http://purl.obolibrary.org/obo/BCGO_9000230 OC-1{tm1.1Mga} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain OC-1{tm1.1Mga} A mouse strain in which the targeted gene, Onecut1 (NCBI Gene ID: 15379), has been modified (allele type: Conditional Null) to targeted mutation 1.1 (MGI ID: OC-1{tm1.1Mga}). This line of mice allows for conditional inactivation of the OC-1 (HNF6) gene using Cre recombinase. Thus, HNF6 function can be assessed in the different tissues in which it is expressed. http://purl.obolibrary.org/obo/BCGO_9000231 Nkx2-2{tm3Suss} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Nkx2-2{tm3Suss} A mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2(TNmut) using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). These mice contain mutations in the central core of the Nkx2.2 TN domain (putative groucho-interaction domain). http://purl.obolibrary.org/obo/BCGO_9000232 Nkx2-2{tm2Suss} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Nkx2-2{tm2Suss} A mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2:rtTA using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). The reverse tetracycline transactivator (rtTA) is knocked into the Nkx2.2 coding region, effectively knocking out one Nkx2.2 allele. http://purl.obolibrary.org/obo/BCGO_9000233 C57/CBAJ-TgN(Glucagon- hHB EGF)Ugfm mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain C57/CBAJ-TgN(Glucagon- hHB EGF)Ugfm A mouse strain containing a transgene in which Diphtheria Toxin Receptor (transgene) is driven by the Gcg promoter (NCBI Gene ID: 14526). Transgenic strain (generated by pronuclear microinjection) of a transgene containing the rat glucagon promoter (1.6kb fragment) upstream of a rabbit beta-globin intron and the coding sequence of the human diphtheria toxin receptor (heparin-binding epidermal growth factor, membrane form). Downstream, there is a rabbit beta-globin stop codon and the polyadenylation signal. http://purl.obolibrary.org/obo/BCGO_9000234 C57/CBAJ-TgN(Glucagon- rtTA)Ugfm mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain C57/CBAJ-TgN(Glucagon- rtTA)Ugfm A mouse strain containing a transgene in which rtTA (transgene) is driven by the Gcg promoter (NCBI Gene ID: 14526). Transgenic strain (generated by pronuclear microinjection) of a transgene containing the rat glucagon promoter (1.6kb fragment) upstream of the coding region of the reverse transactivator doxycycline-dependent. The rtTA is flanked by a rabbit beta-globin intron and downstream there is a stop and polyA signal from the same rabbit beta-globin gene. http://purl.obolibrary.org/obo/BCGO_9000235 C57/CBAJ-Tg(Ins2- HBEGF){6832Ugfm} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain C57/CBAJ-Tg(Ins2- HBEGF){6832Ugfm} A mouse strain containing a transgene in which DTR (transgene) is driven by the Ins promoter (NCBI Gene ID: 16333). Transgenic mice generated by pronuclear microinjection of a transgene encoding the human diphtheria toxin receptor (heparin binding epidermal growth factor, also termed DTR) under the control of the rat insulin II gene promoter (0.6kb-long fragment). The DTR coding sequence is flanked by the rabbit beta-globin intron and stop/polyA sequences. http://purl.obolibrary.org/obo/BCGO_9000237 FVB/NJ-Tg(MIP-Luc-VU)3Pwrs/J mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain FVB/NJ-Tg(MIP-Luc-VU)3Pwrs/J A mouse strain containing a transgene in which Luc (transgene) is driven by the MIP promoter (NCBI Gene ID: 16333). We generated a transgenic mouse expressing the luciferase optical reporter under control of the mouse insulin I promoter (MIP-Luc-VU) and characterized this model in mice with increased or decreased beta-cell mass and after islet transplantation. MIP-Luc-VU mice emitted strong and consistent bioluminescence emanating exclusively from beta-cells of the pancreatic islet. MIP-Luc-VU islets had normal islet architecture and secreted insulin normally in vivo and in vitro. By tracking changes in β cell mass using bioluminescence imaging (BLI) and post-mortem metrics, streptozotocin-induced, diabetic MIP-Luc-VU mice had a progressive decline in bioluminescence that correlated with a decrease in pancreatic insulin content and beta-cell mass. MIP-Luc-VU animals fed a high fat diet displayed a progressive increase in bioluminescence that reflected an immunohistochemically verified increase in beta-cell mass. MIP-Luc-VU islets transplanted beneath the renal capsule or into the liver emitted bioluminescence proportional to the number of islets transplanted and graft insulin content and could be imaged for more than a year. Since bioluminescence in the MIP-Luc-VU mouse model is proportional to beta-cell mass in the setting of increased and decreased beta-cell mass and after transplantation, this approach should be useful for non-invasively assessing beta-cell mass in pre-clinical mouse models of glucose homeostasis, beta-cell growth and regeneration, and diabetes. http://purl.obolibrary.org/obo/BCGO_9000238 Gt(ROSA)26Sor{tm1(Myt1*)Hri} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Gt(ROSA)26Sor{tm1(Myt1*)Hri} A mouse strain in which the targeted gene, ROSA26 (NCBI Gene ID: 14910), has been modified (allele type: Conditional Activating) to ROSA26-loxp-STOP-loxp-Myt1 (MGI ID: Not yet available). Targeted insertion of a LoxP-STOP-LoxP-Myt1 casette into the ROSA26 locus. The presence of Cre recombinase will lead to activation of the 7 zinc finger isoform of Myt1. http://purl.obolibrary.org/obo/BCGO_9000239 Ngn3{tm1(tTA)Hri} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Ngn3{tm1(tTA)Hri} A mouse strain in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Gene Replacement) to Ngn3 tTA knockin (MGI ID: Ngn3tTA). The mouse contains a Ngn3 knock-in allele. IRES-tTA-rabbit beta globin polyA signal replaced the entire Ngn3 cDNA coding sequence. This is therefore also a Ngn3 null allele. Ngn3 is a bHLH transcription factor that is required for the differentiation of endocrine islet and some neuronal cells. http://purl.obolibrary.org/obo/BCGO_9000240 Nkx2-2{tm1Suss} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Nkx2-2{tm1Suss} A mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2:LacZ using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). The lacZ gene has been knocked in to the Nkx2.2 genomic locus using RMCE, effectively replacing the two coding exons. http://purl.obolibrary.org/obo/BCGO_9000241 Nkx2-2{tm4Suss} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Nkx2-2{tm4Suss} A mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2-NK2 mutation using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). The strain carries a mutant Nkx2.2 allele in which conserved residues of the NK2 domain are mutated to alanines. http://purl.obolibrary.org/obo/BCGO_9000242 Pdx1{tm6Cvw} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Pdx1{tm6Cvw} A mouse strain in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{AIId} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). This is a targeted deletion of Area II 5' cis-regulatory region of Pdx1. http://purl.obolibrary.org/obo/BCGO_9000243 Pdx1{tm4Cvw} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Pdx1{tm4Cvw} A mouse strain in which the targeted gene, Pancreatic and Duodenal homeobox 1 (NCBI Gene ID: 18609), has been modified (allele type: Conditional Null) to targeted mutation 4 (MGI ID: Pdx1{tm4(E2)}). This is a conditional null allele of Pdx1. LoxP sites for Cre recombinase were inserted to flank exon 2 of the gene. http://purl.obolibrary.org/obo/BCGO_9000244 Ptf1a{tm2(cre/ESR1)Cvw} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Ptf1a{tm2(cre/ESR1)Cvw} A mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{tm2(cre/ESR1)} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). CreER knock-in into Ptf1a locus replacing part of the exon1 at the translation initiator ATG position using RMCE method. http://purl.obolibrary.org/obo/BCGO_9000245 Pdx1{tm5Cvw} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Pdx1{tm5Cvw} A mouse strain in which the targeted gene, Pancreatic and Duodenal homeobox 1 (NCBI Gene ID: 18609), has been modified (allele type: Other) to targeted mutation 5 (MGI ID: Pdx1{tm5(AI-II-III)}). LoxP sites for cre recombinase were inserted to flank Area I-II-III, a conserved 5' cis-regulatory region of Pdx1. This allele was shown to be a conditional hypomorph by Fujitani et al. (2006) (PMID 16418487). Pdx1{tm3Cvw} (Pdx1{deltaI-II-III}) is generated by Cre-mediated recombination in the germline of this allele. http://purl.obolibrary.org/obo/BCGO_9000246 Dll1{tm1Hri} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Dll1{tm1Hri} A mouse strain in which the targeted gene, Delta-like 1 (NCBI Gene ID: 13388), has been modified (allele type: Conditional Null) to targeted mutation 1 (MGI ID: Dll1{tm1Hri}). This is a targeted mutation of the Notch ligand Dll1, introducing two loxP sites flanking the exons encoding the DSL domain. http://purl.obolibrary.org/obo/BCGO_9000247 Pdx1{tm3Cvw} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Pdx1{tm3Cvw} A mouse strain in which the targeted gene, Pancreatic and Duodenal homeobox 1 (NCBI Gene ID: 18609), has been modified (allele type: Global Mutation) to targeted mutation 3 (MGI ID: Pdx1{tm3(deltaI-II-III)). Area I-II-III, a conserved 5' cis-regulatory region of Pdx1, was removed by Cre mediated recombination in the germline of Pdx1{tm5Cvw} (Pdx1{Flox123}) by crossing to deleter Cre mice. This allele was shown to be a hypomorph. http://purl.obolibrary.org/obo/BCGO_9000248 Ptf1a{tm3Cvw} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Ptf1a{tm3Cvw} A mouse strain in which the targeted gene, Pancreas Specific Transcription Factor, 1a (NCBI Gene ID: 19213), has been modified (allele type: Cassette Acceptor) to Targeted Mutation 3 (MGI ID: Ptf1a{tm3Cvw}). This mouse strain is a conditional null allele of Ptf1a. LoxP sites flanking exon 1 and 2 (entire coding region of Ptf1a). http://purl.obolibrary.org/obo/BCGO_9000661 Insm1{tm1.1Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Insm1{tm1.1Mgn} A mouse strain in which part or all of the targeted gene, insulinoma-associated 1 (NCBI Gene ID: 53626) is replaced to create Insm1{tm1.1(GFP-Cre)} using the Loxed Cassette Acceptor allele Insm1{tm1(LCA)}).

Insm1{GFPCre} mice contain a GFP-Cre fusion protein which replaces the Insm1 coding sequence. These mice express green fluorescent protein (GFP) under control of theInsm1gene locus. Insm1 is expressed in pancreatic primordium starting at E9.5. Insm1 is also expressed in neural precursor cells and tumors of may be used for lineage tracing of Insm1-positive cells in both wild-type and Insm1-null mice.

http://purl.obolibrary.org/obo/BCGO_9000842 Gt(ROSA)26Sor{tm1(GCK*)Ydor} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Gt(ROSA)26Sor{tm1(GCK*)Ydor} A mouse strain containing a transgene in which GCK (transgene) is driven by the ROSA26 promoter (NCBI Gene ID: 14910). Glucokinase containing the Y214C activating mutation, causing severe persistent hyperinsulinemic hypoglycemia (Diabetes 53:2164-2168, 2004) was targeted to the ROSA26 locus, preceded by a lox-stop-lox sequence and followed by IRES-EGFP. http://purl.obolibrary.org/obo/BCGO_9001001 Ptf1a{tm3Macd} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Ptf1a{tm3Macd} A mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{tm3Macd} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). Modified allele of Ptf1a with a biotinylation Tag sequence attached to the amino terminus of Ptf1a. http://purl.obolibrary.org/obo/BCGO_9001101 Sox17{tm1.2Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Sox17{tm1.2Mgn} A mouse strain in which part or all of the targeted gene, SRY-box containing gene 17 (NCBI Gene ID: 20671) is replaced to create Sox17{CreERT2} using the Loxed Cassette Acceptor allele Sox17{tm1(LCA)}). Sox17{CreERT2} mice may be used either to track Sox17-expressing cells or their progeny or to conditionally inactivate genes in Sox17-expressing cells at specific time points by tamoxifen injection. This line is complementary to Sox17-CreGFP and may avoid possible interferences of expression in the extra-embryonic visceral endoderm. We plan to analyze the effects of a direct activation/deletion of the Wnt pathway in the endoderm by crossing the Sox17-CreERT2 with the gain- and loss-of-function of beta-catenin. http://purl.obolibrary.org/obo/BCGO_9001241 Rosa26{tm1.1(R26-60-DR5-TA-Cerulean)Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Rosa26{tm1.1(R26-60-DR5-TA-Cerulean)Mgn} A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{tm1.1(R26-DR5-TA-Cerulean)} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). These mice were generated using RMCE to insert an exchange vector containing a modified Rosa26 promoter linked to a Cerulean fluorescent protein (CFP) reporter gene into mESCs containing a Loxed Cassette Acceptor (LCA) allele within the Rosa26 gene locus. The Rosa26 promoter in this mouse was altered by replacing DNA sequences from -60 to +81 with a multimerized retinoic acid response element (DR5) fused to a TATA box. This mouse will facilitate studies of retinoic acid signaling in an intact animal. http://purl.obolibrary.org/obo/BCGO_9001261 NOD.Cg-Rag1{tm1Mom}Ins2{Akita}Il2rg{tm1Wjl}/Sz mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain NOD.Cg-Rag1{tm1Mom}Ins2{Akita}Il2rg{tm1Wjl}/Sz A mouse strain in which the targeted gene, recombination activating gene 1 (NCBI Gene ID: 19373), has been modified (allele type: Global Null) to (MGI ID: Rag1{tm1Mom}). Backcrossing of the Rag1 null allele onto the NOD/Lt strain background (NOD-Rag1{null} mice) provided a radio-resistant and longer-lived model for human-cell engraftment. Mutations in X-chromosome-linked Il2rg gene cause X-linked severe combined immunodeficiency (XSCID). Immunodeficient NOD-Rag1{null} IL2rg nullmice tolerated much higher levels of irradiation conditioning than did NOD-Prkdcscid IL2rg{null} mice. This immunodeficient mouse also develops spontaneous hyperglycemia based on the Ins2{Akita} mutation. http://purl.obolibrary.org/obo/BCGO_9001262 NOD.Cg-Prkdc{scid}Il2rg{tm1Wjl}/Sz mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain NOD.Cg-Prkdc{scid}Il2rg{tm1Wjl}/Sz A mouse strain in which the targeted gene, interleukin 2 receptor, gamma chain (NCBI Gene ID: 16186), has been modified (allele type: Global Null) to targeted mutation 1 (MGI ID: Il2rg{tm1Wjl}). NOD-scid IL2rg{null} mice are deficient in mature lymphocytes and NK cells, survive beyond 16-month of age, and even after sublethal irradiation resist lymphoma development. Moreover, cytokine-mobilized human peripheral blood stem cells engraft at high levels in NOD-scid IL2rg{null} mice and develop into human CD3+CD4+ and CD3+CD8+ T cells, Ig+B cells, myeloid cells, NK cells and plasmacytoid dentritic cells. http://purl.obolibrary.org/obo/BCGO_9001281 Rosa26{tm1.2(R26-228-DR5-TA-Cerulean)Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Rosa26{tm1.2(R26-228-DR5-TA-Cerulean)Mgn} A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{tm1.2((R26-228-DR5-Cerulean) using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). These mice were generated using RMCE to insert an exchange vector containing a modified Rosa26 promoter linked to a Cerulean fluorescent protein (CFP) reporter gene into mESCs containing a Loxed Cassette Acceptor (LCA) allele within the Rosa26 gene locus. The Rosa26 promoter in this mouse was altered by replacing DNA sequences from -228 to +81 with a multimerized retinoic acid response element (DR5) fused to a TATA box. This mouse will facilitate studies of retinoic acid signaling in an intact animal. http://purl.obolibrary.org/obo/BCGO_9001321 Nkx2-2{tm5(null)Suss} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Nkx2-2{tm5(null)Suss} A mouse strain in which the targeted gene, Nkx2.2 (NCBI Gene ID: 18088), has been modified (allele type: Global Null) to Null (MGI ID: Nkx2.2{tm5(null)}). These mice contain a deletion of the Nkx2.2 coding region to create a null allele. http://purl.obolibrary.org/obo/BCGO_9001342 Nkx6-1{tm2(flox)Msan} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Nkx6-1{tm2(flox)Msan} A mouse strain in which the targeted gene, Nk6 Homeobox 1 (NCBI Gene ID: 18096), has been modified (allele type: Conditional Null) to targeted mutation 1.1 (MGI ID: Nkx6.1{tm1.1Msan}). A conditional allele for nkx6.1 is necessary to study the function of Nkx6.1 in adult mice. A homozygous nkx6.1 null allele results in neonatal lethality due to a paralytic state, which is a direct result of Nkx6.1 function in the development of motor neurons. Conditional loss of Nkx6.1 is achieved through Cre mediated recombination of a floxed exon II of nkx6.1. Our use for a conditional nkx6.1 allele is to study its function in beta cells of the adult pancreas. http://purl.obolibrary.org/obo/BCGO_9001421 NOD.Cg-Rag1{tm1Mom}Prf1{tm1Sdz}/SzJ mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain NOD.Cg-Rag1{tm1Mom}Prf1{tm1Sdz}/SzJ A mouse strain in which the targeted gene, Perforin 1 (Pore forming protein) (NCBI Gene ID: 18646), has been modified (allele type: Global Null) to (MGI ID: ). Mice that are homozygous for both targeted mutations are viable, fertile, normal in size and do not display any gross physical or behavioral abnormalities when housed under specific pathogen free conditions. These double homozygote mutant mice have no mature T or B lymphocytes, no detectable NK cell cytotoxic activity, and lack serum immunoglobulin. The number of nucleated spleen cells is significantly reduced in double mutant mice, when compared to the single homozygote, NOD.129S7(B6)-Rag1tm1Mom/J (Stock No. 003729). Although an increased number of DX5+CD122+ NK cells are found in the spleens of double mutants, these NK cells have impaired cytotoxic activity. The disruption of Prf1 ablates NK cell cytotoxic activity resulting in increased engraftment levels over that observed with Stock No. 003729. All mutant mice develop thymic lymphomas. This double mutant mouse strain may be useful in studies involving engraftment of human hematolymphoid cells. http://purl.obolibrary.org/obo/BCGO_9001701 Foxo1{tm1(DBD)Dac} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Foxo1{tm1(DBD)Dac} A mouse strain in which part or all of the targeted gene, forkhead box O1 (NCBI Gene ID: 56458) is replaced to create Foxo1{DBD} using the Loxed Cassette Acceptor allele Foxo1{tm1(LCA)}).

This line contains a DNA binding-deficient mutant of Foxo1. The mutation may be useful for assessing the contribution of DNA co-activation in the function of Foxo1.

http://purl.obolibrary.org/obo/BCGO_9002061 Foxo1{tm1(GFP)Dac} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Foxo1{tm1(GFP)Dac} A mouse strain in which part or all of the targeted gene, forkhead box O1 (NCBI Gene ID: 56458) is replaced to create Foxo1{GFP} using the Loxed Cassette Acceptor allele Foxo1{tm1(LCA)}). A GFP cDNA has been knocked into the Foxo1 locus at the 3' end of the endogenous Foxo1 cDNA to generate a Foxo1-gfp fusion protein that can be used to study Foxo1 translocation in vivo. http://purl.obolibrary.org/obo/BCGO_9002301 Neurog3{tm1.1(nCre)Ggu} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Neurog3{tm1.1(nCre)Ggu} A mouse strain in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Gene Replacement) to Ngn3{nCre} (MGI ID: Neurog3{nCre}). A nCre-iRES (n-terminal half of Cre followed by internal ribosomal entry site) was inserted after Ngn3ATG. This allele is confirmed to express both nCre and Ngn3 (no visible phenotype in homozygous animals). http://purl.obolibrary.org/obo/BCGO_9002582 Rosa26{(Ngn3.CFP)Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Rosa26{(Ngn3.CFP)Mgn} A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{Ngn3-CFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse contains a bidirectional TetO-regulated fusion gene that has been inserted into a disabled Rosa26 locus. In one direction the tetO/CMV promoter drives expression of CFP (Cerulean). In the other direction it drives Ngn3. Mice containing this allelecan be used to drive the expression of Ngn3 under control of both doxycycline and either an rtTA or tTA transgene. http://purl.obolibrary.org/obo/BCGO_9002702 Rosa26{tm1.4(MafA-Cherry)Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Rosa26{tm1.4(MafA-Cherry)Mgn} A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{MafA-Cherry} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse contains a bidirectional Tet0-regulated fusion gene that has been inserted into adisabled Rosa26 loxed cassette acceptor allele by RMCE. In one direction the tetO/CMV promoter drives expression of a red fluorescent protein (Cherry) while in the other direction it drives MafA expression. http://purl.obolibrary.org/obo/BCGO_9003042 ROSA26{(Nkx2.2.CFP)Suss} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain ROSA26{(Nkx2.2.CFP)Suss} A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{Nkx2.2/CFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In this strain both CFP and myc-tagged Nkx2.2 were inserted into a ROSA26 LCA allele under control of a bidirectional tetO/CMV promoter element. The mouse line will allow us to explore the contribution of Nkx2.2 to progenitor cell population competency by allowing for the manipulation of Nkx2.2 gene expression within the developing pancreas. http://purl.obolibrary.org/obo/BCGO_9004012 Rosa26{(-60.IBRE4.TACerulean)Hri} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Rosa26{(-60.IBRE4.TACerulean)Hri} A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{tm2.1(R26-60-IBRE4-TA-Cerulean)} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse contains aBMP reporter element withina modified ROSA26 promoter followed by a CFP reporter. This mouse is identical to the -228 variant except for the amount of ROSA26 DNA. http://purl.obolibrary.org/obo/BCGO_9004020 Rosa26{tm2Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Rosa26{tm2Mgn} A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{EN-Cherry-Neo} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line expresses mCherry, a red fluorescent protein, under control of the endogenous ROSA26 gene locus. This mouse was generated as part of a study to identify the optimal combination of regulatory elements for fluorescent protein expression from a single gene copy. http://purl.obolibrary.org/obo/BCGO_9004021 Ptf1a{tm2(rtTA)Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Ptf1a{tm2(rtTA)Mgn} A mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{tm1.2(rtTA)Mgn} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). This mouse line expresses the reverse tetracycline transactivator (rtTA) under control of the Ptf1a regulatory sequences. This mouseisuseful for activating expression of various TetO-regulated genes in sites where Ptf1a is normally expressed. http://purl.obolibrary.org/obo/BCGO_9004022 Rosa26{(Nepn.Cherry)Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Rosa26{(Nepn.Cherry)Mgn} A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26[Nepn.Cherry] using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). Nephrocan (Nepn) has been shown to be expressed specifically during early endoderm development. A Nepn promoter driven reporter (Cherry) has been inserted in the Rosa26LCA locus by recombinase mediated cassette exchange. This mouse line will be useful in visualizing whether Nepn can be used as a specific DE marker for beta-cell development. http://purl.obolibrary.org/obo/BCGO_9004025 Rosa26{(mlre1.WT.Cherry)Fpa} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Rosa26{(mlre1.WT.Cherry)Fpa} A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{mlre1.WT-Cherry} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line contains a bidirectional Tet0-regulated fusion gene that has been inserted into a disabled Rosa26 loxed cassette acceptor allele by RMCE. In one direction the tetO/CMV promoter drives expression of a red fluorescent protein (Cherry) while in the other direction it drives a wild type mlre1. mlre1 is an endoplasmic reticulum (ER) membrane kinase response to unfolded protein response (UPR). Activated mlre1 endonucleases leads to the splicing of XBP-1 (a transcription factor which is upregulated in times of ER stress) which transcriptionally increases the expression of ER chaperones and alleviates UPR. These mice may be useful for studying the role of mlre1 in the response to ER stress in the setting of diet induced obesity and insulin resistance. http://purl.obolibrary.org/obo/BCGO_9004026 Rosa26{(mlre1.IG.Cherry)Fpa} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Rosa26{(mlre1.IG.Cherry)Fpa} A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{mlre1.IG-Cherry} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line contains a bidirectional Tet0-regulated fusion gene that has been inserted into a disabled Rosa26 loxed cassette acceptor allele by RMCE. In one direction the tetO/CMV promoter drives expression of a red fluorescent protein (Cherry) while in the other direction it drives a mutant mlre1. mlre1 is an endoplasmic reticulum (ER) membrane kinase response to unfolded protein response (UPR). Activated mlre1 endonucleases leads to the splicing of XBP-1 (a transcription factor which is upregulated in times of ER stress) which transcriptionally increases the expression of ER chaperones and alleviates UPR. These mice may be usefulfor studying the role of mlre1 in the response to ER stress in the setting of diet induced obesity and insulin resistance. http://purl.obolibrary.org/obo/BCGO_9004027 Rosa26{(R26-228-IBRE4-TA-Cerulean)Hri} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Rosa26{(R26-228-IBRE4-TA-Cerulean)Hri} A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{R26-228-IBRE4-TA-Cerulean} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). These mice were generated by performing recombinase mediated cassette exchange on the Rosa26 LCA. The sequence from -228 to +81 of the Rosa26 gene was replaced with a BMP responsive element (IBRE4) fused to a TATA-Cerulean (CFP) reporter. These mice may be useful in visualizing BMP responsiveness. http://purl.obolibrary.org/obo/BCGO_9004030 Rosa26{(TetO.Sox9)Msan} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Rosa26{(TetO.Sox9)Msan} A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Sox9 using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line contains bidirectional TetO-regulated genes inserted into the Rosa26{LCA} allele by RMCE. In one direction, the TetO/CMV promoter drives the expression of the transcription factor Sox9. In the other direction, it drives the expression of the red fluorescent protein mCherry. In this mouse line, when the effector protein rtTA is expressed, Sox9 and mCherry will be over-expressed simultaneously upon administration of doxycyline. http://purl.obolibrary.org/obo/BCGO_9004054 Rosa26{tm3Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Rosa26{tm3Mgn} A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create CFP using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line was made by RMCE in the Rosa26[LCA] allele and has a cyan fluorescent protein (CFP, Cerulean) expressed under the control of the ROSA26 promoter. The CFP sequence is preceded by a translational enhancer and followed by intron-containing rabbit beta-globin polyA sequences. This mouse has ubiquitously expressed CFP protein and can be used for transplantation and other experiments where tracing of source cells is required. http://purl.obolibrary.org/obo/BCGO_9004055 Rosa26{tm4Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Rosa26{tm4Mgn} A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create YFP using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line was made by RMCE in the Rosa26[LCA] allele and has yellow fluorescent protein (YFP, Citrine) expressed under control of the ROSA26 promoter. The YFP sequence is preceded by a translational enhancer and followed by intron-containing rabbit beta-globin polyA sequences. This mouse has ubiquitously expressed YFP protein and can be used for transplantation and other experiments where tracing of source cells is required. http://purl.obolibrary.org/obo/BCGO_9004058 Pdx1{(H2B.Apple)Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Pdx1{(H2B.Apple)Mgn} A mouse strain in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{H2B.Apple} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). This mouse contains a coding sequence for the mApple-H2B fusion protein in order to tag cells expressing Pdx1 with a red fluorescent protein. The generation of a Pdx-1 red fluorescent marker will enable the isolation of pancreatic lineage progenitors by FACS. The presence of the H2B sequences may also be useful in allowing the plane of cell division to be analyzed. http://purl.obolibrary.org/obo/BCGO_9004062 Rosa26{(Pdx1.YFP)Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Rosa26{(Pdx1.YFP)Mgn} A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Pdx1/YFP using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line contains bidirectional TetO-regulated genes inserted into the Rosa26[LCA] allele by RMCE. In one direction, the TetO/CMV promoter will drive expression of Pdx1. In the other direction, it will drive the expression of yellow fluorescent protein (YFP). In this mouse line, when the effector protein rtTA is expressed, Pdx1 and YFP will be over-expressed simultaneously upon administration of doxycyline. http://purl.obolibrary.org/obo/BCGO_9004075 Rosa26{(3TF.Cherry)Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Rosa26{(3TF.Cherry)Mgn} A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create mCherry/MafA/Pdx1/Ngn3 using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line contains bidirectional TetO-regulated genes inserted into the Rosa26[LCA] by RMCE. In one direction, the TetO/CMV promoter drives expression of a polycistronic mRNA with transcription factors MafA, Pdx1, and Ngn3 linked by 2A peptide cleavage sequences. In the other direction, it drives the expression of red fluorescent protein mCherry. In this mouse line, when the effector protein rtTA is expressed, all three transcription factors and mCherry will be over-expressed simultaneously upon administration of doxycyline. http://purl.obolibrary.org/obo/BCGO_9004077 Pdx1{(AIVd)Rwst} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Pdx1{(AIVd)Rwst} A mouse strain in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{area IV deletion} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this mouse line, Area IV of the Pdx1 enhancer (-2168/-1913 relative to the primary transcription start site) was deleted using RMCE in the Pdx1[LCA] allele. This mouse line allows for assessment of the role of these DNA sequences in the regulation and function of Pdx1. http://purl.obolibrary.org/obo/BCGO_9004079 Nkx2.2{(Cre-Knock-in)} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Nkx2.2{(Cre-Knock-in)} A mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{Cre-knock-in)} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this mouse line, one of the two bi-partite Cre molecules, cCre, together with the IRES sequence was knocked into the site directly upstream of the Nkx2.2 start codon using RMCE in the Nkx2.2[LCA] allele. The presence of the IRES sequence allows for transcription of cCre and Nkx2.2 from the native Nkx2.2 locus at the same time. This mouse line allows the labeling of pancreatic epithelium cells that co-express high levels of Ngn3 and Nkx2.2 during mouse embryonic development. http://purl.obolibrary.org/obo/BCGO_9004086 Nkx2.2{(3XHA.Nkx2.2)Suss} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Nkx2.2{(3XHA.Nkx2.2)Suss} A mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{3XHA-Nkx2.2} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this mouse line, RMCE in the Nkx2.2{LCA} allele was used to introduce a triple HA tag in frame at the N-terminus of the transcription factor Nkx2.2. This allows for efficient immunoprecipitation of HA-tagged Nkx2.2 protein from mouse tissues to perform ChIP and protein-protein interaction studies. http://purl.obolibrary.org/obo/BCGO_9004088 Pdx1{(Cre-ER)} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Pdx1{(Cre-ER)} A mouse strain in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1/cre-ER using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this mouse line, the first exon of the transcription factor Pdx1 was replaced with the coding sequence for a Cre-ER fusion protein using RMCE in the Pdx1[LCA] allele. Pdx1-promoter driven Cre-ER expressing mice enable tamoxifen-inducible Cre-LoxP manipulation of pancreatic lineage cells. http://purl.obolibrary.org/obo/BCGO_9004142 NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl}/SzJ mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl}/SzJ A mouse strain in which the targeted gene, protein kinase, DNA activated, catalytic polypeptide (NCBI Gene ID: 19090), has been modified (allele type: Other) to severe combined immunodeficiency (MGI ID: Prkdc{scid}). The NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mice, commonly known as NOD scid gamma (NSG), do not express the Prkdc gene nor the X-linked Il2rg gene. NSG mice are viable, fertile, normal in size and do not display any gross physical or behavioral abnormalities. Histological examination of lymphoid tissues reveals absence of lymphoid cells and some cystic structures in the thymus, an absence of follicles in the spleen and markedly diminished celluarity of lymph nodes. NSG mice are deficient in mature lymphocytes, serum Ig is not detectable and natural killer (NK) cell cytotoxic activity is extremely low. These mice are resistant to lymphoma development even after sublethal irradiation treatment. These mutant mice have been shown to readily support engraftment of human CD34+ hematopoietic stem cells and represent a superior, long-lived model suitable for studies employing xenotransplantation strategies. Please note that the NSG carries the true null interleukin-2 receptor gamma chain mutation and should not be confused with other strains that express a truncated interleukin-2 receptor gamma chain as described in: "Modulation of hematopoiesis in mice with a truncated mutant of the interleukin-2 receptor gamma chain". http://purl.obolibrary.org/obo/BCGO_9004143 NOD.Cg-Rag1{tm1Mom}Ins2{Akita}Il2rg{tm1Wjl}/SzJ mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain NOD.Cg-Rag1{tm1Mom}Ins2{Akita}Il2rg{tm1Wjl}/SzJ A mouse strain in which the targeted gene, insulin II (NCBI Gene ID: 16334), has been modified (allele type: Other) to Akita (MGI ID: Ins2{Akita}). NRG-Akita mice, which are homozygous for the Rag1tm1Mom and the Il2rgtm1Wjl alleles (males are hemizygous for the X-linked Il2rgtm1Wjl allele) and heterozygous for the Ins2Akita allele, develop spontaneous hyperglycermia. No mature T, B or NK cells are detected in flow cytometric analysis of splenocytes from NRG-Akita mutant mice. Granulocyte and macrophage populations are similar to those seen in NRG mice. NRG-Akita mice develop hyperglycemia between 3 and 5 weeks of age. Histological examination at 3 weeks of age reveals normal pancreas morphology, and routine insulin and glucagon staining. By approximately 32 weeks of age, NRG-Akita mice display disorganized, condensed pancreatic islet architecture, with loss of insulin-positive cells. Euglycemia is restored by subrenal transplantation of mouse or human islets or intrapancreatic transplantation of dissociated mouse islet cells. NRG-Akita mice engrafted with human hematopoietic stem cells (HSC) develop humanized immune systems. Approximately 60% of the human HSC engrafted NRG-Akita mice reject human islet allografts. http://purl.obolibrary.org/obo/BCGO_9004145 Ngn3{(HA.LCA)} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Ngn3{(HA.LCA)} A mouse strain in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Cassette Acceptor) to (MGI ID: ). This mouse line was made by gene targeting and designed to express an HA-tagged version of the transcription factor Ngn3. The Lox71 and Lox2272 sites were inserted flanking the Ngn3 coding sequence. Within the flanked region an HA-tag was placed at the N-terminus of the Ngn3 protein. This allele can be used to study chromatin and protein-protein interactions of Ngn3. Additionally, the Lox71 and Lox2272 sites allow for manipulations of the flanked region by RMCE. http://purl.obolibrary.org/obo/BCGO_9004146 Pax4{(HA.LCA)Ggu} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Pax4{(HA.LCA)Ggu} A mouse strain in which the targeted gene, paired box 4 (NCBI Gene ID: 18506), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Pax4{tm1(LCA)Ggu}). This mouse line was made by gene targeting and designed to express an HA-tagged version of the transcription factor Pax4. The Lox71 and Lox2272 sites were inserted flanking the last coding exon of the Pax4 gene. Within the flanked region an HA-tag was placed at the C-terminus of the PAX4 protein. This allele can be used to study chromatin and protein-protein interactions of PAX4. Additionally, the Lox71 and Lox2272 sites allow for manipulations of the flanked region by RMCE in the future. http://purl.obolibrary.org/obo/BCGO_9004147 Rosa26{(Setd5.GFP)Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Rosa26{(Setd5.GFP)Mgn} A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Setd5/GFP using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line was generated by RMCE in the Rosa26[LCA] allele. A coding sequence for green fluorescent protein (GFP) was inserted into the first exon of the Setd5 gene. This exon is located upstream of the Rosa26 transcribed sequence and is transcribed in an opposite orientation. The GFP-polyA cassette, transcribed from the Setd5 promoter, knocks out Setd5 transcription and provides a reporter for Setd5 gene expression. The purpose of this mouse line is to study the molecular function of the Setd5 gene. http://purl.obolibrary.org/obo/BCGO_9004149 Ptf1a{(tdTomato)} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Ptf1a{(tdTomato)} A mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{td.TOM} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). This mouse cell line was generated by RMCE in the Ptf1a[LCA] allele. Pancreata of this mouse line express both td.Tomato (a red fluorescent protein) and an N-terminal epitope tagged Strep/Flag (NSF) fusion of the transcription factor Ptf1a. This line may be used in a variety of applications such as FACS sorting of Ptf1a expressing cells, chromatin immunoprecipitation, and proteomic analyses. http://purl.obolibrary.org/obo/BCGO_9004150 Nkx2.2{(Cre.EGFP)Suss} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Nkx2.2{(Cre.EGFP)Suss} A mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{Cre-EGFP} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this mouse, a coding portion of the transcription factor Nkx2.2 was replaced with a Cre-EGFP cassette, in frame to the Nkx2.2 ATG. This allows for sites of Nkx2.2 gene expression to be identified in mice using direct immunofluorescence, FACS purification of Nkx2.2 expressing cells, and lineage tracing using Nkx2.2 driven Cre expression. http://purl.obolibrary.org/obo/BCGO_9004152 Rosa26{(TetO.NRSF)Msan} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Rosa26{(TetO.NRSF)Msan} A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create NRSF using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line contains bidirectional TetO-regulated genes inserted into the Rosa26[LCA] allele by RMCE. In one direction, the TetO/CMV promoter drives the expression of the transcription factor NRSF/REST. In the other direction, it drives the expression of red fluorescent protein mCherry. In this mouse line, when the effector protein rtTA is expressed, NRSF and mCherry will be simultaneously over-expressed upon administration of doxycyline. http://purl.obolibrary.org/obo/BCGO_9004153 Gt(ROSA)26Sor{tm2.1(mix1b-mCherry)Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Gt(ROSA)26Sor{tm2.1(mix1b-mCherry)Mgn} A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{(R26-228-AR8-TA-mCherry)} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line was generated by RMCE in the Rosa26[LCA] allele. In this mouse line, the Rosa26 gene sequence (-228 to +81) was replaced by the Foxh1/Smad2-dependent, Mix2-derived Activin response element (AR8) fused to a TATA-mCherry reporter. These mice may be useful to assess Activin, Nodal, and TGFbeta responsiveness. http://purl.obolibrary.org/obo/BCGO_9004278 Ghrl{tm1(Cre-eGFP)Suss} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Ghrl{tm1(Cre-eGFP)Suss} A mouse strain in which part or all of the targeted gene, Ghrelin (NCBI Gene ID: 58991) is replaced to create Ghrl Cre-eGFP CEV using the Loxed Cassette Acceptor allele Ghrl{LCA}). Ghrl{Cre-eGGP} mice contain a Cre-eGFP fusion protein which replaces the Ghrelin coding sequence. These mice expressc Cre-eGFP phusion protein under control of the Ghrelin gene locus. The Ghrl{Cre-eGGP} mice may be used to track ghrelin-expressing cells progeny,or to conditionally inactivate genes in ghrelin-expressing cells. http://purl.obolibrary.org/obo/BCGO_9004533 Pdx1{CreMgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Pdx1{CreMgn} A mouse strain in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{Cre} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this mouse strain, the first exon of Pdx1 is replaced with coding sequence for Cre recombinase using RMCE in the Pdx1{LCA} allele. Generation of Pdx-promoter driven Cre expressing mice will enable Cre-LoxP manipulation of pancreatic lineage cells. http://purl.obolibrary.org/obo/BCGO_9004534 Rosa26{228.TOP.CFPHri} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Rosa26{228.TOP.CFPHri} A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{228.TOP.CFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In this mouse strain the Rosa26 gene sequence from -228 to +81 was replaced by a Wnt response element (7xTcf/Lef binding site) fused to a TATA-Cerulean (CFP) reporter. These mice may be useful in assessing Canonical Wnt responsiveness. http://purl.obolibrary.org/obo/BCGO_9004537 Rosa26{228.3TF.GFP-CreMgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Rosa26{228.3TF.GFP-CreMgn} A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create ROSA26{228.3TF.GFP-Cre} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse strain contains TetO-regulated genes inserted into the Rosa 26{LCA} allele by RMCE. TetO/miniCMV promoter is placed at -228 position upstream of putative ROSA26 transcription start site and drives the expression of a polycistronic mRNA with transcription factors MafA, Pdx1, and Ngn3 together with GFP-Cre fusion protein linked by 2A peptide cleavage sequences. These mice will be able to simultaneously over-express all three transcription factors and GFP-Cre upon administration of doxycyline when the effector protein rtTA is expressed. http://purl.obolibrary.org/obo/BCGO_9004538 Ngn3{T2A.nCreGgu} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Ngn3{T2A.nCreGgu} A mouse strain in which part or all of the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925) is replaced to create Ngn3{T2A.nCre} using the Loxed Cassette Acceptor allele ). In this mouse line, one of the two bi-partite Cre molecules, nCre, was knocked in upstream of Ngn3 coding sequence by RMCE in Ngn3{HA.LCA} ES cell line. nCre sequence is expressed from policistronic mRNA linked by 2a peptide to Ngn3 coding sequence allowing for simultanious expression of both proteins from the Ngn3 promoter. This mouse line, in combination with Nkx2.2{cCre} mouse line, allows for the labeling of pancreatic epithelium cells that co-express high levels of Ngn3 and Nkx2.2 during mouse embryonic development. http://purl.obolibrary.org/obo/BCGO_9004556 Nkx2.2{T2A.cCreGgu} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Nkx2.2{T2A.cCreGgu} A mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{T2A.cCre} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this line, one of the two bi-partite Cre molecules, cCre, is placed downstream of Nkx2.2 coding sequence fused with 2a peptide using RMCE in the Nkx2.2[LCA] allele. The presence of the T2A sequence allows for transcription of Nkx2.2 and cCre from the native Nkx2.2 locus at the same time. This mouse line allows the labeling of pancreatic epithelium cells that co-express high levels of Ngn3 and Nkx2.2 during mouse embryonic development. http://purl.obolibrary.org/obo/BCGO_9004560 Rosa26{mIre1.N906A.CherryMgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Rosa26{mIre1.N906A.CherryMgn} A mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26.mIre1.N906A.Cherry using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse contains bidirectional TetO-regulated genes inserted into the Rosa26.LCA allele by RMCE. In one direction the TetO/CMV promoter drives the expression of point mutant (N906A) of IRE1, an ER transmembrane kinase response to unfolded protein response (UPR). In the other direction it drives the expression of red fluorescent protein mCherry. This mouse can be used to simultaneously over-express Ire1 (N906A) and mCherry upon administration of doxycyline when the effector protein rtTA is expressed. This line can be used to study the roles of IRE1 in the response to ER stress, diet induced obesity and insulin resistance. http://purl.obolibrary.org/obo/BCGO_9004561 Sst{rTTA.LCA.Mgn} mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain Sst{rTTA.LCA.Mgn} A mouse strain in which the targeted gene, Somatostatin (NCBI Gene ID: 20604), has been modified (allele type: Gene Replacement) to (MGI ID: Sst{rTTA.LCA}). TheSst.rTTA.LCA mice are designed to express a tet-inducible reverse-transactivator under control of somatostatin promoter. Lox66 and Lox2272 sites are inserted flanking 500bp of Sst promoter region, Sst exons I and II and Sst poly A site. The rTTA-beta-globin poly A cassete is put in place of Sst coding exons (I and II). The mice can be used to drive tet-inducible expression in somatostatin expressing cells (Delta-cells). Additionally, the Lox66 and Lox2272 sites allow for manipulations of the flanked region by RMCE in the future. http://purl.obolibrary.org/obo/BCGO_9004611 NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} Tg(HLA-A/H2-D/B2M)1Dvs/SzJ mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} Tg(HLA-A/H2-D/B2M)1Dvs/SzJ A mouse strain that is immunodeficient and express human HLA class 1 heavy and light chains. This strain may be useful as a human hematopoietic engraftment host that supports the maturation of human T cells with transplantation http://jaxmice.jax.org/strain/014570.html. http://purl.obolibrary.org/obo/BCGO_9004612 NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} H2-Ab1{tm1Gru} Tg(HLA-DRB1)31Dmz/SzJ mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} H2-Ab1{tm1Gru} Tg(HLA-DRB1)31Dmz/SzJ A mouse strain that lacks expression of the murine Prkdc gene, the X-linked Il2rg gene, and MHC class II, but express the human leukocyte antigen DR4 gene. These mice may be useful for targeting human CD4{+} T cells in transplantation studies in the absence of xeno-GVHD.More details are available at http://jaxmice.jax.org/strain/017637.html. http://purl.obolibrary.org/obo/OBCS_0000164 Extraction of Differential Gene Expression software http://purl.obolibrary.org/obo/BCGO_0000060 differential expression software EDGE A software that is used for the differential gene expression significance analysis of DNA microarray experiments for both standard and time course experiments. The outputs consist of bothe p-values and q-values. http://purl.obolibrary.org/obo/OBCS_0000165 Patterns from Gene Expression software http://purl.obolibrary.org/obo/BCGO_0000060 differential expression software PaGE A software that can be used to produce lists of differentially expressed genes with confidence measures attached. These lists are generated via a False Discovery Rate (FDR) method of controlling the false positives. Patterns from Gene Expression (PaGE) is more than a differential expression analysis tool. PaGE is a tool to attach descriptive, dependable, and easily interpretable expression patterns to genes across multiple conditions, each represented by a set of replicated array experiments. http://purl.obolibrary.org/obo/OBCS_0000166 GLobal Identifier of Target Regions software http://purl.obolibrary.org/obo/IAO_0000010 software GLITR A software that is used to identify transcription factor binding sites in a genome that have been enriched with aligned reads generated from ChIP-Seq technology. http://purl.obolibrary.org/obo/CHEBI_33261 organosulfur compound http://purl.obolibrary.org/obo/CHEBI_26835 sulfur molecular entity An organosulfur compound is a compound containing at least one carbon-sulfur bond. http://purl.obolibrary.org/obo/CHEBI_38101 organonitrogen heterocyclic compound http://purl.obolibrary.org/obo/CHEBI_35352 organonitrogen compound Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms. http://purl.obolibrary.org/obo/CHEBI_5686 heterocyclic compound http://purl.obolibrary.org/obo/CHEBI_33595 cyclic compound A cyclic compound having as ring members atoms of at least two different elements. http://purl.obolibrary.org/obo/CHEBI_25367 molecule http://purl.obolibrary.org/obo/CHEBI_36357 polyatomic entity Any polyatomic entity that is an electrically neutral entity consisting of more than one atom. http://purl.obolibrary.org/obo/CHEBI_61120 nucleobase-containing molecular entity http://purl.obolibrary.org/obo/CHEBI_33833 heteroarene Any compound that has a nucleobase as a part. http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity http://purl.obolibrary.org/obo/CHEBI_24431 chemical entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. http://purl.obolibrary.org/obo/CHEBI_24431 chemical entity http://purl.obolibrary.org/obo/BFO_0000040 material entity A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. http://purl.obolibrary.org/obo/CHEBI_24532 organic heterocyclic compound http://purl.obolibrary.org/obo/CHEBI_33832 organic cyclic compound A cyclic compound having as ring members atoms of carbon and at least of one other element. http://purl.obolibrary.org/obo/CHEBI_24651 hydroxides http://purl.obolibrary.org/obo/CHEBI_33579 main group molecular entity Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)). http://purl.obolibrary.org/obo/CHEBI_24870 ion http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity A molecular entity having a net electric charge. http://purl.obolibrary.org/obo/CHEBI_25741 oxide http://purl.obolibrary.org/obo/CHEBI_37577 heteroatomic molecular entity An oxide is a chemical compound of oxygen with other chemical elements. http://purl.obolibrary.org/obo/CHEBI_28659 phosphorus atom http://purl.obolibrary.org/obo/CHEBI_33318 main group element atom A pnictogen that has formula P. http://purl.obolibrary.org/obo/CHEBI_33250 atom http://purl.obolibrary.org/obo/CHEBI_24431 chemical entity A chemical entity constituting the smallest component of an element having the chemical properties of the element. http://purl.obolibrary.org/obo/CHEBI_33285 heteroorganic entity http://purl.obolibrary.org/obo/CHEBI_50860 organic molecular entity A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms. http://purl.obolibrary.org/obo/CHEBI_33304 chalcogen molecular entity http://purl.obolibrary.org/obo/CHEBI_33675 p-block molecular entity Any p-block molecular entity containing a chalcogen. http://purl.obolibrary.org/obo/CHEBI_33318 main group element atom http://purl.obolibrary.org/obo/CHEBI_33250 atom An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table. http://purl.obolibrary.org/obo/CHEBI_33675 p-block molecular entity http://purl.obolibrary.org/obo/CHEBI_33579 main group molecular entity A p-block molecular entity is a molecular entity containing one or more atoms of a p-block element. http://purl.obolibrary.org/obo/CHEBI_33832 organic cyclic compound http://purl.obolibrary.org/obo/CHEBI_33595 cyclic compound Any organic molecule that consists of atoms connected in the form of a ring. http://purl.obolibrary.org/obo/CHEBI_35406 oxoanion http://purl.obolibrary.org/obo/CHEBI_33273 polyatomic anion An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen. http://purl.obolibrary.org/obo/CHEBI_36357 polyatomic entity http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity Any molecular entity consisting of more than one atom. http://purl.obolibrary.org/obo/CHEBI_36358 polyatomic ion http://purl.obolibrary.org/obo/CHEBI_36357 polyatomic entity An ion consisting of more than one atom. http://purl.obolibrary.org/obo/CHEBI_36962 organochalcogen compound http://purl.obolibrary.org/obo/CHEBI_33304 chalcogen molecular entity An organochalcogen compound is a compound containing at least one carbon-chalcogen bond. http://purl.obolibrary.org/obo/CHEBI_37577 heteroatomic molecular entity http://purl.obolibrary.org/obo/CHEBI_36357 polyatomic entity A molecular entity consisting of two or more chemical elements. http://purl.obolibrary.org/obo/CHEBI_37972 phosphorus-32 atom http://purl.obolibrary.org/obo/CHEBI_28659 phosphorus atom The radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days. http://purl.obolibrary.org/obo/CHEBI_37973 phosphorus-33 atom http://purl.obolibrary.org/obo/CHEBI_28659 phosphorus atom The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2. http://purl.obolibrary.org/obo/CHEBI_38313 diazines http://purl.obolibrary.org/obo/CHEBI_25693 organic heteromonocyclic compound Any organic heterocyclic compound containing a benzene ring in which two of the C-H fragments have been replaced by isolobal nitrogens (the diazine parent structure). http://purl.obolibrary.org/obo/PR_000015424 transcription factor SOX-17 http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human SOX17 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000016043 T-cell acute lymphocytic leukemia protein 1 http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human TAL1 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PATO_0000001 quality http://purl.obolibrary.org/obo/BFO_0000019 quality A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities. http://purl.obolibrary.org/obo/PATO_0000025 composition http://purl.obolibrary.org/obo/PATO_0000141 structure A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts. http://purl.obolibrary.org/obo/PATO_0000033 concentration of http://purl.obolibrary.org/obo/PATO_0002182 molecular quality A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance. http://purl.obolibrary.org/obo/PATO_0000051 morphology http://purl.obolibrary.org/obo/PATO_0001241 physical object quality A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. http://purl.obolibrary.org/obo/PATO_0000052 shape http://purl.obolibrary.org/obo/PATO_0000051 morphology A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). http://purl.obolibrary.org/obo/PATO_0000069 deviation(from_normal) http://purl.obolibrary.org/obo/PATO_0000068 qualitative A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. http://purl.obolibrary.org/obo/PATO_0000117 size http://purl.obolibrary.org/obo/PATO_0000051 morphology A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. http://purl.obolibrary.org/obo/PATO_0000141 structure http://purl.obolibrary.org/obo/PATO_0000051 morphology A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. http://purl.obolibrary.org/obo/PATO_0000165 time http://purl.obolibrary.org/obo/PATO_0001018 physical quality A quality in which events occur in sequence. http://purl.obolibrary.org/obo/PATO_0000169 viability http://purl.obolibrary.org/obo/PATO_0001995 organismal quality An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population. http://purl.obolibrary.org/obo/PATO_0000261 maturity http://purl.obolibrary.org/obo/PATO_0001995 organismal quality A quality of a single physical entity which is held by a bearer when the latter exhibits complete growth, differentiation, or development. http://purl.obolibrary.org/obo/PATO_0000411 circular http://purl.obolibrary.org/obo/PATO_0000947 elliptic A shape quality inhering in a bearer by virtue of the bearer's being such that every part of the surface or the circumference is equidistant from the center. http://purl.obolibrary.org/obo/PATO_0000461 normal http://purl.obolibrary.org/obo/PATO_0000069 deviation(from_normal) A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. http://purl.obolibrary.org/obo/PATO_0000586 increased size http://purl.obolibrary.org/obo/PATO_0002305 increased object quality A size quality which is relatively high. http://purl.obolibrary.org/obo/PATO_0000947 elliptic http://purl.obolibrary.org/obo/PATO_0002318 superelliptic A spheroid quality inhering in a bearer by virtue of the bearer's being oval with two axes of symmetry, as produced by a conical section. 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/PATO_0000001 quality A quality which inheres in a continuant. http://purl.obolibrary.org/obo/PATO_0001335 bacterial mating type http://purl.obolibrary.org/obo/PATO_0001895 mating type A mating type that indicates whether the F plasmid has integrated into the chromosome. http://purl.obolibrary.org/obo/PATO_0001337 yeast mating type http://purl.obolibrary.org/obo/PATO_0001895 mating type A yeast mating type. http://purl.obolibrary.org/obo/PATO_0001342 Saccharomyces cerevisiae mating type http://purl.obolibrary.org/obo/PATO_0001337 yeast mating type A S. cerevisiae mating type. http://purl.obolibrary.org/obo/PATO_0001343 Schizosaccharomyces pombe mating type http://purl.obolibrary.org/obo/PATO_0001337 yeast mating type A S. pombe mating type determined by the gene configuration on the mat1 locus. http://purl.obolibrary.org/obo/PATO_0001393 euploid http://purl.obolibrary.org/obo/PATO_0001374 ploidy A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes. http://purl.obolibrary.org/obo/PATO_0001397 cellular potency http://purl.obolibrary.org/obo/PATO_0001396 cellular quality A cellular quality that arises by virtue of whether the bearer's disposition to differentiate into one or more mature cell types. http://purl.obolibrary.org/obo/PATO_0001400 unipotent http://purl.obolibrary.org/obo/PATO_0001397 cellular potency A cellular potency that is the capacity to produce only one differentiated cell type. http://purl.obolibrary.org/obo/PATO_0001401 oligopotent http://purl.obolibrary.org/obo/PATO_0001397 cellular potency A cellular potency that is the capacity to form multiple differentiated cell types of a specific lineage and lack self renewing capacity. http://purl.obolibrary.org/obo/PATO_0001402 multipotent http://purl.obolibrary.org/obo/PATO_0001397 cellular potency A cellular potency that is the capacity to form multiple differentiated cell types. http://purl.obolibrary.org/obo/PATO_0001404 nucleate quality http://purl.obolibrary.org/obo/PATO_0001396 cellular quality A cellular quality inhering in a bearer by virtue of bearer's number of nuclei. http://purl.obolibrary.org/obo/PATO_0001405 anucleate http://purl.obolibrary.org/obo/PATO_0001404 nucleate quality A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus. http://purl.obolibrary.org/obo/PATO_0001407 mononucleate http://purl.obolibrary.org/obo/PATO_0001404 nucleate quality A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus. http://purl.obolibrary.org/obo/PATO_0001410 striated http://purl.obolibrary.org/obo/PATO_0000052 shape A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel. http://purl.obolibrary.org/obo/PATO_0001501 immature http://purl.obolibrary.org/obo/PATO_0000261 maturity A quality inhering in a bearer by virtue of the bearer's lacking complete growth, differentiation, or development. http://purl.obolibrary.org/obo/PATO_0001701 mature http://purl.obolibrary.org/obo/PATO_0000261 maturity A quality inhering in a bearer by virtue of the bearer's exhibiting complete growth, differentiation, or development. http://purl.obolibrary.org/obo/PATO_0001857 concave http://purl.obolibrary.org/obo/PATO_0002005 concavity A shape quality in a bearer by virtue of the bearer's curving inward. http://purl.obolibrary.org/obo/PATO_0001873 cylindrical http://purl.obolibrary.org/obo/PATO_0002007 convex 3-D shape A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section. http://purl.obolibrary.org/obo/PATO_0001874 discoid http://purl.obolibrary.org/obo/PATO_0001873 cylindrical A shape quality inhering in a bearer by virtue of the bearer's being cylindrical, in which the height is less than the diameter. http://purl.obolibrary.org/obo/PATO_0001895 mating type http://purl.obolibrary.org/obo/PATO_0000047 biological sex A biological sex quality inhering in an individual or a population that undergo sexual reproduction. http://purl.obolibrary.org/obo/PATO_0002003 population quality http://purl.obolibrary.org/obo/PATO_0001241 physical object quality A quality that inheres in an entire population or part of a population. http://purl.obolibrary.org/obo/PATO_0002005 concavity http://purl.obolibrary.org/obo/PATO_0000052 shape Surface shape that refers to the inward or outward curvature of the surface. http://purl.obolibrary.org/obo/PATO_0002006 2-D shape http://purl.obolibrary.org/obo/PATO_0000052 shape A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity. http://purl.obolibrary.org/obo/PATO_0002007 convex 3-D shape http://purl.obolibrary.org/obo/PATO_0002266 3-D shape A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave. http://purl.obolibrary.org/obo/PATO_0002039 biconcave http://purl.obolibrary.org/obo/PATO_0001857 concave A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces. http://purl.obolibrary.org/obo/PATO_0002070 affinity http://purl.obolibrary.org/obo/PATO_0002182 molecular quality A molecular quality that arises from the molecular attraction exerted between two atoms or compounds. http://purl.obolibrary.org/obo/PATO_0002094 basophilic http://purl.obolibrary.org/obo/PATO_0002070 affinity An affinity inhering in a tissue constituent by virtue of the bearer exhibiting a molecular interaction for basic dyes under specific ph conditions. http://purl.obolibrary.org/obo/PATO_0002182 molecular quality http://purl.obolibrary.org/obo/PATO_0001241 physical object quality A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc. http://purl.obolibrary.org/obo/PATO_0002266 3-D shape http://purl.obolibrary.org/obo/PATO_0000052 shape A shape that inheres in a 3 dimensional entity. http://purl.obolibrary.org/obo/PATO_0002300 increased quality http://purl.obolibrary.org/obo/PATO_0000069 deviation(from_normal) A quality that has a value that is increased compared to normal or average. http://purl.obolibrary.org/obo/PATO_0002305 increased object quality http://purl.obolibrary.org/obo/PATO_0002300 increased quality A quality of an object that has a value that is increased compared to normal or average. http://purl.obolibrary.org/obo/PATO_0002318 superelliptic http://purl.obolibrary.org/obo/PATO_0002006 2-D shape A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt http://purl.obolibrary.org/obo/PATO_0002478 transversely striated http://purl.obolibrary.org/obo/PATO_0001410 striated A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel, that are oriented transversely relative to the long axis of the bearer. http://purl.obolibrary.org/obo/UBERON_0000002 uterine cervix http://purl.obolibrary.org/obo/UBERON_0005156 reproductive structure Lower, narrow portion of the uterus where it joins with the top end of the vagina. http://purl.obolibrary.org/obo/UBERON_0000017 exocrine pancreas http://purl.obolibrary.org/obo/UBERON_0004119 endoderm-derived structure The part of the pancreas that is part of the exocrine system and which produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells [GO]. http://purl.obolibrary.org/obo/UBERON_0000033 head http://purl.obolibrary.org/obo/UBERON_0000475 organism subdivision The head is the anterior-most division of the body [GO]. http://purl.obolibrary.org/obo/UBERON_0000473 testis http://purl.obolibrary.org/obo/UBERON_0003133 reproductive organ A gonad of a male animal. A gonad produces and releases sperm. http://purl.obolibrary.org/obo/UBERON_0000947 aorta http://purl.obolibrary.org/obo/UBERON_0003509 arterial blood vessel The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation http://purl.obolibrary.org/obo/UBERON_0000991 gonad http://purl.obolibrary.org/obo/UBERON_0003133 reproductive organ Reproductive organ that produces and releases eggs (ovary) or sperm (testis). http://purl.obolibrary.org/obo/UBERON_0001003 skin epidermis http://purl.obolibrary.org/obo/UBERON_0007376 outer epithelium The outer layer of the skin[WP]. cellular, multilayered epithelium derived from the ectoderm[ZFA]. http://purl.obolibrary.org/obo/UBERON_0001135 smooth muscle tissue http://purl.obolibrary.org/obo/UBERON_0002385 muscle tissue Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO]. Tissue which consists of smooth muscle . Examples: Arrector muscle of hair, Muscularis mucosae. http://purl.obolibrary.org/obo/UBERON_0001156 ascending colon http://purl.obolibrary.org/obo/UBERON_0000168 segment of colon Segment of the colon which is continuous with the cecum proximally and the transverse colon distally.[FMA,modified] http://purl.obolibrary.org/obo/UBERON_0001235 adrenal cortex http://purl.obolibrary.org/obo/UBERON_0004120 mesoderm-derived structure the thick outer layer of the adrenal gland that produces and secretes steroid hormones such as corticosterone, estrone and aldosterone http://purl.obolibrary.org/obo/UBERON_0001264 pancreas http://purl.obolibrary.org/obo/BCGO_0000071 pancreatic material An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]. http://purl.obolibrary.org/obo/UBERON_0001296 myometrium http://purl.obolibrary.org/obo/UBERON_0005156 reproductive structure the smooth muscle coat of the uterus, which forms the main mass of the organ and surrounds and supports the endometrium http://purl.obolibrary.org/obo/UBERON_0001638 vein http://purl.obolibrary.org/obo/UBERON_0001981 blood vessel Any of the tubular branching vessels that carry blood from the capillaries toward the heart. http://purl.obolibrary.org/obo/UBERON_0001684 mandible http://purl.obolibrary.org/obo/UBERON_0004742 dentary A dentary bone that is the only bone in one of the lateral halves of the lower jaw skeleton. http://purl.obolibrary.org/obo/UBERON_0001817 lacrimal gland http://purl.obolibrary.org/obo/UBERON_0019319 exocrine gland of integumental system The lacrimal glands are paired almond-shaped glands, located in or near the orbital region, that secrete the aqueous layer of the tear film.[WP]. http://purl.obolibrary.org/obo/UBERON_0001821 sebaceous gland http://purl.obolibrary.org/obo/UBERON_0019319 exocrine gland of integumental system A holocrine gland that secretes sebum into the hair follicles, or in hairless areas into ducts.[MP]. http://purl.obolibrary.org/obo/UBERON_0001987 placenta http://purl.obolibrary.org/obo/UBERON_0005156 reproductive structure organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell. http://purl.obolibrary.org/obo/UBERON_0002037 cerebellum http://purl.obolibrary.org/obo/UBERON_0010314 structure with developmental contribution from neural crest Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA]. http://purl.obolibrary.org/obo/UBERON_0002285 telencephalic ventricle http://purl.obolibrary.org/obo/UBERON_0010314 structure with developmental contribution from neural crest A brain ventricle that is part of a telencephalon. In mammals and species with an evaginated telencephalon, this is one of a pair of lateral structures, one in each hemisphere http://purl.obolibrary.org/obo/UBERON_0002369 adrenal gland http://purl.obolibrary.org/obo/UBERON_0015212 lateral structure Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. http://purl.obolibrary.org/obo/UBERON_0002371 bone marrow http://purl.obolibrary.org/obo/UBERON_0012429 hemopoietic tissue the soft tissue that fills the cavities of bones http://purl.obolibrary.org/obo/UBERON_0002385 muscle tissue http://purl.obolibrary.org/obo/UBERON_0004120 mesoderm-derived structure Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. http://purl.obolibrary.org/obo/UBERON_0002420 basal ganglion http://purl.obolibrary.org/obo/UBERON_0003528 brain gray matter An individual member of a collection of basal ganglia. Basal ganglia are subcortical masses of gray matter in the forebrain and midbrain that are richly interconnected and so viewed as a functional system. The nuclei usually included are the caudate nucleus (caudoputamen in rodents), putamen, globus pallidus, substantia nigra (pars compacta and pars reticulata) and the subthalamic nucleus. Some also include the nucleus accumbens and ventral pallidum[NIF,modified]. http://purl.obolibrary.org/obo/UBERON_0003129 skull http://purl.obolibrary.org/obo/UBERON_0000477 anatomical cluster Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP]. http://purl.obolibrary.org/obo/UBERON_0004086 brain ventricle http://purl.obolibrary.org/obo/UBERON_0003947 brain ventricle/choroid plexus one of the system of communicating cavities in the brain that are continuous with the central canal of the spinal cord, that like it are derived from the medullary canal of the embryo, that are lined with an epithelial ependyma, and that contain a serous fluid http://purl.obolibrary.org/obo/UBERON_0004363 pharyngeal arch artery http://purl.obolibrary.org/obo/UBERON_0015787 upper respiratory conduit One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP] http://purl.obolibrary.org/obo/UBERON_0007329 pancreatic duct http://purl.obolibrary.org/obo/UBERON_0004119 endoderm-derived structure A duct that is part of the pancreas and connected to the duodenum. http://purl.obolibrary.org/obo/UBERON_0018707 bladder organ http://purl.obolibrary.org/obo/UBERON_0009856 sac A membranous sac in animals that serves as the receptacle of a liquid or contains gas. http://purl.obolibrary.org/obo/BFO_0000002 continuant http://purl.obolibrary.org/obo/BFO_0000001 entity An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. http://purl.obolibrary.org/obo/BFO_0000003 occurrent http://purl.obolibrary.org/obo/BFO_0000001 entity An entity that has temporal parts and that happens, unfolds or develops through time. http://purl.obolibrary.org/obo/BFO_0000004 independent continuant http://purl.obolibrary.org/obo/BFO_0000002 continuant A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. http://purl.obolibrary.org/obo/BFO_0000005 obsolete dependent continuant http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. http://purl.obolibrary.org/obo/BFO_0000015 process http://purl.obolibrary.org/obo/BFO_0000003 occurrent An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. http://purl.obolibrary.org/obo/BFO_0000017 realizable entity http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant http://purl.obolibrary.org/obo/BFO_0000002 continuant b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) http://purl.obolibrary.org/obo/BFO_0000023 role http://purl.obolibrary.org/obo/BFO_0000017 realizable entity A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. http://purl.obolibrary.org/obo/BFO_0000031 generically dependent continuant http://purl.obolibrary.org/obo/BFO_0000002 continuant A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. http://purl.obolibrary.org/obo/BFO_0000035 process boundary http://purl.obolibrary.org/obo/BFO_0000003 occurrent p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) http://purl.obolibrary.org/obo/BFO_0000040 material entity http://purl.obolibrary.org/obo/BFO_0000004 independent continuant An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. http://purl.obolibrary.org/obo/BFO_0000140 continuant fiat boundary http://purl.obolibrary.org/obo/BFO_0000141 immaterial entity b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) http://purl.obolibrary.org/obo/BFO_0000144 process profile http://purl.obolibrary.org/obo/BFO_0000015 process b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) http://purl.obolibrary.org/obo/BFO_0000145 relational quality http://purl.obolibrary.org/obo/BFO_0000019 quality b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) http://purl.obolibrary.org/obo/CLO_0000001 cell line cell http://purl.obolibrary.org/obo/CL_0000010 cultured cell A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture http://purl.obolibrary.org/obo/CLO_0000019 immortal cell line cell http://purl.obolibrary.org/obo/CLO_0000001 cell line cell A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line. http://purl.obolibrary.org/obo/CLO_0000031 cell line http://purl.obolibrary.org/obo/OBI_0100060 cultured cell population A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). http://purl.obolibrary.org/obo/CLO_0009828 immortal cell line http://purl.obolibrary.org/obo/CLO_0000031 cell line A cell line that is expected to be capable of indefinite propagation in an vitro culture. http://purl.obolibrary.org/obo/ENVO_00001998 soil http://purl.obolibrary.org/obo/ENVO_00010483 environmental material Any material within 2 m from the Earth's surface that is in contact with the atmosphere, with the exclusion of living organisms, areas with continuous ice not covered by other material, and water bodies deeper than 2 m. http://purl.obolibrary.org/obo/ENVO_00010483 environmental material http://purl.obolibrary.org/obo/BFO_0000040 material entity A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. http://purl.obolibrary.org/obo/GAZ_00000448 geographical 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_0000003 measurement unit label http://purl.obolibrary.org/obo/IAO_0000009 datum label A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. http://purl.obolibrary.org/obo/IAO_0000007 action specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity a directive information entity that describes an action the bearer will take http://purl.obolibrary.org/obo/IAO_0000009 datum label http://purl.obolibrary.org/obo/IAO_0000030 information content entity A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label http://purl.obolibrary.org/obo/IAO_0000010 software http://purl.obolibrary.org/obo/IAO_0000104 plan specification Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. http://purl.obolibrary.org/obo/IAO_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_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_0000078 curation status specification http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. http://purl.obolibrary.org/obo/IAO_0000100 data set http://purl.obolibrary.org/obo/IAO_0000027 data item A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. http://purl.obolibrary.org/obo/IAO_0000101 image http://purl.obolibrary.org/obo/IAO_0000308 figure An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part http://purl.obolibrary.org/obo/IAO_0000027 data item data about an ontology part is a data item about a part of an ontology, for example a term http://purl.obolibrary.org/obo/IAO_0000104 plan specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. http://purl.obolibrary.org/obo/IAO_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_0000225 obsolescence reason specification http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. http://purl.obolibrary.org/obo/IAO_0000308 figure http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. http://purl.obolibrary.org/obo/IAO_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_0000311 publication http://purl.obolibrary.org/obo/IAO_0000310 document A document that has been accepted by a publisher 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_0000590 written name http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that denotes a particular in reality. http://purl.obolibrary.org/obo/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_0000045 waiting http://purl.obolibrary.org/obo/OBI_0600009 exposure of material to environment not actively doing anything to a material for a duration of time. http://purl.obolibrary.org/obo/OBI_0000047 processed material http://purl.obolibrary.org/obo/BFO_0000040 material entity Is a material entity that is created or changed during material processing. http://purl.obolibrary.org/obo/OBI_0000049 mass spectrometer http://purl.obolibrary.org/obo/OBI_0000832 measurement device A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum http://purl.obolibrary.org/obo/OBI_0000052 microarray platform http://purl.obolibrary.org/obo/OBI_0001034 environmental control device A microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI. http://purl.obolibrary.org/obo/OBI_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_0000066 investigation http://purl.obolibrary.org/obo/OBI_0000011 planned process a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). http://purl.obolibrary.org/obo/OBI_0000067 evaluant role http://purl.obolibrary.org/obo/BFO_0000023 role a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role http://purl.obolibrary.org/obo/OBI_0000075 diagnosis textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity diagnosis is an assessment of a disease or injury, its likely prognosis and treatment. http://purl.obolibrary.org/obo/OBI_0000079 culture medium http://purl.obolibrary.org/obo/OBI_0000047 processed material a processed material that provides the needed nourishment for microorganisms or cells grown in vitro. http://purl.obolibrary.org/obo/OBI_0000096 protocol testing objective http://purl.obolibrary.org/obo/OBI_0000208 methodology testing objective Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols. http://purl.obolibrary.org/obo/OBI_0000097 participant under investigation role http://purl.obolibrary.org/obo/BFO_0000023 role A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected. http://purl.obolibrary.org/obo/OBI_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_0000109 biological vector role http://purl.obolibrary.org/obo/OBI_0000319 material to be added role a biological vector role is a material to be added role that is realized by the process of transmitting material to the organism that is the target of the transmission. http://purl.obolibrary.org/obo/OBI_0000112 specimen role http://purl.obolibrary.org/obo/BFO_0000023 role a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation http://purl.obolibrary.org/obo/OBI_0000113 sequence feature identification objective http://purl.obolibrary.org/obo/OBI_0000015 biological feature identification objective Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide. http://purl.obolibrary.org/obo/OBI_0000115 intervention design http://purl.obolibrary.org/obo/OBI_0500000 study design An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays. http://purl.obolibrary.org/obo/OBI_0000118 gene list http://purl.obolibrary.org/obo/IAO_0000100 data set A data set of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis. http://purl.obolibrary.org/obo/OBI_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_0000164 cDNA library http://purl.obolibrary.org/obo/OBI_0000731 recombinant vector Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process. ALT DEF (PRS):: a cDNA library is a collection of host cells, typically E.Coli cells but not exclusively. modified by transfer of plasmid DNA molecule used as vector containing a fragment or totality of cDNA molecule (the insert) . cDNA library may have an array of role and applications. http://purl.obolibrary.org/obo/OBI_0000181 population http://purl.obolibrary.org/obo/BFO_0000040 material entity a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area http://purl.obolibrary.org/obo/OBI_0000185 imaging assay http://purl.obolibrary.org/obo/OBI_0000070 assay An imaging assay is an assay to produce a picture of an entity. definition_source: OBI. 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_0000231 enzymatic cleavage http://purl.obolibrary.org/obo/OBI_0000094 material processing enzymatic cleavage is a protocol application to digest the fraction of input material that is susceptible to that enzyme http://purl.obolibrary.org/obo/OBI_0000232 hardware optimization objective http://purl.obolibrary.org/obo/OBI_0000134 hardware testing objective Hardware_optimization is a hardware_testing_objective describing a study designed to identify the best hardware. http://purl.obolibrary.org/obo/OBI_0000242 software testing objective http://purl.obolibrary.org/obo/OBI_0000208 methodology testing objective Software_testing_objective is a hardware_optimization role describing a study designed to examine the effects of using different software or software parameters, e.g. data processing software. http://purl.obolibrary.org/obo/OBI_0000245 organization http://purl.obolibrary.org/obo/BFO_0000040 material entity An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. http://purl.obolibrary.org/obo/OBI_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_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_0000275 analyte role http://purl.obolibrary.org/obo/BFO_0000023 role A role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role http://purl.obolibrary.org/obo/OBI_0000278 disease stage http://purl.obolibrary.org/obo/GO_0008150 biological_process a part of an occurrence of a disease process which is associated with position in the normal progression of the disease http://purl.obolibrary.org/obo/OBI_0000281 intraperitoneal injection http://purl.obolibrary.org/obo/OBI_0000429 intraperitoneal administration is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe http://purl.obolibrary.org/obo/OBI_0000319 material to be added role http://purl.obolibrary.org/obo/BFO_0000023 role material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process http://purl.obolibrary.org/obo/OBI_0000338 drawing a conclusion based on data http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion http://purl.obolibrary.org/obo/OBI_0000339 planning http://purl.obolibrary.org/obo/BFO_0000015 process a process of creating or modifying a plan specification http://purl.obolibrary.org/obo/OBI_0000341 histological sample preparation http://purl.obolibrary.org/obo/OBI_0000659 specimen collection process histological sample preparation is the preparation of an input tissue via slicing and labeling to make tissue microstructure of interest visible in a future histology assay http://purl.obolibrary.org/obo/OBI_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_0000361 ion source http://purl.obolibrary.org/obo/OBI_0000968 device An ion source is a device that is part of a mass spectrometer that ionizes the material under analysis. The ions are then transported by magnetic or electric fields to the mass analyzer. Techniques for ionization have been key to determining what types of samples can be analyzed by mass spectrometry. Electron ionization and chemical ionization are used for gases and vapors. In chemical ionization sources, the material is ionized by chemical ion-molecule reactions during collisions in the source. Two techniques often used with liquid and solid biological samples include electrospray ionization (due to John Fenn PMID 2675315.) and matrix-assisted laser desorption/ionization (MALDI, due to M. Karas and F. Hillenkamp (Measuring Mass: From Positive Rays to Proteins by Michael A. Grayson (Editor) (ISBN 0-941901-31-9))). http://purl.obolibrary.org/obo/OBI_0000364 ion detector http://purl.obolibrary.org/obo/OBI_0000832 measurement device An ion detector is a device that measures and records the charge induced or current produced when an ion passes by or hits a surface. In a scanning instrument the signal produced in the detector during the course of the scan versus where the instrument is in the scan (at what m/Q) will produce a mass spectrum, a record of ions as a function of m/Q. http://purl.obolibrary.org/obo/OBI_0000367 light emission function http://purl.obolibrary.org/obo/OBI_0000374 excitation function A light emission function is an excitation function to excite a material to a specific excitation state that it emits light. http://purl.obolibrary.org/obo/OBI_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_0000374 excitation function http://purl.obolibrary.org/obo/BFO_0000034 function A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons. http://purl.obolibrary.org/obo/OBI_0000376 synthesizing function http://purl.obolibrary.org/obo/BFO_0000034 function A synthesizing function is a function to assemble new output materials from distinct input materials. The output materials typically consist of chemically distinct monomeric objects or object aggregate polymers. http://purl.obolibrary.org/obo/OBI_0000377 perturb function http://purl.obolibrary.org/obo/BFO_0000034 function A perturb function is a function that disrupts the normal function of a system induced through either internal or external means. External means of perturbation include: (1) displacement fields in the physical sense - e.g., temperature change, osmotic shock, pressure change; (2) application of small molecules such as drugs or toxins to perturb the function of specific pathways or application of surfactants to perturb the normal function of plasma membrane. Internal means of perturbation include: (1) manipulation of gene function via gene knockout or transcript knockdown via RNAi; (2) directed genetic mutation leading to minimal aa alterations that interfere with peptide function. http://purl.obolibrary.org/obo/OBI_0000378 filter function http://purl.obolibrary.org/obo/OBI_0000372 material separation function A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through http://purl.obolibrary.org/obo/OBI_0000379 mechanical function http://purl.obolibrary.org/obo/BFO_0000034 function A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force). http://purl.obolibrary.org/obo/OBI_0000383 transfer function http://purl.obolibrary.org/obo/BFO_0000034 function A transfer function is a function to displace a material from one location to another. http://purl.obolibrary.org/obo/OBI_0000385 ionization function http://purl.obolibrary.org/obo/BFO_0000034 function An ionization function is a function to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. http://purl.obolibrary.org/obo/OBI_0000387 cool function http://purl.obolibrary.org/obo/BFO_0000034 function A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material. http://purl.obolibrary.org/obo/OBI_0000397 image acquisition function http://purl.obolibrary.org/obo/OBI_0000453 measure function An image acquisition function is a function to acquire an image of a material http://purl.obolibrary.org/obo/OBI_0000399 solid support function http://purl.obolibrary.org/obo/BFO_0000034 function A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement http://purl.obolibrary.org/obo/OBI_0000401 environment control function http://purl.obolibrary.org/obo/BFO_0000034 function An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature. http://purl.obolibrary.org/obo/OBI_0000403 sort function http://purl.obolibrary.org/obo/OBI_0000372 material separation function A sort function is a function to distinguish material components based on some associated physical quality or entity and to partition the separate components into distinct fractions according to a defined order. http://purl.obolibrary.org/obo/OBI_0000406 PCR product http://purl.obolibrary.org/obo/CHEBI_4705 double-stranded DNA is double stranded DNA that is the specified output of a polymerase chain reaction http://purl.obolibrary.org/obo/OBI_0000409 nucleic acid template role http://purl.obolibrary.org/obo/OBI_0000025 reference substance role a reference substance role which inheres in nucleic acid material entity and is realized in the process of using the nucleic acid bearing the template role as a reference during synthesis of a reverse copy. http://purl.obolibrary.org/obo/OBI_0000411 cloning vector role http://purl.obolibrary.org/obo/OBI_0000109 biological vector role a vector role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning. http://purl.obolibrary.org/obo/OBI_0000416 cloning insert role http://purl.obolibrary.org/obo/BFO_0000023 role cloning insert role is a role which inheres in DNA or RNA and is realized by the process of being inserted into a cloning vector in a cloning process. http://purl.obolibrary.org/obo/OBI_0000419 reverse transcriptase http://purl.obolibrary.org/obo/OBI_0000427 enzyme enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity) http://purl.obolibrary.org/obo/OBI_0000422 syringe http://purl.obolibrary.org/obo/OBI_0000968 device a processed material which is used to introduce or draw fluids from a material entity. A syringe is made of a piston and body. the movement of the piston in the body determines the amount/volume of fluid to inject or draw http://purl.obolibrary.org/obo/OBI_0000425 averaging objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation. http://purl.obolibrary.org/obo/OBI_0000426 injection http://purl.obolibrary.org/obo/OBI_0000274 adding a material entity into a target injection is process which aims at introducing a compound or a mixture into a material entity (either biological entity or instrument) by relying on devices such as syringe or injector connection, attached or forced into a vascular system (veins of an organism or tubes of a machine) or in a tissue. http://purl.obolibrary.org/obo/OBI_0000427 enzyme http://purl.obolibrary.org/obo/BFO_0000040 material entity (protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity) http://purl.obolibrary.org/obo/OBI_0000429 intraperitoneal administration http://purl.obolibrary.org/obo/OBI_0600007 administering substance in vivo The administration of a substance into the peritoneum of an organism http://purl.obolibrary.org/obo/OBI_0000430 plasmid http://purl.obolibrary.org/obo/CHEBI_4705 double-stranded DNA plasmid = DNA and has_quality circular and has_function (is_realized_as some gene expression) GO:0010467 http://purl.obolibrary.org/obo/OBI_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_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_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_0000443 analyte assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. http://purl.obolibrary.org/obo/OBI_0000444 target of material addition role http://purl.obolibrary.org/obo/BFO_0000023 role target of material addition role is a role realized by an entity into which a material is added in a material addition process http://purl.obolibrary.org/obo/OBI_0000451 normalized data set http://purl.obolibrary.org/obo/IAO_0000100 data set A data set that is produced as the output of a normalization data transformation. http://purl.obolibrary.org/obo/OBI_0000453 measure function http://purl.obolibrary.org/obo/BFO_0000034 function Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference. http://purl.obolibrary.org/obo/OBI_0000455 consume data function http://purl.obolibrary.org/obo/BFO_0000034 function Process data function is a function that is borne by in a material entity by virtue of its structure. When realized the material entity consumes data. http://purl.obolibrary.org/obo/OBI_0000457 manufacturing http://purl.obolibrary.org/obo/OBI_0000094 material processing Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process http://purl.obolibrary.org/obo/OBI_0000458 manufacturing objective http://purl.obolibrary.org/obo/OBI_0000456 material transformation objective is the objective to manufacture a material of a certain function (device) http://purl.obolibrary.org/obo/OBI_0000471 study design execution http://purl.obolibrary.org/obo/OBI_0000011 planned process a planned process that realizes the concretization of a study design http://purl.obolibrary.org/obo/OBI_0000571 manufacturer role http://purl.obolibrary.org/obo/BFO_0000023 role Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. http://purl.obolibrary.org/obo/OBI_0000626 DNA sequencing http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay DNA sequencing is a sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument. http://purl.obolibrary.org/obo/OBI_0000634 DNA methylation profiling assay http://purl.obolibrary.org/obo/OBI_0002020 epigenetic modification assay an assay which aims to provide information about state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion. http://purl.obolibrary.org/obo/OBI_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_0000650 differential expression analysis data transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation A differential expression analysis data transformation is a data transformation that has objective differential expression analysis and that consists of http://purl.obolibrary.org/obo/OBI_0000651 urine specimen http://purl.obolibrary.org/obo/OBI_0001479 tissue specimen 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_0000654 device setting http://purl.obolibrary.org/obo/BFO_0000019 quality a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device http://purl.obolibrary.org/obo/OBI_0000668 error correction data transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation An error correction data transformation is a data transformation that has the objective of error correction, where the aim is to remove (correct for) erroneous contributions from the input to the data transformation. http://purl.obolibrary.org/obo/OBI_0000671 sample from organism http://purl.obolibrary.org/obo/OBI_0001479 tissue specimen 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_0000680 whole organism preparation http://purl.obolibrary.org/obo/OBI_0100051 specimen A material entity which is the output of a process in which one or more whole organisms are prepared in a way to make it easier to study them, and in which the great majority of organismal parts are maintained http://purl.obolibrary.org/obo/OBI_0000681 separation into different composition objective http://purl.obolibrary.org/obo/OBI_0000639 material separation objective A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities). http://purl.obolibrary.org/obo/OBI_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_0000690 immunoprecipitation http://purl.obolibrary.org/obo/OBI_0600014 material component separation is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity http://purl.obolibrary.org/obo/OBI_0000691 ABI 377 automated sequencer http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer is a DNA sequencer which is manufactured by Applied Biosystems corporation (formerly Perkin-Elmer). It allows automated chain termination DNA sequencing. It has part polyacrylamide gel electrophoresis system and a laser -based detection system to detect fluorescence intensity emitted by the dyes attached to the dideoxyterminator nucleotides or to the primers. http://purl.obolibrary.org/obo/OBI_0000694 animal feeding http://purl.obolibrary.org/obo/OBI_0000011 planned process animal feeding is a process in which animals are provided with food http://purl.obolibrary.org/obo/OBI_0000696 AB SOLiD System http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation http://purl.obolibrary.org/obo/OBI_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_0000705 Edman degradation http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay is a process which produces a sequence from an input peptide or protein. In this process, the amino-terminal (N-terminal) residue is labeled and cleaved from the peptide without disrupting the peptide bonds between other amino acid residues. http://purl.obolibrary.org/obo/OBI_0000706 SOLiD sequencing http://purl.obolibrary.org/obo/OBI_0000723 DNA sequencing by ligation is a DNA sequencing which allows sequence identification by relying on the following steps: 1. Primers hybridize to the P1 adapter sequence within the library template. 2. A set of four fluorescently labeled di-base probes compete for ligation to the sequencing primer. Specificity of the di-base probe is achieved by interrogating every 1st and 2nd base in each ligation reaction. 3. Multiple cycles of ligation, detection and cleavage are performed with the number of cycles determining the eventual read length. 4. Following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n-1 position for a second round of ligation cycles http://purl.obolibrary.org/obo/OBI_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_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 http://purl.obolibrary.org/obo/OBI_0000626 DNA sequencing is a DNA sequencing which relies on DNA ligase activity to perform chain extension during the sequencing reaction step. http://purl.obolibrary.org/obo/OBI_0000725 host role http://purl.obolibrary.org/obo/BFO_0000023 role host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role http://purl.obolibrary.org/obo/OBI_0000730 pyrosequencing http://purl.obolibrary.org/obo/OBI_0000734 DNA sequencing by synthesis is a DNA sequencing which allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. The template DNA is immobilized, and solutions of A, C, G, and T nucleotides are added and removed after the reaction, sequentially. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions which produce chemiluminescent signals allows the determination of the sequence of the template. ssDNA template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase, ATP sulfurylase, luciferase and apyrase, and with the substrates adenosine 5-prime phosphosulfate (APS) and luciferin. http://purl.obolibrary.org/obo/OBI_0000731 recombinant vector http://purl.obolibrary.org/obo/OBI_0000047 processed material A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector. http://purl.obolibrary.org/obo/OBI_0000734 DNA sequencing by synthesis http://purl.obolibrary.org/obo/OBI_0000626 DNA sequencing is a DNA sequencing which relies on DNA polymerase activity to perform chain extension during the sequencing reaction step. http://purl.obolibrary.org/obo/OBI_0000737 cloning vector http://purl.obolibrary.org/obo/OBI_1110108 material to be added A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site. http://purl.obolibrary.org/obo/OBI_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_0000748 bisulfite sequencing http://purl.obolibrary.org/obo/OBI_0001266 DNA methylation profiling by high throughput sequencing assay An assay which allows to determine the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location. http://purl.obolibrary.org/obo/OBI_0000800 cross linking http://purl.obolibrary.org/obo/OBI_0000094 material processing A process in which bonds are created that link one polymer to another http://purl.obolibrary.org/obo/OBI_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_0000809 amplified DNA http://purl.obolibrary.org/obo/CHEBI_16991 deoxyribonucleic acid DNA that has been produced in an enzymatic amplification process http://purl.obolibrary.org/obo/OBI_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_0000831 DNA residue methylation http://purl.obolibrary.org/obo/PATO_0002182 molecular quality a quality of a DNA residue that has a methyl group attached to it http://purl.obolibrary.org/obo/OBI_0000832 measurement device http://purl.obolibrary.org/obo/OBI_0000968 device A device in which a measure function inheres. http://purl.obolibrary.org/obo/OBI_0000834 high molecular weight DNA extract http://purl.obolibrary.org/obo/OBI_0001051 DNA extract The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas. http://purl.obolibrary.org/obo/OBI_0000838 material maintenance http://purl.obolibrary.org/obo/OBI_0000011 planned process a process with that achieves the objective to maintain some or all of the characteristics of an input material over time http://purl.obolibrary.org/obo/OBI_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_0000852 record of missing knowledge http://purl.obolibrary.org/obo/IAO_0000030 information content entity a information content entity created to indicate that information about something is not available to the person recording it. http://purl.obolibrary.org/obo/OBI_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_0000858 record of unknown sex http://purl.obolibrary.org/obo/OBI_0000852 record of missing knowledge a record indicating that the biological sex of an organism is not known. http://purl.obolibrary.org/obo/OBI_0000859 cytoplasmic RNA extraction http://purl.obolibrary.org/obo/OBI_0666666 RNA extraction A RNA extraction process in which the desired output material is RNA in the cytoplasm. http://purl.obolibrary.org/obo/OBI_0000862 nuclear RNA extract http://purl.obolibrary.org/obo/OBI_0000880 RNA extract A RNA extract that is the output of an extraction process in which RNA molecules found in the nucleus, including mRNA precursors (pre-mRNA), are extracted. http://purl.obolibrary.org/obo/OBI_0000869 polyA RNA extract http://purl.obolibrary.org/obo/OBI_0000880 RNA extract A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3' end are purified. http://purl.obolibrary.org/obo/OBI_0000873 pre-mortem specimen http://purl.obolibrary.org/obo/OBI_0001506 specimen with pre- or post-mortem status a specimen that was taken from a live organism http://purl.obolibrary.org/obo/OBI_0000876 cytoplasmic RNA extract http://purl.obolibrary.org/obo/OBI_0000880 RNA extract A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted. http://purl.obolibrary.org/obo/OBI_0000880 RNA extract http://purl.obolibrary.org/obo/OBI_0001010 nucleic acid extract an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen. http://purl.obolibrary.org/obo/OBI_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_0000894 protein extract http://purl.obolibrary.org/obo/OBI_0000423 extract a protein extract is the output of an extraction process from tissues or cell cultures resulting in a solution of cellular and/or organellar proteins in buffer solution used to prevent degradation, http://purl.obolibrary.org/obo/OBI_0000895 total RNA extract http://purl.obolibrary.org/obo/OBI_0000880 RNA extract A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen. http://purl.obolibrary.org/obo/OBI_0000899 organellar RNA extract http://purl.obolibrary.org/obo/OBI_0000880 RNA extract A RNA extract that is the output of an extraction process in which RNA molecules found in an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus, are extracted. http://purl.obolibrary.org/obo/OBI_0000902 post mortem specimen http://purl.obolibrary.org/obo/OBI_0001506 specimen with pre- or post-mortem status a specimen that was taken from a dead organism http://purl.obolibrary.org/obo/OBI_0000905 sequence feature annotation http://purl.obolibrary.org/obo/IAO_0000030 information content entity Information about a sequence region http://purl.obolibrary.org/obo/OBI_0000908 labeled DNA extract http://purl.obolibrary.org/obo/OBI_0001143 labeled nucleic acid extract a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments. http://purl.obolibrary.org/obo/OBI_0000915 freezing storage http://purl.obolibrary.org/obo/OBI_0302893 storage A storage process in temperature that maintenance the frozen status of the stored entities. http://purl.obolibrary.org/obo/OBI_0000921 labeled RNA extract http://purl.obolibrary.org/obo/OBI_0001143 labeled nucleic acid extract a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments. http://purl.obolibrary.org/obo/OBI_0000922 frozen specimen http://purl.obolibrary.org/obo/OBI_0001472 specimen with known storage state A specimen that has been frozen in order to store it. http://purl.obolibrary.org/obo/OBI_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_0000927 lyophilization storage http://purl.obolibrary.org/obo/OBI_0302893 storage a storage process with input material entity and output freeze dried material for long time storage http://purl.obolibrary.org/obo/OBI_0000931 study intervention http://purl.obolibrary.org/obo/OBI_0000011 planned process the part of the execution of an intervention design study which is varied between two or more subjects in the study http://purl.obolibrary.org/obo/OBI_0000932 material separation device http://purl.obolibrary.org/obo/OBI_0000968 device A device with a separation function realized in a planed process http://purl.obolibrary.org/obo/OBI_0000934 intramuscular injection http://purl.obolibrary.org/obo/OBI_0600007 administering substance in vivo is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe http://purl.obolibrary.org/obo/OBI_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_0000950 paraffin specimen http://purl.obolibrary.org/obo/OBI_0001472 specimen with known storage state a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin http://purl.obolibrary.org/obo/OBI_0000951 compound treatment design http://purl.obolibrary.org/obo/OBI_0000115 intervention design an intervention design in which the treatment is the administration of a compound http://purl.obolibrary.org/obo/OBI_0000953 processed specimen http://purl.obolibrary.org/obo/OBI_0100051 specimen A specimen that has been intentionally physically modified. http://purl.obolibrary.org/obo/OBI_0000954 subcutaneous injection http://purl.obolibrary.org/obo/OBI_0600007 administering substance in vivo is the injection of a material entity (bearing the administered substance role) into the hypodermis (bearing the target role) of an organism using a syringe http://purl.obolibrary.org/obo/OBI_0000965 lyophilized specimen http://purl.obolibrary.org/obo/OBI_0001472 specimen with known storage state a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage. http://purl.obolibrary.org/obo/OBI_0000967 container http://purl.obolibrary.org/obo/OBI_0000968 device A device that can be used to restrict the location of material entities over time http://purl.obolibrary.org/obo/OBI_0000971 fresh specimen http://purl.obolibrary.org/obo/OBI_0001472 specimen with known storage state a specimen that is output of a specimen creation process used for an investigation without storage. http://purl.obolibrary.org/obo/OBI_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_0000977 paraffin storage http://purl.obolibrary.org/obo/OBI_0302893 storage a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage http://purl.obolibrary.org/obo/OBI_0000981 agar stab specimen http://purl.obolibrary.org/obo/OBI_0001472 specimen with known storage state a specimen that is output of a process that cell culture inoculated into agar for long term storage. http://purl.obolibrary.org/obo/OBI_0000985 growth condition intervention design http://purl.obolibrary.org/obo/OBI_0000115 intervention design A study design in which the independent variable is the environmental condition in which the specimen is growing http://purl.obolibrary.org/obo/OBI_0000989 PCR instrument http://purl.obolibrary.org/obo/OBI_0400116 thermal cycler A device that is used to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence. http://purl.obolibrary.org/obo/OBI_0000994 intravenous injection http://purl.obolibrary.org/obo/OBI_0600007 administering substance in vivo is the injection of a material entity (bearing the administered substance role) into the vein (bearing the target role) of an organism using a syringe http://purl.obolibrary.org/obo/OBI_0000995 administration of material to specimen http://purl.obolibrary.org/obo/OBI_0000274 adding a material entity into a target The directed combination of a material entity with a specimen. http://purl.obolibrary.org/obo/OBI_0000997 growth environment http://purl.obolibrary.org/obo/BFO_0000040 material entity The collection of material entities and their qualities that are located near a live organism, tissue or cell and can influence its growth. http://purl.obolibrary.org/obo/OBI_0001003 agar stab storage http://purl.obolibrary.org/obo/OBI_0302893 storage a storage process with input cell culture and agar and output agar stab for long time storage http://purl.obolibrary.org/obo/OBI_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_0001028 feature extraction http://purl.obolibrary.org/obo/OBI_0200000 data transformation A planed process with objective of obtaining quantified values from an image. http://purl.obolibrary.org/obo/OBI_0001032 light emission device http://purl.obolibrary.org/obo/OBI_0000968 device a device which has a function to emit light. http://purl.obolibrary.org/obo/OBI_0001033 perturbation device http://purl.obolibrary.org/obo/OBI_0000968 device A perturbation device is a device which is designed to perform a perturb function http://purl.obolibrary.org/obo/OBI_0001034 environmental control device http://purl.obolibrary.org/obo/OBI_0000968 device An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity. http://purl.obolibrary.org/obo/OBI_0001051 DNA extract http://purl.obolibrary.org/obo/OBI_0001010 nucleic acid extract The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas. http://purl.obolibrary.org/obo/OBI_0001069 array manufacturer role http://purl.obolibrary.org/obo/OBI_0000571 manufacturer role a manufacturer role which is played by the person or organization that manufactured the array http://purl.obolibrary.org/obo/OBI_0001088 tandem mass spectrometer http://purl.obolibrary.org/obo/OBI_0000049 mass spectrometer A mass spectrometer in which ions are subjected to two or more sequential stages of analysis (which may be separated spatially or temporally) according to the quotient mass/charge. http://purl.obolibrary.org/obo/OBI_0001140 spike-in quality control role http://purl.obolibrary.org/obo/OBI_0000025 reference substance role a reference substance role that is borne by a material entity with a known amount which is mixed into the evaluant of assays for quality control or data normalization purposes http://purl.obolibrary.org/obo/OBI_0001141 individual organism identifier http://purl.obolibrary.org/obo/IAO_0000577 centrally registered identifier symbol a CRID symbol used to distinguish one individual organism from another. http://purl.obolibrary.org/obo/OBI_0001142 dye swap quality control role http://purl.obolibrary.org/obo/OBI_0000025 reference substance role a reference substance role that is borne by a material entity used in a dye swap design experiment for quality control or data normalization purposes http://purl.obolibrary.org/obo/OBI_0001146 binding assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay with the objective to characterize the disposition of two or more material entities to form a complex. http://purl.obolibrary.org/obo/OBI_0001147 cell culture expansion http://purl.obolibrary.org/obo/OBI_0000094 material processing a processual entity that results in the increase of cell numbers http://purl.obolibrary.org/obo/OBI_0001148 gene knock out http://purl.obolibrary.org/obo/OBI_0600043 genetic transformation a genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods. http://purl.obolibrary.org/obo/OBI_0001149 gene knock in http://purl.obolibrary.org/obo/OBI_0600043 genetic transformation a genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion. http://purl.obolibrary.org/obo/OBI_0001150 chromosomal substitution http://purl.obolibrary.org/obo/OBI_0600043 genetic transformation A genetic transformation in which all, or part, of a chromosome from a donor replaces that of the recipient. It does not include chromosome recombination. For single gene insertion, use the term 'gene knock in'. http://purl.obolibrary.org/obo/OBI_0001151 genetically modified material http://purl.obolibrary.org/obo/OBI_0000047 processed material a material entity, organism or cell, that is the output of a genetic transformation process. http://purl.obolibrary.org/obo/OBI_0001152 transfection http://purl.obolibrary.org/obo/OBI_0600043 genetic transformation a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA or RNA into a cell http://purl.obolibrary.org/obo/OBI_0001153 genetic transformation objective http://purl.obolibrary.org/obo/OBI_0000456 material transformation objective a material transformation objective aims to create genetically modified organism or cell http://purl.obolibrary.org/obo/OBI_0001154 induced mutation http://purl.obolibrary.org/obo/OBI_0600043 genetic transformation a genetic transformation that the modification of the genetic material (either coding or non-coding) of an organism is caused by mutagenic compounds or irradiation. http://purl.obolibrary.org/obo/OBI_0001156 age since planting measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since planting, the process of placing a plant in media (e.g. soil) to allow it to grow, which excludes sowing. http://purl.obolibrary.org/obo/OBI_0001157 age since hatching measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since hatching, the process of emergence from an egg. http://purl.obolibrary.org/obo/OBI_0001158 age measurement assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that measures the duration of temporal interval of a process that is part of the life of the bearer, where the initial time point of the measured process is the beginning of some transitional state of the bearer such as birth or when planted. http://purl.obolibrary.org/obo/OBI_0001159 age since egg laying measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since egg laying, the process of the production of egg(s) by an organism. http://purl.obolibrary.org/obo/OBI_0001160 assay validation objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification an objective specification to check the accuracy or the quality of the results of an assay by comparison with independent results http://purl.obolibrary.org/obo/OBI_0001161 age since germination measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since germination, the process consisting of physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth. http://purl.obolibrary.org/obo/OBI_0001162 validation by reverse transcription PCR design http://purl.obolibrary.org/obo/OBI_0500000 study design a study design in which checks the accuracy or the quality of the result of an assay by comparing with reverse transcription PCR results http://purl.obolibrary.org/obo/OBI_0001163 age since eclosion measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since eclosion, the process of emergence of an adult insect from its pupa or cocoon. http://purl.obolibrary.org/obo/OBI_0001164 age since sowing measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since sowing, the process of placing a seed or spore in some media with the intention to invoke germination. http://purl.obolibrary.org/obo/OBI_0001165 age since coitus measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since coitus, the process of copulation that occurs during the process of sexual reproduction. http://purl.obolibrary.org/obo/OBI_0001166 validation by real time PCR design http://purl.obolibrary.org/obo/OBI_0500000 study design a study design in which the accuracy or the quality of the result of an assay is checked by comparing with real time PCR results http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum http://purl.obolibrary.org/obo/BCGO_0000095 age datum A time measurement datum that is the result of measurement of age of an organism http://purl.obolibrary.org/obo/OBI_0001168 age since fertilization measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. http://purl.obolibrary.org/obo/OBI_0001169 age since birth measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother. http://purl.obolibrary.org/obo/OBI_0001170 reverse transcription polymerase chain reaction assay http://purl.obolibrary.org/obo/OBI_0000070 assay an assay that evaluates the concentration of RNA in a sample in which an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional or real-time PCR. http://purl.obolibrary.org/obo/OBI_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 http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay RNA sequencing is a sequencing process which uses ribonucleic acid as input and results in a the creation of RNA sequence information artifact http://purl.obolibrary.org/obo/OBI_0001181 binding datum http://purl.obolibrary.org/obo/IAO_0000027 data item A data item that states if two or more material entities have the disposition to form a complex, and if so, how strong that disposition is. http://purl.obolibrary.org/obo/OBI_0001195 operator variation design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that assesses the operator performance and relation to data consistency and quality. http://purl.obolibrary.org/obo/OBI_0001197 comparative genome hybridization by array design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that detects genomic copy number variations using microarray technology. http://purl.obolibrary.org/obo/OBI_0001199 in vivo design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model. http://purl.obolibrary.org/obo/OBI_0001200 genotyping by high throughput sequencing design http://purl.obolibrary.org/obo/OBI_0001444 genotyping design A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using high througput sequencing techniques. http://purl.obolibrary.org/obo/OBI_0001202 innate behavior design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which the innate behavior of the organism is examined, e.g. path finding in bees. http://purl.obolibrary.org/obo/OBI_0001205 cell component comparison design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that compares samples from different cell components. http://purl.obolibrary.org/obo/OBI_0001211 ex vivo design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design where all or part of an organism is removed and studied in vitro, e.g. part of a mouse is removed and cultured in vitro. A cell culture with an established cell line is an in vitro experiment. http://purl.obolibrary.org/obo/OBI_0001214 normalization testing design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that tests different normalization procedures. http://purl.obolibrary.org/obo/OBI_0001225 genetic population background information http://purl.obolibrary.org/obo/OBI_0001404 genetic characteristics information a genetic characteristics information which is a part of genotype information that identifies the population of organisms http://purl.obolibrary.org/obo/OBI_0001226 environmental history design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc. http://purl.obolibrary.org/obo/OBI_0001234 epigenetic modification identification objective http://purl.obolibrary.org/obo/OBI_0000131 molecular feature identification objective A molecular feature identification objective that aims to detect epigenetic modifications, such as DNA methylation, histone modifications. http://purl.obolibrary.org/obo/OBI_0001235 transcription profiling by tiling array assay http://purl.obolibrary.org/obo/OBI_0000424 transcription profiling assay An assay in which the transcriptome of a biological sample is analysed using a tiling path array. http://purl.obolibrary.org/obo/OBI_0001239 transcription profiling by high throughput sequencing design http://purl.obolibrary.org/obo/OBI_0001430 transcription profiling design A study design in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and/or to quantitate transcript abundance http://purl.obolibrary.org/obo/OBI_0001247 genotyping by high throughput sequencing assay http://purl.obolibrary.org/obo/OBI_0000435 genotyping assay An assay in which high througput sequencer is used to detect polymorphisms in DNA samples http://purl.obolibrary.org/obo/OBI_0001252 array platform variation design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which the array platform is compared, e.g. Agilent versus Affymetrix. http://purl.obolibrary.org/obo/OBI_0001258 ChIP-seq design http://purl.obolibrary.org/obo/OBI_0001425 protein binding site identification design A study design which aims to identify protein and DNA interactions using a combination of chromatin immunoprecipitation and high throughput sequencing. Massively parallel sequence analyses are used in conjunction with whole-genome sequence databases to analyze the interaction pattern of any protein with DNA, or the pattern of any epigenetic chromatin modifications. http://purl.obolibrary.org/obo/OBI_0001259 translational bias design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that characterizes the association of transcripts and translation machinery. http://purl.obolibrary.org/obo/OBI_0001266 DNA methylation profiling by high throughput sequencing assay http://purl.obolibrary.org/obo/OBI_0000634 DNA methylation profiling assay An assay in which the methylation state of DNA is determined and is compared between samples using sequencing based technology http://purl.obolibrary.org/obo/OBI_0001274 genotyping by array assay http://purl.obolibrary.org/obo/OBI_0000435 genotyping assay An assay in which an array is used to detect polymorphisms in DNA samples http://purl.obolibrary.org/obo/OBI_0001278 DNA methylation profiling by array design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which the methylation state of DNA is determined and is compared between samples using array technology. http://purl.obolibrary.org/obo/OBI_0001282 translation profiling assay http://purl.obolibrary.org/obo/OBI_0000443 analyte assay An assay in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, which mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation. http://purl.obolibrary.org/obo/OBI_0001285 in vitro design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that is done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture. http://purl.obolibrary.org/obo/OBI_0001286 RNAi profiling by array design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which experiment double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression. http://purl.obolibrary.org/obo/OBI_0001290 transcription profiling by array design http://purl.obolibrary.org/obo/OBI_0001430 transcription profiling design A study design that identifies forms and abundance of transcripts in the genome using microarray technology. http://purl.obolibrary.org/obo/OBI_0001293 disease state design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress. http://purl.obolibrary.org/obo/OBI_0001294 wild type organism genotype information http://purl.obolibrary.org/obo/OBI_0001305 genotype information a genotype information about an organism and includes information that there are no known modifications to the genetic background. Generally it is the genotype information of a representative individual from a class of organisms. http://purl.obolibrary.org/obo/OBI_0001304 RNAi profiling by array assay http://purl.obolibrary.org/obo/OBI_0000443 analyte assay An assay in which double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression. http://purl.obolibrary.org/obo/OBI_0001305 genotype information http://purl.obolibrary.org/obo/OBI_0001404 genetic characteristics information a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc. http://purl.obolibrary.org/obo/OBI_0001306 RNA stability design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that examines the stability and/or decay of RNA transcripts. http://purl.obolibrary.org/obo/OBI_0001310 species comparison design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that assays differences between distinct species. http://purl.obolibrary.org/obo/OBI_0001313 transcription profiling by RT-PCR design http://purl.obolibrary.org/obo/OBI_0001430 transcription profiling design A study design which aims to examine the transcriptome of a biological sample by reverse transcription PCR (RT-PCR). http://purl.obolibrary.org/obo/OBI_0001318 proteomic profiling by array assay http://purl.obolibrary.org/obo/OBI_0000443 analyte assay An assay that proteins in a sample are detected, quantified or otherwise analysed, e.g. antibody profiling using an array based technology http://purl.obolibrary.org/obo/OBI_0001323 microRNA profiling by array design http://purl.obolibrary.org/obo/OBI_0001430 transcription profiling design A study design in which a microRNA array is used to analyse the microRNA component of the transcriptome. http://purl.obolibrary.org/obo/OBI_0001328 organism development design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that assays events associated with development. Development applies to organism(s) acquiring a mature state. http://purl.obolibrary.org/obo/OBI_0001329 family history design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which the family history such as traits, characteristics, susceptibility to disease is studied. http://purl.obolibrary.org/obo/OBI_0001331 transcription profiling identification objective http://purl.obolibrary.org/obo/OBI_0000131 molecular feature identification objective A molecular feature identification objective that aims to characterize the abundance of transcripts http://purl.obolibrary.org/obo/OBI_0001332 DNA methylation profiling by array assay http://purl.obolibrary.org/obo/OBI_0000634 DNA methylation profiling assay An assay in which the methylation state of DNA is determined and is compared between samples using array technology http://purl.obolibrary.org/obo/OBI_0001335 microRNA profiling by array assay http://purl.obolibrary.org/obo/OBI_0001926 microRNA profiling assay An assay in which a microRNA array is used to analyse the microRNA component of the transcriptome. http://purl.obolibrary.org/obo/OBI_0001336 quality control testing design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which some aspects of the experiment is quality controlled for the purposes of quality assurance. http://purl.obolibrary.org/obo/OBI_0001337 clinical history design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that the organism's clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied. http://purl.obolibrary.org/obo/OBI_0001352 allele information http://purl.obolibrary.org/obo/OBI_0001364 genetic alteration information a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition. http://purl.obolibrary.org/obo/OBI_0001358 post-transcriptional modification design http://purl.obolibrary.org/obo/OBI_0000115 intervention design A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting. http://purl.obolibrary.org/obo/OBI_0001361 transcription profiling by RT-PCR assay http://purl.obolibrary.org/obo/OBI_0000424 transcription profiling assay An assay in which the transcriptome of a biological sample is analysed by reverse transcription PCR (RT-PCR) http://purl.obolibrary.org/obo/OBI_0001364 genetic alteration information http://purl.obolibrary.org/obo/OBI_0001404 genetic characteristics information a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc. http://purl.obolibrary.org/obo/OBI_0001365 cellular process design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that aims to study the processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. http://purl.obolibrary.org/obo/OBI_0001369 wild type allele information http://purl.obolibrary.org/obo/OBI_0001352 allele information an allele information that is about the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism. http://purl.obolibrary.org/obo/OBI_0001374 injury design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which the response of an organism(s) to injury or damage is studied. http://purl.obolibrary.org/obo/OBI_0001377 organism status comparison design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that compares samples from live and dead organisms. http://purl.obolibrary.org/obo/OBI_0001387 genotyping by array design http://purl.obolibrary.org/obo/OBI_0001444 genotyping design A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using microarray technology. http://purl.obolibrary.org/obo/OBI_0001396 stimulus or stress design http://purl.obolibrary.org/obo/OBI_0000115 intervention design A study design in which the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc. http://purl.obolibrary.org/obo/OBI_0001398 protein and DNA interaction identification objective http://purl.obolibrary.org/obo/OBI_0000113 sequence feature identification objective A sequence feature identification objective that aims to characterize the interactions between protein and DNA which includes identification of transcription factor binding sites. http://purl.obolibrary.org/obo/OBI_0001401 protocol optimization design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design where different protocols or protocol parameters are compared aims to find an optimized protocol http://purl.obolibrary.org/obo/OBI_0001404 genetic characteristics information http://purl.obolibrary.org/obo/IAO_0000027 data item a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes. http://purl.obolibrary.org/obo/OBI_0001408 imprinting design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design where differences in genetic imprinting of maternally- and paternally-inherited chromosomes (e.g., due to in vivo differences in chemical modification and/or chromatin structure) are compared. http://purl.obolibrary.org/obo/OBI_0001409 cell cycle design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that assays events that occur in relation to the cell cycle, which is the period between the formation of a cell, by division of its mother cell and the time when the cell itself divides to form two daughter cells. http://purl.obolibrary.org/obo/OBI_0001410 translation profiling design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, where mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation. http://purl.obolibrary.org/obo/OBI_0001411 cell type comparison design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that compares cells of different type, for example different cell lines. http://purl.obolibrary.org/obo/OBI_0001417 ChIP-chip by tiling array design http://purl.obolibrary.org/obo/OBI_0001403 ChIP-chip design A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and tiling microarray (chip) assays. http://purl.obolibrary.org/obo/OBI_0001418 dose response design http://purl.obolibrary.org/obo/OBI_0000951 compound treatment design A study design that examines the relationship between the size of the administered dose and the extent of the response. http://purl.obolibrary.org/obo/OBI_0001419 ChIP-chip by tiling array assay http://purl.obolibrary.org/obo/OBI_0001248 ChIP-chip assay An assay where chromatin immunoprecipitation (ChIP) is used in combination with tiling microarray technology http://purl.obolibrary.org/obo/OBI_0001422 organism part comparison design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that compares tissues, regions, organs within or between organisms http://purl.obolibrary.org/obo/OBI_0001425 protein binding site identification design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that investigates protein binding sites on nucleic acids. http://purl.obolibrary.org/obo/OBI_0001426 sex comparison design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that assays differences associated with an organism's sex, gender or mating type. http://purl.obolibrary.org/obo/OBI_0001427 transcription profiling by tiling array design http://purl.obolibrary.org/obo/OBI_0001430 transcription profiling design A study design in which gene expression on a genome-wide basis is evaluated, without bias toward coding or noncoding regions, using tiling arrays containing oligonucleotides that are either overlapping or spaced at regular intervals. http://purl.obolibrary.org/obo/OBI_0001429 cell differentiation design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that assays events associated with cell development or differentiation. http://purl.obolibrary.org/obo/OBI_0001430 transcription profiling design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that identifies forms and abundance of transcripts in the genome. http://purl.obolibrary.org/obo/OBI_0001432 operon identification design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that identifies locations and members of operons in a genome. http://purl.obolibrary.org/obo/OBI_0001435 DNA methylation profiling by high throughput sequencing design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which the methylation state of DNA is determined and is compared between samples using high throughput sequencing technology. http://purl.obolibrary.org/obo/OBI_0001440 all pairs design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which all specimens are compared to every other specimen. http://purl.obolibrary.org/obo/OBI_0001441 proteomic profiling by array design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which proteins in a sample are detected, quantified or otherwise analysed, e.g. antibody profiling using an array based technology http://purl.obolibrary.org/obo/OBI_0001444 genotyping design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs. http://purl.obolibrary.org/obo/OBI_0001448 individual genetic characteristics comparison design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design where genotype, haplotype, or other individual genetic characteristics are compared. http://purl.obolibrary.org/obo/OBI_0001454 pathogenicity design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design in which an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed. http://purl.obolibrary.org/obo/OBI_0001460 genetic modification design http://purl.obolibrary.org/obo/OBI_0000115 intervention design A study design in which an organism(s) is studied that has had genetic material removed, rearranged, mutagenized or added, such as in a knock out. http://purl.obolibrary.org/obo/OBI_0001463 transcription profiling by array assay http://purl.obolibrary.org/obo/OBI_0000424 transcription profiling assay An assay in which the transcriptome of a biological sample is analysed using array technology. http://purl.obolibrary.org/obo/OBI_0001464 strain comparison design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species. http://purl.obolibrary.org/obo/OBI_0001468 cell specimen http://purl.obolibrary.org/obo/OBI_0100051 specimen A specimen primarily composed of cells collected from a multicellular organism or a cell culture 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_0001474 lowess group transformation http://purl.obolibrary.org/obo/OBI_0001477 lowess transformation A lowess transformation where a potentially different normalization curve is generated and used for two or more groups (delineated by some criteria); criteria could include blocks (e.g. print-tip groups) on an array, or the day on which mass spectrometry was performed. http://purl.obolibrary.org/obo/OBI_0001477 lowess transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A data transformation of normalizing ratio data by using a locally weighted polynomial regression (typically after a log transformation). The regression can be performed on log ratios resulting from the relation of two data sets versus the average log intensity data from the same two data sets or it can be performed on raw or log transformed values from one data set versus values from another. The goal could be to remove intensity-dependent dye-specific effects from the set of pair wise ratios. This method can be applied globally, or limited by one or more specified criteria. http://purl.obolibrary.org/obo/OBI_0001479 tissue specimen http://purl.obolibrary.org/obo/OBI_0100051 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_0001481 lowess global transformation http://purl.obolibrary.org/obo/OBI_0001477 lowess transformation A lowess transformation where the same normalization curve is used for all members of the data set; e.g. Features on an array, picked spots on a gel, or measured metabolites in a sample. http://purl.obolibrary.org/obo/OBI_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_0001498 atmosphere http://purl.obolibrary.org/obo/OBI_0000997 growth environment A growth environment pertaining to the atmospheric conditions that is used to culture or grow an organism. http://purl.obolibrary.org/obo/OBI_0001504 dissection http://purl.obolibrary.org/obo/OBI_0000094 material processing A planned process that separates and isolates tissues for surgical purposes, or for the analysis or study of their structures. http://purl.obolibrary.org/obo/OBI_0001505 purification http://purl.obolibrary.org/obo/OBI_0600014 material component separation A planned process to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest http://purl.obolibrary.org/obo/OBI_0001506 specimen with pre- or post-mortem status http://purl.obolibrary.org/obo/OBI_0100051 specimen A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism. http://purl.obolibrary.org/obo/OBI_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_0001588 binding http://purl.obolibrary.org/obo/GO_0008150 biological_process The process of material entities forming complexes. http://purl.obolibrary.org/obo/OBI_0001700 immunoprecipitation assay http://purl.obolibrary.org/obo/OBI_0000443 analyte assay An assay with the objective to determine presence of an analyte by mixing a solution of antigen and antibody and separating out bound antigen:antibody complexes using immunoprecipitation. Either the antibody has known specificy, and the antigen mixture is tested for the presence of a specific antigen, or the antigen solution is well defined and the antibody solution is tested for the presence of antigen specific antibodies. http://purl.obolibrary.org/obo/OBI_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_0001854 protein and RNA interaction identification objective http://purl.obolibrary.org/obo/OBI_0000113 sequence feature identification objective A sequence feature identification objective that aims to characterize the interactions between protein and RNA. http://purl.obolibrary.org/obo/OBI_0001865 assay array http://purl.obolibrary.org/obo/OBI_0000968 device A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface. http://purl.obolibrary.org/obo/OBI_0001866 secondary cultured cell http://purl.obolibrary.org/obo/CL_0000010 cultured cell A cultured cell that has been passaged or derives from a cell that has been passaged in culture. http://purl.obolibrary.org/obo/OBI_0001867 establishing cell line http://purl.obolibrary.org/obo/OBI_0600036 establishing cell culture a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset). http://purl.obolibrary.org/obo/OBI_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_0001912 cell freezing medium http://purl.obolibrary.org/obo/OBI_0000047 processed material A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles. http://purl.obolibrary.org/obo/OBI_0001916 DNA replication identification objective http://purl.obolibrary.org/obo/OBI_0000131 molecular feature identification objective A molecular feature identification objective that aims to examine charateristics of DNA replication, such as replication time. http://purl.obolibrary.org/obo/OBI_0001917 chromosome conformation identification objective http://purl.obolibrary.org/obo/OBI_0000131 molecular feature identification objective A molecular feature identification objective that aims to determine spatial organization of chromatin. http://purl.obolibrary.org/obo/OBI_0001923 protein sequencing by tandem mass spectrometry assay http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay A sequencing assay in which amino acid sequences of proteins is determined using multiple rounds of mass spectrometry and molecule fragmentation. http://purl.obolibrary.org/obo/OBI_0001931 scalar value specification http://purl.obolibrary.org/obo/OBI_0001933 value specification A value specification that consists of two parts: a numeral and a unit label http://purl.obolibrary.org/obo/OBI_0001933 value specification http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity that specifies a value within a classification scheme or on a quantitative scale. http://purl.obolibrary.org/obo/OBI_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_0001956 assay using chromatin immunoprecipitation http://purl.obolibrary.org/obo/OBI_0001700 immunoprecipitation assay an assay which uses immunoprecipitation and which produces data about protein-DNA interaction or DNA epigenetic modification http://purl.obolibrary.org/obo/OBI_0001957 hardware testing design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that aims to compare different types of hardware for performance, reproducibility, accuracy and precision. http://purl.obolibrary.org/obo/OBI_0001958 systematic review study design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design for identifying in the literature prior studies of a pre-determined phenomenon or set of related phenomena according to certain criteria, extracting findings from these studies, and summarizing these findings and/or attempting to draw new conclusions from them which were not justified by any of the individual, prior studies. Many systematic reviews also assess the quality of the studies so reviewed. http://purl.obolibrary.org/obo/OBI_0001965 decision analysis study design http://purl.obolibrary.org/obo/OBI_0500000 study design a study design that has a decision analysis objective specification as part http://purl.obolibrary.org/obo/OBI_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_0002020 epigenetic modification assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that identifies epigenetic modification including histone modifications, open chromatin, and DNA methylation. 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_0100066 organ section http://purl.obolibrary.org/obo/OBI_0000047 processed material A processed material which derives from an organ and results from a process of dissection or histological sample preparation a portion(formerly an organ section is portion of an organ removed from the context of the organ) http://purl.obolibrary.org/obo/OBI_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_0200021 linlog transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A linlog transformation is a data transformation, described in PMID 16646782, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (9) of this paper, where values below an appropriately determined threshold (dependent on the row i) are transformed via a polynomial of degree 1, and values above this threshold are transformed via a logarithm. http://purl.obolibrary.org/obo/OBI_0200023 loess global transformation http://purl.obolibrary.org/obo/OBI_0200071 loess transformation A loess global transformation is a loess transformation where only one loess fitting is performed, utilizing one subset of (or possibly all of) the data points in the input so that there is only one resulting loess curve y=f(x) which is used for the transformation. http://purl.obolibrary.org/obo/OBI_0200024 loess group transformation http://purl.obolibrary.org/obo/OBI_0200071 loess transformation A loess group transformation is a loess transformation where the input is partitioned into groups and for each group a loess fitting is performed, utilizing a subset of (or possibly all of) the data points in that group. Thus, a collection of loess curves y=f_i(x) is generated, one per group. Each (x, y) in the input is transformed into (x, y-f_i(x)), where f_i(x) is the curve corresponding to the group to which that data point belongs. http://purl.obolibrary.org/obo/OBI_0200025 loess scale group transformation http://purl.obolibrary.org/obo/OBI_0200185 scaling data transformation A loess scale group transformation is a data transformation consisting in the application of a scale adjustment following a loess group transformation, to render the group variances for the second variable (y) similar. Has objective scaling. http://purl.obolibrary.org/obo/OBI_0200026 total intensity transformation single http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A total intensity transformation single is a data transformation that takes as input an n-dimensional (real) vector and multiplies each component of this vector by a coefficient, where the coefficient is obtained by taking the sum of the input components or of a subset of these, multiplied by a constant of choice. http://purl.obolibrary.org/obo/OBI_0200027 total intensity transformation paired http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A total intensity transformation paired is a data transformation that takes as input two n-dimensional (real) vectors and multiplies each component of the first vector by a coefficient, where the coefficient is obtained by taking the ratio of the sum of the second input components or of a subset of these by the sum of the first input components or of a subset of these (the same subset is used for the two vectors). http://purl.obolibrary.org/obo/OBI_0200028 quantile transformation http://purl.obolibrary.org/obo/OBI_0200181 center calculation data transformation A quantile transformation is a data transformation that takes as input a collection of data sets, where each can be thought as an n-dimensional (real) vector, and which transforms each data set so that the resulting output data sets have equal quantiles. http://purl.obolibrary.org/obo/OBI_0200031 differential expression analysis objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions. http://purl.obolibrary.org/obo/OBI_0200055 dye swap merge http://purl.obolibrary.org/obo/OBI_0200057 replicate analysis A dye swap merge is a replicate analysis which takes as input data from paired two-channel microarray assays where the sample labeled with one dye in the first assay is labeled with the other dye in the second assay and vice versa. The output for each reporter is obtained by combining its (raw or possibly pre-processed) M values in the two assays, where the M value in an assay is defined as the difference of the log intensities in the two channels. This can be used as a normalization step, when appropriate assumptions are met. http://purl.obolibrary.org/obo/OBI_0200056 moving average http://purl.obolibrary.org/obo/OBI_0200170 averaging data transformation A moving average is a data transformation in which center calculations, usually mean calculations, are performed on values within a sliding window across the input data set. http://purl.obolibrary.org/obo/OBI_0200057 replicate analysis http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A replicate analysis is a data transformation in which data from replicates are combined, e.g. through descriptive statistics calculations, and the results might be utilized for a variety of purposes, like assessing reproducibility, identifying outliers, normalizing, etc. http://purl.obolibrary.org/obo/OBI_0200071 loess transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A loess transformation is a data transformation that takes as input a collection of real number pairs (x, y) and, after performing (one or more) loess fittings, utilizes the resulting curves to transform each (x, y) in the input into (x, y-f(x)) where f(x) is one of the fitted curves. http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification An objective specification to transformation input data into output data http://purl.obolibrary.org/obo/OBI_0200167 data normalization objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A normalization objective is a data transformation objective where the aim is to remove systematic sources of variation to put the data on equal footing in order to create a common base for comparisons. http://purl.obolibrary.org/obo/OBI_0200168 correction objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation A normalization data transformation is a data transformation that has objective normalization. http://purl.obolibrary.org/obo/OBI_0200170 averaging data transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation An averaging data transformation is a data transformation that has objective averaging. http://purl.obolibrary.org/obo/OBI_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_0200181 center calculation data transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation A center calculation data transformation is a data transformation that has objective of center calculation. http://purl.obolibrary.org/obo/OBI_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_0200185 scaling data transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation A scaling data transformation is a data transformation that has objective scaling. 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_0300310 sequential design http://purl.obolibrary.org/obo/OBI_0000115 intervention design Any design in which the decision as to whether to enroll the next patient, pair of patients, or block of patients is determined by whether the cumulative treatment difference for all previous patients is within specified limits. Enrollment is continued if the difference does not exceed the limits. It is terminated if it does http://purl.obolibrary.org/obo/OBI_0300311 observation design http://purl.obolibrary.org/obo/OBI_0500000 study design observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists. http://purl.obolibrary.org/obo/OBI_0302716 pool of specimens http://purl.obolibrary.org/obo/OBI_0000953 processed specimen A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish. http://purl.obolibrary.org/obo/OBI_0302859 genetically modified organism http://purl.obolibrary.org/obo/OBI_0100026 organism an organism that is the output of a genetic 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_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_0302887 staining http://purl.obolibrary.org/obo/OBI_0000094 material processing Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound. 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_0302889 irradiation http://purl.obolibrary.org/obo/OBI_0000094 material processing irradiation is a process by which a material entity is exposed to radiative energy, which could be ionizing radiation (such as gamma rays or X-rays) or not such as UV light or microwaves http://purl.obolibrary.org/obo/OBI_0302892 enzymatic ligation http://purl.obolibrary.org/obo/OBI_0000094 material processing An enzymatic ligation is a planned process in which molecules are joined by covalent bonds through the action of an material entity with a ligase activity http://purl.obolibrary.org/obo/OBI_0302893 storage http://purl.obolibrary.org/obo/OBI_0000838 material maintenance A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability http://purl.obolibrary.org/obo/OBI_0302894 cell lysis http://purl.obolibrary.org/obo/OBI_0600006 killing cell lysis is a process by which cell membrane integrity of live cells is compromised and leads to cell death. Cell lysis may be achieved by means of viral action or osmotic shock. http://purl.obolibrary.org/obo/OBI_0302902 immobilization http://purl.obolibrary.org/obo/OBI_0000094 material processing immbolization is a process by which material entity become (possibly covalently but not necessarily) attached to the surface of another material entity used a substratum. 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_0400044 flow cytometer http://purl.obolibrary.org/obo/OBI_0400137 cytometer A flow_cytometer is an instrument for counting, examining and sorting microscopic particles in suspension. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of single cells flowing through an optical and/or electronic detection apparatus. A flow cytometer is an instrument that can be used to quantitatively measure the properties of individual cells in a flowing medium. http://purl.obolibrary.org/obo/OBI_0400065 light source http://purl.obolibrary.org/obo/OBI_0001032 light emission device A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser. http://purl.obolibrary.org/obo/OBI_0400078 obscuration bar http://purl.obolibrary.org/obo/OBI_0000932 material separation device An obscuration bar is a an optical subsystem which is a strip of metal or other material that serves to block out direct light from the illuminating beam. The obscuration bar prevents the bright light scattered in the forward directions from burning out the collection device. http://purl.obolibrary.org/obo/OBI_0400079 optical filter http://purl.obolibrary.org/obo/OBI_0000932 material separation device An optical filter is an optical subsystem that selectively transmits light having certain properties (often, a particular range of wavelengths, that is, range of colours of light), while blocking the remainder. They are commonly used in photography, in many optical instruments, and to colour stage lighting Optical filters can be arranged to segregate and collect light by wave length. http://purl.obolibrary.org/obo/OBI_0400082 photodetector http://purl.obolibrary.org/obo/OBI_0000832 measurement device A photodetector is a device used to detect and measure the intensity of radiant energy through photoelectric action. In a cytometer, photodetectors measure either the number of photons of laser light scattered on impact with a cell (for example), or the flourescence emitted by excitation of a fluorescent dye. http://purl.obolibrary.org/obo/OBI_0400099 flow cytometer sorter http://purl.obolibrary.org/obo/OBI_0400044 flow cytometer A flow_cytometer_sorter is a flow_cytometer that analyzes and separates or sorts particles passing through (based on properties measured during analysis) to collect cells of interest. 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_0400104 array scanner http://purl.obolibrary.org/obo/OBI_0000398 image creation device An processed material which acquires images of fluorescence (induced with lasers) from labeled molecules on the surface of the microarray chip 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_0000932 material separation 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_0400108 heating block http://purl.obolibrary.org/obo/OBI_0001034 environmental control device A heating block is an instrument or part of an instrument which raises or maintains the temperature of a sample to a defined constant temperature during certain parts of an assay http://purl.obolibrary.org/obo/OBI_0400109 homogenizer http://purl.obolibrary.org/obo/OBI_0001033 perturbation device A homogenizer is an instrument for the homogenization of various types of material, such as tissue, plant, food, soil, and many others. http://purl.obolibrary.org/obo/OBI_0400110 hybridization chamber http://purl.obolibrary.org/obo/OBI_0001034 environmental control device A device which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide. http://purl.obolibrary.org/obo/OBI_0400111 hybridization station http://purl.obolibrary.org/obo/OBI_0001034 environmental control device A device which is used to maintain the temperature of one or more hybridization_chamber(s) at a defined, constant temperature. http://purl.obolibrary.org/obo/OBI_0400113 oligonucleotide synthesizer http://purl.obolibrary.org/obo/OBI_0001034 environmental control device An instrument used to chemically synthesize oligonucleotides. http://purl.obolibrary.org/obo/OBI_0400114 sonicator http://purl.obolibrary.org/obo/OBI_0001033 perturbation device A device that converts a variable electrical current to mechanical vibration of a metallic probe. The device is used for the lysis of cells, the mixing of compounds or solutions, to framgent molecules of DNA, or to create emulsions. http://purl.obolibrary.org/obo/OBI_0400115 spectrophotometer http://purl.obolibrary.org/obo/OBI_0000832 measurement device A spectrophotometer is an instrument that measures the intensity of light as a function of the color, or more specifically, the wavelength of light, transmitted by a substance. http://purl.obolibrary.org/obo/OBI_0400119 microarray wash station http://purl.obolibrary.org/obo/OBI_0001034 environmental control device a device that is used to wash Affymetrix-type arrays. http://purl.obolibrary.org/obo/OBI_0400120 temperature control bath http://purl.obolibrary.org/obo/OBI_0001034 environmental control device A temperature_control_bath is a device that has the function to regulate the temperature of a material, the function to contain fluid and the function to vary and maintain the temperature of the contained fluid. Heat exchange (energy transfer) between the material and the heating element is facilitated via the contained fluid. A temperature_control_bath is composed of a container, a heating element and/or a cooling element and a means to adjust the needed temperature. In most cases also a timer and a means to stir the fluid is provided as well. http://purl.obolibrary.org/obo/OBI_0400137 cytometer http://purl.obolibrary.org/obo/OBI_0000832 measurement device A cytometer is an instrument for counting and measuring cells. 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_0400153 droplet sorter http://purl.obolibrary.org/obo/OBI_0000932 material separation device A droplet sorter is part_of a flow cytometer sorter that converts the carrier fluid stream into individual droplets, and these droplets are directed into separate locations for recovery (enriching the original sample for particles of interest based on qualities determined by gating) or disposal. http://purl.obolibrary.org/obo/OBI_0400155 water bath http://purl.obolibrary.org/obo/OBI_0400120 temperature control bath A water bath is a temperature control bath in which a water acts as contact medium enabling temperature transfer from the heating element or cooling element to the sample. The temperature can be controlled in the 0 to 100 degree centigrade range (under normal pressure). http://purl.obolibrary.org/obo/OBI_0400168 microtome http://purl.obolibrary.org/obo/OBI_0000932 material separation device A microtome is a mechanical instrument used to cut biological specimens into very thin segments for further treatment (e.g. ISH) and ultimately microscopic or histologic examination. Most microtomes provide cooling facilities (cryo-microtome) and use a steel blade to cut a slice of defined thickness. Some are automatic, and some are driven by hand. http://purl.obolibrary.org/obo/OBI_0500001 clinical study design http://purl.obolibrary.org/obo/OBI_0500000 study design Plan for the precise procedure to be followed in a clinical trial, including planned and actual timing of events, choice of control group, method of allocating treatments, blinding methods; assigns a subject to pass through one or more epochs in the course of a trial. Specific design elements, e.g., crossover, parallel; dose-escalation [Modified from Pocock, Clinical Trials: A Practical Approach] http://purl.obolibrary.org/obo/OBI_0500002 repeated measure design http://purl.obolibrary.org/obo/OBI_0000115 intervention design a study design which use the same individuals and exposure them to a set of conditions. The effect of order and practice can be confounding factor in such designs http://purl.obolibrary.org/obo/OBI_0500003 cross over design http://purl.obolibrary.org/obo/OBI_0500002 repeated measure design a repeated measure design which ensures that experimental units receive, in sequence, the treatment (or the control), and then, after a specified time interval (aka *wash-out periods*), switch to the control (or treatment). In this design, subjects (patients in human context) serve as their own controls, and randomization may be used to determine the ordering which a subject receives the treatment and control http://purl.obolibrary.org/obo/OBI_0500004 n-to-1 design http://purl.obolibrary.org/obo/OBI_0500003 cross over design N-of-1 design is a cross-over design in which the same patient is repeatedly randomised to receive either the experimental treatment or its control (Senn, 1993). http://purl.obolibrary.org/obo/OBI_0500005 matched pairs design http://purl.obolibrary.org/obo/OBI_0500000 study design A matched pair design is a study design which use groups of individuals associated (hence matched) to each other based on a set of criteria, one member going to one treatment, the other member receiving the other treatment. http://purl.obolibrary.org/obo/OBI_0500007 randomized complete block design http://purl.obolibrary.org/obo/OBI_0000115 intervention design A randomized complete block design is_a study design which assigns randomly treatments to block. The number of units per block equals the number of treatment so each block receives each treatment exactly once (hence the qualifier 'complete'). The design was originally devised from field trials used in agronomy and agriculture. The analysis assumes that there is no interaction between block and treatment. The method was then used in other settings So The randomised complete block design is a design in which the subjects are matched according to a variable which the experimenter wishes to control. The subjects are put into groups (blocks) of the same size as the number of treatments. The members of each block are then randomly assigned to different treatment groups. http://purl.obolibrary.org/obo/OBI_0500008 balanced incomplete block design http://purl.obolibrary.org/obo/OBI_0500014 factorial design balanced incomplete block design is a kind of factorial design where all treatment pairs occur together within a block an equal number ?? times. ??ii' is the number of times treatment i occurs with i' http://purl.obolibrary.org/obo/OBI_0500009 loop design http://purl.obolibrary.org/obo/OBI_0500000 study design A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular design http://purl.obolibrary.org/obo/OBI_0500010 reference design http://purl.obolibrary.org/obo/OBI_0500000 study design A reference experiment design type is where all samples are compared to a common reference. http://purl.obolibrary.org/obo/OBI_0500011 latin square design http://purl.obolibrary.org/obo/OBI_0500007 randomized complete block design Latin square design is_a study design which allows in its simpler form controlling 2 levels of nuisance variables (also known as blocking variables).he 2 nuisance factors are divided into a tabular grid with the property that each row and each column receive each treatment exactly once. http://purl.obolibrary.org/obo/OBI_0500012 graeco latin square design http://purl.obolibrary.org/obo/OBI_0500007 randomized complete block design Greco-Latin square design is a study design which relates to Latin square design http://purl.obolibrary.org/obo/OBI_0500013 hyper graeco latin square design http://purl.obolibrary.org/obo/OBI_0500007 randomized complete block design PRS to do http://purl.obolibrary.org/obo/OBI_0500014 factorial design http://purl.obolibrary.org/obo/OBI_0500000 study design factorial design is_a study design which is used to evaluate two or more factors simultaneously. The treatments are combinations of levels of the factors. The advantages of factorial designs over one-factor-at-a-time experiments is that they are more efficient and they allow interactions to be detected. In statistics, a factorial design experiment is an experiment whose design consists of two or more factors, each with discrete possible values or levels, and whose experimental units take on all possible combinations of these levels across all such factors. Such an experiment allows studying the effect of each factor on the response variable, as well as the effects of interactions between factors on the response variable. http://purl.obolibrary.org/obo/OBI_0500015 2x2 factorial design http://purl.obolibrary.org/obo/OBI_0500014 factorial design a factorial design which has 2 experimental factors (aka independent variables) and 2 factor levels per experimental factors http://purl.obolibrary.org/obo/OBI_0500016 fractional factorial design http://purl.obolibrary.org/obo/OBI_0500014 factorial design A fractional factorial design is_a study design in which only an adequately chosen fraction of the treatment combinations required for the complete factorial experiment is selected to be run http://purl.obolibrary.org/obo/OBI_0500017 dye swap design http://purl.obolibrary.org/obo/OBI_0500000 study design An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip http://purl.obolibrary.org/obo/OBI_0500018 replicate design http://purl.obolibrary.org/obo/OBI_0500000 study design A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. http://purl.obolibrary.org/obo/OBI_0500019 self vs self design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that investigates variance and error estimates in the experimental system, and is where the same extract is compared. http://purl.obolibrary.org/obo/OBI_0500020 time series design http://purl.obolibrary.org/obo/OBI_0500000 study design Groups of assays that are related as part of a time series. 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_0600007 administering substance in vivo http://purl.obolibrary.org/obo/OBI_0000274 adding a material entity into a target A process by which a substance is intentionally given to an organism resulting in exposure of the organism to that substance. http://purl.obolibrary.org/obo/OBI_0600009 exposure of material to environment http://purl.obolibrary.org/obo/OBI_0000011 planned process a planned process in which an input material is exposed to a defined set of conditions in a controlled environment. The environment is a specified input. http://purl.obolibrary.org/obo/OBI_0600011 acclimatization http://purl.obolibrary.org/obo/OBI_0600009 exposure of material to environment A protocol application in which an object is left in an environment for some period of time, until some qualities of interest are in equilibrium with that environment. 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_0600022 excision http://purl.obolibrary.org/obo/OBI_0600014 material component separation the use physical means to remove a portion of a substance from the rest http://purl.obolibrary.org/obo/OBI_0600023 non specific enzymatic cleavage http://purl.obolibrary.org/obo/OBI_0000231 enzymatic cleavage a protocol application to digest the fraction of input material that is susceptible to that enzyme http://purl.obolibrary.org/obo/OBI_0600024 maintaining cell culture http://purl.obolibrary.org/obo/OBI_0000838 material maintenance a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing http://purl.obolibrary.org/obo/OBI_0600028 artificially induced reverse transcription http://purl.obolibrary.org/obo/OBI_0000094 material processing a protocol with the objective to transcribe single-stranded RNA into complementary DNA (cDNA) http://purl.obolibrary.org/obo/OBI_0600033 cell permeabilization http://purl.obolibrary.org/obo/OBI_0000094 material processing A protocol application to permeabilize cell membranes, allowing molecules to more easily pass through the membrane than was possible prior to the protocol application http://purl.obolibrary.org/obo/OBI_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_0600041 concentrate http://purl.obolibrary.org/obo/OBI_0600014 material component separation a protocol application to create an output material with an increased density of a material of interest that is part of the input material by separating other parts of the input material http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay http://purl.obolibrary.org/obo/OBI_0000070 assay the use of a chemical or biochemical means to infer the sequence of a biomaterial http://purl.obolibrary.org/obo/OBI_0600048 vector mediated amplification http://purl.obolibrary.org/obo/OBI_0600064 recombinant vector cloning The process of creating a copy of some biological entity in cell culture http://purl.obolibrary.org/obo/OBI_0600050 specific enzymatic cleavage http://purl.obolibrary.org/obo/OBI_0000231 enzymatic cleavage a protocol application to digest the fraction of input material that is susceptible to that enzyme http://purl.obolibrary.org/obo/OBI_0600056 protease cleavage http://purl.obolibrary.org/obo/OBI_0000231 enzymatic cleavage protease cleavage is an enzymatic cleavage which relies on enzyme with protease activity to act on proteins and produce polypeptides (protein fragments). http://purl.obolibrary.org/obo/OBI_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_1110021 infection http://purl.obolibrary.org/obo/OBI_1110122 pathologic process the detrimental process in which an infectious agent colonizes or replicates in a host environment http://purl.obolibrary.org/obo/OBI_1110022 adaptive immune receptor http://purl.obolibrary.org/obo/GO_0043234 protein complex is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes. http://purl.obolibrary.org/obo/OBI_1110055 obsolete_disease http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class placeholder to be imported from disease ontology http://purl.obolibrary.org/obo/OBI_1110093 disposition to infect an organism http://purl.obolibrary.org/obo/BFO_0000016 disposition Is a role borne by an agent, and realized when in contact with or inside another organism in which it is capable of replicating and causing disease http://purl.obolibrary.org/obo/OBI_1110108 material to be added http://purl.obolibrary.org/obo/BFO_0000040 material entity a material that is added to another one in a material combination process http://purl.obolibrary.org/obo/OBI_1110109 target of material addition http://purl.obolibrary.org/obo/BFO_0000040 material entity A material entity into which another is being added in a material combinatino process http://purl.obolibrary.org/obo/OBI_1110122 pathologic process http://purl.obolibrary.org/obo/GO_0008150 biological_process abnormal, harmful processes caused by or associated with a disease http://purl.obolibrary.org/obo/OGMS_0000015 clinical history http://purl.obolibrary.org/obo/IAO_0000030 information content entity A series of statements representing health-relevant qualities of a patient and of a patient's family. http://purl.obolibrary.org/obo/OGMS_0000023 phenotype http://purl.obolibrary.org/obo/BFO_0000019 quality A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. http://purl.obolibrary.org/obo/OGMS_0000031 disease http://purl.obolibrary.org/obo/BFO_0000016 disposition A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. http://purl.obolibrary.org/obo/OGMS_0000063 disease course http://purl.obolibrary.org/obo/GO_0008150 biological_process The totality of all processes through which a given disease instance is realized. http://purl.obolibrary.org/obo/OGMS_0000090 treatment http://purl.obolibrary.org/obo/OBI_0000011 planned process A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder http://purl.obolibrary.org/obo/PATO_0000011 age http://purl.obolibrary.org/obo/PATO_0000165 time A time quality inhering in a bearer by virtue of how long the bearer has existed. http://purl.obolibrary.org/obo/PATO_0000047 biological sex http://purl.obolibrary.org/obo/PATO_0001995 organismal quality An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. http://purl.obolibrary.org/obo/PATO_0000146 temperature http://purl.obolibrary.org/obo/PATO_0001018 physical quality A physical quality of the thermal energy of a system. http://purl.obolibrary.org/obo/PATO_0000383 female http://purl.obolibrary.org/obo/PATO_0001894 phenotypic sex A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. http://purl.obolibrary.org/obo/PATO_0000384 male http://purl.obolibrary.org/obo/PATO_0001894 phenotypic sex A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. http://purl.obolibrary.org/obo/PATO_0001338 mixed sex http://purl.obolibrary.org/obo/PATO_0002003 population quality A biological sex quality inhering in a population of multiple sexes. http://purl.obolibrary.org/obo/PATO_0001339 biomaterial purity http://purl.obolibrary.org/obo/PATO_0000025 composition A composition quality inhering in an bearer by virtue of the bearer's homogeneity of a biomaterial. http://purl.obolibrary.org/obo/PATO_0001340 hermaphrodite http://purl.obolibrary.org/obo/PATO_0001894 phenotypic sex A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual. http://purl.obolibrary.org/obo/PATO_0001341 a mating type (yeast) http://purl.obolibrary.org/obo/PATO_0001342 Saccharomyces cerevisiae mating type A S. cerevisiae mating type cells that secrete a pheromone that in alpha haploids stimulates processes that lead to mating. http://purl.obolibrary.org/obo/PATO_0001344 alpha mating type (yeast) http://purl.obolibrary.org/obo/PATO_0001342 Saccharomyces cerevisiae mating type A S. cerevisiae mating type cells that secrete a pheromone that stimulates a haploids. http://purl.obolibrary.org/obo/PATO_0001345 h minus http://purl.obolibrary.org/obo/PATO_0001343 Schizosaccharomyces pombe mating type A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 locus. http://purl.obolibrary.org/obo/PATO_0001346 h plus http://purl.obolibrary.org/obo/PATO_0001343 Schizosaccharomyces pombe mating type A S. pombe mating type determined by the mat1-Pc and mat1-Pi on the mat1 locus. http://purl.obolibrary.org/obo/PATO_0001347 F mating type http://purl.obolibrary.org/obo/PATO_0001335 bacterial mating type A bacterial mating type indicating the presence of F plasmid in a bacterial cell. http://purl.obolibrary.org/obo/PATO_0001348 F minus mating type http://purl.obolibrary.org/obo/PATO_0001335 bacterial mating type A bacterial mating type indicating the absence of F plasmid in a bacterial cell. http://purl.obolibrary.org/obo/PATO_0001374 ploidy http://purl.obolibrary.org/obo/PATO_0001396 cellular quality A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism. http://purl.obolibrary.org/obo/PATO_0001375 haploid http://purl.obolibrary.org/obo/PATO_0001393 euploid A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes. http://purl.obolibrary.org/obo/PATO_0001377 polyploid http://purl.obolibrary.org/obo/PATO_0001393 euploid A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes. http://purl.obolibrary.org/obo/PATO_0001385 aneuploid http://purl.obolibrary.org/obo/PATO_0001374 ploidy A ploidy quality inhering in a bearer by virtue of the bearer's containing a non-integral multiple of the monoploid number, due to extra or missing chromosomes. http://purl.obolibrary.org/obo/PATO_0001394 diploid http://purl.obolibrary.org/obo/PATO_0001393 euploid A ploidy quality inhering in a bearer by virtue of the bearer's having two copies (homologs) of each chromosome, usually one from the mother and one from the father. http://purl.obolibrary.org/obo/PATO_0001396 cellular quality http://purl.obolibrary.org/obo/PATO_0001241 physical object quality A monadic quality of continuant that exists at the cellular level of organisation. http://purl.obolibrary.org/obo/PATO_0001421 alive http://purl.obolibrary.org/obo/PATO_0000169 viability A viability quality inhering in a bearer by virtue of the bearer's condition before death. http://purl.obolibrary.org/obo/PATO_0001422 dead http://purl.obolibrary.org/obo/PATO_0000169 viability A viability quality inhering in a bearer by virtue of the cessation of the bearer's life. http://purl.obolibrary.org/obo/PATO_0001985 frozen http://purl.obolibrary.org/obo/PATO_0000146 temperature A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point. http://purl.obolibrary.org/obo/PATO_0001995 organismal quality http://purl.obolibrary.org/obo/PATO_0001241 physical object quality A quality that inheres in an entire organism or part of an organism. http://purl.obolibrary.org/obo/PR_000000001 protein http://purl.obolibrary.org/obo/CHEBI_16670 peptide An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA. http://purl.obolibrary.org/obo/PR_000001004 CD4 molecule http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence. http://purl.obolibrary.org/obo/PR_000023089 DNA ligase http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the Escherichia coli K-12 ligA gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/REO_0000171 molecular label role http://purl.obolibrary.org/obo/BFO_0000023 role a reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay. http://purl.obolibrary.org/obo/REO_0000280 molecular label http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity a molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay http://purl.obolibrary.org/obo/SO_0000001 region http://purl.obolibrary.org/obo/SO_0000110 sequence_feature 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_0001411 biological_region 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/SO_0000276 miRNA http://purl.obolibrary.org/obo/SO_0000655 ncRNA Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors. http://purl.obolibrary.org/obo/SO_0000988 circular http://purl.obolibrary.org/obo/SO_0000443 polymer_attribute A quality of a nucleotide polymer that has no terminal nucleotide residues. http://purl.obolibrary.org/obo/UO_0000001 length unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label A unit which is a standard measure of the distance between two points. http://purl.obolibrary.org/obo/UO_0000002 mass unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label A unit which is a standard measure of the amount of matter/energy of a physical object. http://purl.obolibrary.org/obo/UO_0000003 time unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label A unit which is a standard measure of the dimension in which events occur in sequence. http://purl.obolibrary.org/obo/UO_0000005 temperature unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter. http://purl.obolibrary.org/obo/UO_0000006 substance unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label A unit which is a standardised quantity of an element or compound with uniform composition. http://purl.obolibrary.org/obo/UO_0000008 meter http://purl.obolibrary.org/obo/UO_0000045 base unit A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second. http://purl.obolibrary.org/obo/UO_0000009 kilogram http://purl.obolibrary.org/obo/UO_0000045 base unit A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France. http://purl.obolibrary.org/obo/UO_0000010 second http://purl.obolibrary.org/obo/UO_0000045 base unit A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. http://purl.obolibrary.org/obo/UO_0000015 centimeter http://purl.obolibrary.org/obo/UO_0000001 length unit A length unit which is equal to one hundredth of a meter or 10^[-2] m. http://purl.obolibrary.org/obo/UO_0000016 millimeter http://purl.obolibrary.org/obo/UO_0000001 length unit A length unit which is equal to one thousandth of a meter or 10^[-3] m. http://purl.obolibrary.org/obo/UO_0000017 micrometer http://purl.obolibrary.org/obo/UO_0000001 length unit A length unit which is equal to one millionth of a meter or 10^[-6] m. http://purl.obolibrary.org/obo/UO_0000018 nanometer http://purl.obolibrary.org/obo/UO_0000001 length unit A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m. http://purl.obolibrary.org/obo/UO_0000021 gram http://purl.obolibrary.org/obo/UO_0000002 mass unit A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg. http://purl.obolibrary.org/obo/UO_0000022 milligram http://purl.obolibrary.org/obo/UO_0000002 mass unit A mass unit which is equal to one thousandth of a gram or 10^[-3] g. http://purl.obolibrary.org/obo/UO_0000023 microgram http://purl.obolibrary.org/obo/UO_0000002 mass unit A mass unit which is equal to one millionth of a gram or 10^[-6] g. http://purl.obolibrary.org/obo/UO_0000024 nanogram http://purl.obolibrary.org/obo/UO_0000002 mass unit A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g. http://purl.obolibrary.org/obo/UO_0000025 picogram http://purl.obolibrary.org/obo/UO_0000002 mass unit A mass unit which is equal to 10^[-12] g. http://purl.obolibrary.org/obo/UO_0000027 degree Celsius http://purl.obolibrary.org/obo/UO_0000005 temperature unit A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K. http://purl.obolibrary.org/obo/UO_0000031 minute http://purl.obolibrary.org/obo/UO_0000003 time unit A time unit which is equal to 60 seconds. http://purl.obolibrary.org/obo/UO_0000032 hour http://purl.obolibrary.org/obo/UO_0000003 time unit A time unit which is equal to 3600 seconds or 60 minutes. http://purl.obolibrary.org/obo/UO_0000033 day http://purl.obolibrary.org/obo/UO_0000003 time unit A time unit which is equal to 24 hours. http://purl.obolibrary.org/obo/UO_0000034 week http://purl.obolibrary.org/obo/UO_0000003 time unit A time unit which is equal to 7 days. http://purl.obolibrary.org/obo/UO_0000035 month http://purl.obolibrary.org/obo/UO_0000003 time unit A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days. http://purl.obolibrary.org/obo/UO_0000036 year http://purl.obolibrary.org/obo/UO_0000003 time unit A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days. http://purl.obolibrary.org/obo/UO_0000039 micromole http://purl.obolibrary.org/obo/UO_0000006 substance unit A substance unit equal to a millionth of a mol or 10^[-6] mol. http://purl.obolibrary.org/obo/UO_0000041 nanomole http://purl.obolibrary.org/obo/UO_0000006 substance unit A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol. http://purl.obolibrary.org/obo/UO_0000042 picomole http://purl.obolibrary.org/obo/UO_0000006 substance unit A substance unit equal to 10^[-12] mol. http://purl.obolibrary.org/obo/UO_0000051 concentration unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label A unit which represents a standard measurement of how much of a given substance there is mixed with another substance. http://purl.obolibrary.org/obo/UO_0000062 molar http://purl.obolibrary.org/obo/UO_0000061 unit of molarity A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L). http://purl.obolibrary.org/obo/UO_0000063 millimolar http://purl.obolibrary.org/obo/UO_0000061 unit of molarity A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M. http://purl.obolibrary.org/obo/UO_0000064 micromolar http://purl.obolibrary.org/obo/UO_0000061 unit of molarity A unit of molarity which is equal to one millionth of a molar or 10^[-6] M. http://purl.obolibrary.org/obo/UO_0000066 picomolar http://purl.obolibrary.org/obo/UO_0000061 unit of molarity A unit of molarity which is equal to 10^[-12] M. http://purl.obolibrary.org/obo/UO_0000095 volume unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. http://purl.obolibrary.org/obo/UO_0000097 cubic centimeter http://purl.obolibrary.org/obo/UO_0000095 volume unit A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml. http://purl.obolibrary.org/obo/UO_0000098 milliliter http://purl.obolibrary.org/obo/UO_0000095 volume unit A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter. http://purl.obolibrary.org/obo/UO_0000099 liter http://purl.obolibrary.org/obo/UO_0000095 volume unit A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter. http://purl.obolibrary.org/obo/UO_0000101 microliter http://purl.obolibrary.org/obo/UO_0000095 volume unit A volume unit which is equal to one millionth of a liter or 10^[-6] L. http://purl.obolibrary.org/obo/UO_0000102 nanoliter http://purl.obolibrary.org/obo/UO_0000095 volume unit A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L. http://purl.obolibrary.org/obo/UO_0000103 picoliter http://purl.obolibrary.org/obo/UO_0000095 volume unit A volume unit which is equal to 10^[-12] L. http://purl.obolibrary.org/obo/UO_0000163 mass percentage http://purl.obolibrary.org/obo/UO_0000187 percent A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture. http://purl.obolibrary.org/obo/UO_0000164 mass volume percentage http://purl.obolibrary.org/obo/UO_0000187 percent A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture. http://purl.obolibrary.org/obo/UO_0000165 volume percentage http://purl.obolibrary.org/obo/UO_0000205 volume per unit volume A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution. http://purl.obolibrary.org/obo/UO_0000175 gram per liter http://purl.obolibrary.org/obo/UO_0000052 mass density unit A mass unit density which is equal to mass of an object in grams divided by the volume in liters. http://purl.obolibrary.org/obo/UO_0000176 milligram per milliliter http://purl.obolibrary.org/obo/UO_0000052 mass density unit A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters. http://purl.obolibrary.org/obo/UO_0000196 pH http://purl.obolibrary.org/obo/UO_0000186 dimensionless unit A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+). http://purl.obolibrary.org/obo/UO_0000207 milliliter per liter http://purl.obolibrary.org/obo/UO_0000205 volume per unit volume A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution. http://purl.obolibrary.org/obo/UO_0000208 gram per deciliter http://purl.obolibrary.org/obo/UO_0000052 mass density unit A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters. http://purl.obolibrary.org/obo/CHEBI_26912 oxolanes http://purl.obolibrary.org/obo/CHEBI_38104 oxacycle Any oxacycle having an oxolane (tetrahydrofuran) skeleton. http://purl.obolibrary.org/obo/CHEBI_15956 biotin http://purl.obolibrary.org/obo/CHEBI_51570 biotins An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins. http://purl.obolibrary.org/obo/CHEBI_15986 polynucleotide http://purl.obolibrary.org/obo/CHEBI_33694 biomacromolecule A nucleobase-containing molecular entity with a polymeric structure comprised of a linear sequence of 13 or more nucleotide residues. http://purl.obolibrary.org/obo/CHEBI_16991 deoxyribonucleic acid http://purl.obolibrary.org/obo/CHEBI_33696 nucleic acid High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. http://purl.obolibrary.org/obo/CHEBI_17137 hydrogensulfite http://purl.obolibrary.org/obo/CHEBI_33482 sulfur oxoanion A sulfur oxoanion that has formula HO3S. http://purl.obolibrary.org/obo/CHEBI_18154 polysaccharide http://purl.obolibrary.org/obo/CHEBI_33694 biomacromolecule A biomacromolecule consisting of large numbers of monosaccharide residues linked glycosidically. This term is commonly used only for those containing more than ten monosaccharide residues. http://purl.obolibrary.org/obo/CHEBI_33696 nucleic acid http://purl.obolibrary.org/obo/CHEBI_15986 polynucleotide A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. http://purl.obolibrary.org/obo/CHEBI_33838 nucleoside http://purl.obolibrary.org/obo/CHEBI_21731 N-glycosyl compound An N-glycosyl compound that has both a nucleobase, normally adenine, guanine, xanthine, thymine, cytosine or uracil, and either a ribose or deoxyribose as functional parents. http://purl.obolibrary.org/obo/CHEBI_72695 organic molecule http://purl.obolibrary.org/obo/CHEBI_50860 organic molecular entity Any molecule that consists of at least one carbon atom as part of the electrically neutral entity. http://purl.obolibrary.org/obo/CL_0000000 cell http://purl.obolibrary.org/obo/BFO_0000040 material entity A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. http://purl.obolibrary.org/obo/CL_0000001 primary cultured cell http://purl.obolibrary.org/obo/CL_0000010 cultured cell A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged. http://purl.obolibrary.org/obo/CL_0000003 native cell http://purl.obolibrary.org/obo/CL_0000000 cell A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). http://purl.obolibrary.org/obo/CL_0000010 cultured cell http://purl.obolibrary.org/obo/CL_0000578 experimentally modified cell in vitro A cell in vitro that is or has been maintained or propagated as part of a cell culture. http://purl.obolibrary.org/obo/CL_0000021 female germ cell http://purl.obolibrary.org/obo/CL_0000586 germ cell Female germ cell is a germ cell that supports female gamete production. http://purl.obolibrary.org/obo/CL_0000023 oocyte http://purl.obolibrary.org/obo/CL_0000021 female germ cell A female germ cell that has entered meiosis. http://purl.obolibrary.org/obo/CL_0000034 stem cell http://purl.obolibrary.org/obo/CL_0011115 precursor cell 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://purl.obolibrary.org/obo/CL_0008001 hematopoietic precursor cell 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, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119. 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. http://purl.obolibrary.org/obo/CL_0000039 germ line cell http://purl.obolibrary.org/obo/CL_0000548 animal cell A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring. http://purl.obolibrary.org/obo/CL_0000040 monoblast http://purl.obolibrary.org/obo/CL_0002194 monopoietic cell A myeloid progenitor cell committed to the monocyte lineage. This cell is CD11b-positive, has basophilic cytoplasm, euchromatin, and the presence of a nucleolus. http://purl.obolibrary.org/obo/CL_0000048 multi fate stem cell http://purl.obolibrary.org/obo/CL_0002371 somatic cell A stem cell that can give rise to multiple lineages of cells. http://purl.obolibrary.org/obo/CL_0000049 common myeloid progenitor http://purl.obolibrary.org/obo/CL_0002032 hematopoietic oligopotent progenitor cell A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages. http://purl.obolibrary.org/obo/CL_0000050 megakaryocyte-erythroid progenitor cell http://purl.obolibrary.org/obo/CL_0011115 precursor cell A progenitor cell committed to the megakaryocyte and erythroid lineages. http://purl.obolibrary.org/obo/CL_0000051 common lymphoid progenitor http://purl.obolibrary.org/obo/CL_0011115 precursor cell A oligopotent progenitor cell committed to the lymphoid lineage. http://purl.obolibrary.org/obo/CL_0000055 non-terminally differentiated cell http://purl.obolibrary.org/obo/CL_0011115 precursor cell A precursor cell with a limited number of potential fates. http://purl.obolibrary.org/obo/CL_0000056 myoblast http://purl.obolibrary.org/obo/CL_0000680 muscle precursor cell A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair. http://purl.obolibrary.org/obo/CL_0000057 fibroblast http://purl.obolibrary.org/obo/CL_0002320 connective tissue cell A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. http://purl.obolibrary.org/obo/CL_0000066 epithelial cell http://purl.obolibrary.org/obo/CL_0000548 animal cell A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina. http://purl.obolibrary.org/obo/CL_0000071 blood vessel endothelial cell http://purl.obolibrary.org/obo/CL_0002139 endothelial cell of vascular tree An endothelial cell that lines the vasculature. http://purl.obolibrary.org/obo/CL_0000081 blood cell http://purl.obolibrary.org/obo/CL_0000988 hematopoietic cell A cell found predominately in the blood. http://purl.obolibrary.org/obo/CL_0000083 epithelial cell of pancreas http://www.ebi.ac.uk/efo/EFO_0002966 pancreatic cell An epithelial cell of the pancreas. http://purl.obolibrary.org/obo/CL_0000084 T cell http://purl.obolibrary.org/obo/CL_0000542 lymphocyte A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex. http://purl.obolibrary.org/obo/CL_0000094 granulocyte http://purl.obolibrary.org/obo/CL_0000766 myeloid leukocyte A leukocyte with abundant granules in the cytoplasm. http://purl.obolibrary.org/obo/CL_0000115 endothelial cell http://purl.obolibrary.org/obo/CL_0002078 meso-epithelial cell 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_0000133 neurectodermal cell http://purl.obolibrary.org/obo/CL_0000221 ectodermal cell Ectoderm destined to be nervous tissue. http://purl.obolibrary.org/obo/CL_0000134 mesenchymal stem cell http://purl.obolibrary.org/obo/CL_0002320 connective tissue cell A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. This cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs. http://purl.obolibrary.org/obo/CL_0000136 fat cell http://purl.obolibrary.org/obo/CL_0002320 connective tissue cell A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides. http://purl.obolibrary.org/obo/CL_0000147 pigment cell http://purl.obolibrary.org/obo/CL_0000325 stuff accumulating cell A pigment cell is a cell that contains pigment granules. http://purl.obolibrary.org/obo/CL_0000148 melanocyte http://purl.obolibrary.org/obo/CL_0002371 somatic cell A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance. http://purl.obolibrary.org/obo/CL_0000150 glandular epithelial cell http://purl.obolibrary.org/obo/CL_0002371 somatic cell A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules. http://purl.obolibrary.org/obo/CL_0000151 secretory cell http://purl.obolibrary.org/obo/CL_0000003 native cell A cell that specializes in controlled release of one or more substances. http://purl.obolibrary.org/obo/CL_0000152 exocrine cell http://purl.obolibrary.org/obo/CL_0000151 secretory cell A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct. 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_0000164 enteroendocrine cell http://purl.obolibrary.org/obo/CL_0000163 endocrine cell An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas. http://purl.obolibrary.org/obo/CL_0000169 type B pancreatic cell http://purl.obolibrary.org/obo/CL_0008024 pancreatic endocrine cell A cell that secretes insulin and is located towards the center of the islets of Langerhans. http://purl.obolibrary.org/obo/CL_0000170 glucagon secreting cell http://purl.obolibrary.org/obo/CL_0000167 peptide hormone secreting cell A cell that secretes glucagon. http://purl.obolibrary.org/obo/CL_0000171 pancreatic A cell http://purl.obolibrary.org/obo/CL_0008024 pancreatic endocrine 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://purl.obolibrary.org/obo/CL_0008024 pancreatic endocrine 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_0000181 metabolising cell http://purl.obolibrary.org/obo/CL_0000003 native cell A cell whose primary function is intermediary metabolism. http://purl.obolibrary.org/obo/CL_0000182 hepatocyte http://purl.obolibrary.org/obo/CL_0002371 somatic cell The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated. http://purl.obolibrary.org/obo/CL_0000183 contractile cell http://purl.obolibrary.org/obo/CL_0000003 native cell A cell whose primary function is to shorten. http://purl.obolibrary.org/obo/CL_0000187 muscle cell http://purl.obolibrary.org/obo/CL_0002371 somatic cell A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns. http://purl.obolibrary.org/obo/CL_0000211 electrically active cell http://purl.obolibrary.org/obo/CL_0000003 native cell A cell whose function is determined by the generation or the reception of an electric signal. http://purl.obolibrary.org/obo/CL_0000213 lining cell http://purl.obolibrary.org/obo/CL_0000215 barrier cell A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism. http://purl.obolibrary.org/obo/CL_0000215 barrier cell http://purl.obolibrary.org/obo/CL_0000003 native cell A cell whose primary function is to prevent the transport of stuff across compartments. http://purl.obolibrary.org/obo/CL_0000219 motile cell http://purl.obolibrary.org/obo/CL_0000003 native cell A cell that moves by its own activities. http://purl.obolibrary.org/obo/CL_0000221 ectodermal cell http://purl.obolibrary.org/obo/CL_0002321 embryonic cell A cell of the outer of the three germ layers of the embryo. http://purl.obolibrary.org/obo/CL_0000222 mesodermal cell http://purl.obolibrary.org/obo/CL_0002321 embryonic cell A cell of the middle germ layer of the embryo. http://purl.obolibrary.org/obo/CL_0000223 endodermal cell http://purl.obolibrary.org/obo/CL_0002321 embryonic cell A cell of the inner of the three germ layers of the embryo. http://purl.obolibrary.org/obo/CL_0000225 anucleate cell http://purl.obolibrary.org/obo/CL_0000003 native cell A cell that lacks a nucleus. http://purl.obolibrary.org/obo/CL_0000226 single nucleate cell http://purl.obolibrary.org/obo/CL_0002242 nucleate cell A cell with a single nucleus. 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 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_0000236 B cell http://purl.obolibrary.org/obo/CL_0000945 lymphocyte of B lineage A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity. http://purl.obolibrary.org/obo/CL_0000325 stuff accumulating cell http://purl.obolibrary.org/obo/CL_0000003 native cell A cell that is specialised to accumulate a particular substance(s). http://purl.obolibrary.org/obo/CL_0000333 migratory neural crest cell http://purl.obolibrary.org/obo/CL_0002321 embryonic cell A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body. http://purl.obolibrary.org/obo/CL_0000393 electrically responsive cell http://purl.obolibrary.org/obo/CL_0000211 electrically active cell A cell whose function is determined by its response to an electric signal. http://purl.obolibrary.org/obo/CL_0000412 polyploid cell http://purl.obolibrary.org/obo/CL_0000003 native cell A cell whose nucleus, or nuclei, each contain more than two haploid genomes. http://purl.obolibrary.org/obo/CL_0000448 white fat cell http://purl.obolibrary.org/obo/CL_0000136 fat cell Fat cells with light coloration and few mitochondria. They contain a scant ring of cytoplasm surrounding a single large lipid droplet or vacuole. http://purl.obolibrary.org/obo/CL_0000451 dendritic cell http://purl.obolibrary.org/obo/CL_0000738 leukocyte A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative). http://purl.obolibrary.org/obo/CL_0000458 serotonin secreting cell http://purl.obolibrary.org/obo/CL_0000457 biogenic amine secreting cell A cell type that secretes 5-Hydroxytryptamine (serotonin). http://purl.obolibrary.org/obo/CL_0000502 type D enteroendocrine cell http://purl.obolibrary.org/obo/CL_0000172 somatostatin secreting cell A cell found throughout the gastrointestinal tract and in the pancreas. They secrete somatostatin in both an endocrine and paracrine manner. Somatostatin inhibits gastrin, cholecystokinin, insulin, glucagon, pancreatic enzymes, and gastric hydrochloric acid. A variety of substances which inhibit gastric acid secretion (vasoactive intestinal peptide, calcitonin gene-related peptide, cholecystokinin, beta-adrenergic agonists, and gastric inhibitory peptide) are thought to act by releasing somatostatin. http://purl.obolibrary.org/obo/CL_0000513 cardiac muscle myoblast http://purl.obolibrary.org/obo/CL_0010021 cardiac myoblast A precursor cell destined to differentiate into cardiac muscle cell. http://purl.obolibrary.org/obo/CL_0000541 melanoblast http://purl.obolibrary.org/obo/CL_0002371 somatic cell A cell that originates from the neural crest and differentiates into a pigment cell. http://purl.obolibrary.org/obo/CL_0000542 lymphocyte http://purl.obolibrary.org/obo/CL_0002242 nucleate cell A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. http://purl.obolibrary.org/obo/CL_0000547 proerythroblast http://purl.obolibrary.org/obo/CL_0002242 nucleate cell An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers. 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. This cell is CD71-positive and lacks hematopoeitic lineage markers. http://purl.obolibrary.org/obo/CL_0000550 polychromatophilic erythroblast http://purl.obolibrary.org/obo/CL_0000765 erythroblast A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers. http://purl.obolibrary.org/obo/CL_0000552 orthochromatic erythroblast http://purl.obolibrary.org/obo/CL_0000765 erythroblast The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated. 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. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative). http://purl.obolibrary.org/obo/CL_0000556 megakaryocyte http://purl.obolibrary.org/obo/CL_1001610 bone marrow hematopoietic cell A giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow; mature blood platelets are released from its cytoplasm. http://purl.obolibrary.org/obo/CL_0000557 granulocyte monocyte progenitor cell http://purl.obolibrary.org/obo/CL_0011115 precursor cell A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata1 or 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 that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds. http://purl.obolibrary.org/obo/CL_0000559 promonocyte http://purl.obolibrary.org/obo/CL_0002194 monopoietic cell A precursor in the monocytic series, being a cell intermediate in development between the monoblast and monocyte. This cell is CD11b-positive and has fine azurophil granules. http://purl.obolibrary.org/obo/CL_0000566 angioblastic mesenchymal cell http://purl.obolibrary.org/obo/CL_0000134 mesenchymal stem cell A mesenchymal stem cell capable of developing into blood vessel endothelium. http://purl.obolibrary.org/obo/CL_0000576 monocyte http://purl.obolibrary.org/obo/CL_0011115 precursor cell Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells. http://purl.obolibrary.org/obo/CL_0000578 experimentally modified cell in vitro http://purl.obolibrary.org/obo/CL_0001034 cell in vitro A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. http://purl.obolibrary.org/obo/CL_0000586 germ cell http://purl.obolibrary.org/obo/CL_0000039 germ line cell The reproductive cell in multicellular organisms. http://purl.obolibrary.org/obo/CL_0000622 acinar cell http://purl.obolibrary.org/obo/CL_0000154 protein secreting 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_0000623 natural killer cell http://purl.obolibrary.org/obo/CL_0000542 lymphocyte A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells. http://purl.obolibrary.org/obo/CL_0000696 PP cell http://purl.obolibrary.org/obo/CL_0000167 peptide hormone secreting cell A cell that stores and secretes pancreatic polypeptide hormone. 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_0000737 striated muscle cell http://purl.obolibrary.org/obo/CL_0000187 muscle cell Muscle cell which has as its direct parts myofilaments organized into sarcomeres. http://purl.obolibrary.org/obo/CL_0000738 leukocyte http://purl.obolibrary.org/obo/CL_0000988 hematopoietic cell An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. http://purl.obolibrary.org/obo/CL_0000746 cardiac muscle cell http://purl.obolibrary.org/obo/CL_0002494 cardiocyte Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei. http://purl.obolibrary.org/obo/CL_0000763 myeloid cell http://purl.obolibrary.org/obo/CL_0000988 hematopoietic cell A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage. 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_0011115 precursor cell A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers. http://purl.obolibrary.org/obo/CL_0000766 myeloid leukocyte http://purl.obolibrary.org/obo/CL_0000763 myeloid cell A cell of the monocyte, granulocyte, or mast cell lineage. http://purl.obolibrary.org/obo/CL_0000767 basophil http://purl.obolibrary.org/obo/CL_0000094 granulocyte Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive. http://purl.obolibrary.org/obo/CL_0000771 eosinophil http://purl.obolibrary.org/obo/CL_0000094 granulocyte Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive. http://purl.obolibrary.org/obo/CL_0000775 neutrophil http://purl.obolibrary.org/obo/CL_0000094 granulocyte Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. http://purl.obolibrary.org/obo/CL_0000825 pro-NK cell http://purl.obolibrary.org/obo/CL_0000838 lymphoid lineage restricted progenitor cell A lymphoid progenitor cell that is committed to the natural killer cell lineage, expressing CD122 (IL-15) receptor, but lacking many of the phenotypic characteristics of later stages of natural killer cell development such as expression of NK activating and inhibitory molecules. In human this cell has the phenotype CD34-positive, CD45RA-positive, CD10-positive, CD117-negative, and CD161 negative. http://purl.obolibrary.org/obo/CL_0000826 pro-B cell http://purl.obolibrary.org/obo/CL_0000838 lymphoid lineage restricted progenitor cell A progenitor cell of the B cell lineage, with some lineage specific activity such as early stages of recombination of B cell receptor genes, but not yet fully committed to the B cell lineage until the expression of PAX5 occurs. http://purl.obolibrary.org/obo/CL_0000827 pro-T cell http://purl.obolibrary.org/obo/CL_0000838 lymphoid lineage restricted progenitor cell A lymphoid progenitor cell of the T cell lineage, with some lineage specific marker expression, but not yet fully committed to the T cell lineage. http://purl.obolibrary.org/obo/CL_0000835 myeloblast http://purl.obolibrary.org/obo/CL_0002242 nucleate cell The most primitive precursor in the granulocytic series, having fine, evenly distributed chromatin, several nucleoli, a high nuclear-to-cytoplasmic ration (5:1-7:1), and a nongranular basophilic cytoplasm. They reside in the bone marrow. http://purl.obolibrary.org/obo/CL_0000836 promyelocyte http://purl.obolibrary.org/obo/CL_0002242 nucleate cell A precursor in the granulocytic series, being a cell intermediate in development between a myeloblast and myelocyte, that has distinct nucleoli, a nuclear-to-cytoplasmic ratio of 5:1 to 3:1, and containing a few primary cytoplasmic granules. Markers for this cell are fucosyltransferase FUT4-positive, CD33-positive, integrin alpha-M-negative, low affinity immunoglobulin gamma Fc region receptor III-negative, and CD24-negative. http://purl.obolibrary.org/obo/CL_0000837 hematopoietic multipotent progenitor cell http://purl.obolibrary.org/obo/CL_0008001 hematopoietic precursor cell A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans. http://purl.obolibrary.org/obo/CL_0000838 lymphoid lineage restricted progenitor cell http://purl.obolibrary.org/obo/CL_0011115 precursor cell A progenitor cell restricted to the lymphoid lineage. http://purl.obolibrary.org/obo/CL_0000839 myeloid lineage restricted progenitor cell http://purl.obolibrary.org/obo/CL_0011115 precursor cell A progenitor cell restricted to the myeloid lineage. http://purl.obolibrary.org/obo/CL_0000842 mononuclear cell http://purl.obolibrary.org/obo/CL_0002087 nongranular leukocyte A leukocyte with a single non-segmented nucleus in the mature form. http://purl.obolibrary.org/obo/CL_0000945 lymphocyte of B lineage http://purl.obolibrary.org/obo/CL_0000542 lymphocyte A lymphocyte of B lineage is a lymphocyte that expresses CD19 on the cell surface. An additional defining characteristic is the commitment to express an immunoglobulin complex. http://purl.obolibrary.org/obo/CL_0000988 hematopoietic cell http://purl.obolibrary.org/obo/CL_0002371 somatic cell A cell of a hematopoietic lineage. http://purl.obolibrary.org/obo/CL_0001021 CD34-positive, CD38-positive common lymphoid progenitor http://purl.obolibrary.org/obo/CL_0000995 CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor A common lymphoid progenitor that is CD10-positive, CD45RA-positive, CD34-positive and CD38-positive. http://purl.obolibrary.org/obo/CL_0001024 CD34-positive, CD38-negative hematopoietic stem cell http://purl.obolibrary.org/obo/CL_0000037 hematopoietic stem cell CD133-positive hematopoietic stem cell is a hematopoietic stem cell that is CD34-positive, CD90-positive, and CD133-positive. http://purl.obolibrary.org/obo/CL_0001026 CD34-positive, CD38-positive common myeloid progenitor http://purl.obolibrary.org/obo/CL_0001059 common myeloid progenitor, CD34-positive A common myeloid progenitor that is CD34-positive, CD38-positive, IL3ra-low, CD10-negative, CD7-negative, CD45RA-negative, and IL-5Ralpha-negative. http://purl.obolibrary.org/obo/CL_0001027 CD7-negative lymphoid progenitor cell http://purl.obolibrary.org/obo/CL_0001012 CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor CD7-negative lymphoid progenitor cell is a lymphoid progenitor cell that is CD34-positive, CD7-negative and CD45RA-negative. http://purl.obolibrary.org/obo/CL_0001034 cell in vitro http://purl.obolibrary.org/obo/CL_0000000 cell A cell that is maintained or propagated in a controlled artificial environment for use in an investigation. http://purl.obolibrary.org/obo/CL_0001035 bone cell http://purl.obolibrary.org/obo/CL_0000548 animal cell A connective tissue cell found in bone. http://purl.obolibrary.org/obo/CL_0001059 common myeloid progenitor, CD34-positive http://purl.obolibrary.org/obo/CL_0011115 precursor cell A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages. These cells are CD34-positive, and express Gata1, Gata2, C/EBPa, and Pu.1. http://purl.obolibrary.org/obo/CL_0001060 hematopoietic oligopotent progenitor cell, lineage-negative http://purl.obolibrary.org/obo/CL_0002032 hematopoietic oligopotent progenitor cell A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers. http://purl.obolibrary.org/obo/CL_0002009 macrophage dendritic cell progenitor http://purl.obolibrary.org/obo/CL_0011115 precursor cell A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages. http://purl.obolibrary.org/obo/CL_0002031 hematopoietic lineage restricted progenitor cell http://purl.obolibrary.org/obo/CL_0008001 hematopoietic precursor cell A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells. http://purl.obolibrary.org/obo/CL_0002032 hematopoietic oligopotent progenitor cell http://purl.obolibrary.org/obo/CL_0008001 hematopoietic precursor cell A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers. 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 A hematopoietic multipotent progenitor cell that is CD34-positive, CD38-negative, CD45RA-negative, and CD90-negative. http://purl.obolibrary.org/obo/CL_0002064 pancreatic acinar cell http://purl.obolibrary.org/obo/CL_1001599 pancreas exocrine glandular cell A secretory cell found in pancreatic acini that secretes digestive enzymes and mucins. This cell is a typical zymogenic cell, have a basal nucleus and basophilic cytoplasm consisting of regular arrays of granular endoplasmic reticulum with mitochondria and dense secretory granules. http://purl.obolibrary.org/obo/CL_0002067 type A enterocrine cell http://purl.obolibrary.org/obo/CL_0000170 glucagon secreting cell An enterocrine cell that produces glucagon. http://purl.obolibrary.org/obo/CL_0002076 endo-epithelial cell http://purl.obolibrary.org/obo/CL_0002371 somatic cell An epithelial cell derived from endoderm. http://purl.obolibrary.org/obo/CL_0002078 meso-epithelial cell http://purl.obolibrary.org/obo/CL_0002371 somatic cell Epithelial cell derived from mesoderm or mesenchyme. http://purl.obolibrary.org/obo/CL_0002079 pancreatic ductal cell http://purl.obolibrary.org/obo/CL_1001433 epithelial cell of exocrine pancreas Epithelial cell found in the ducts of the pancreas. This cell type contributes to the high luminal pH. http://purl.obolibrary.org/obo/CL_0002087 nongranular leukocyte http://purl.obolibrary.org/obo/CL_0000738 leukocyte A leukocyte that lacks granules. http://purl.obolibrary.org/obo/CL_0002092 bone marrow cell http://purl.obolibrary.org/obo/CL_0001035 bone cell A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells. http://purl.obolibrary.org/obo/CL_0002139 endothelial cell of vascular tree http://purl.obolibrary.org/obo/CL_0000115 endothelial cell An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. http://purl.obolibrary.org/obo/CL_0002191 granulocytopoietic cell http://purl.obolibrary.org/obo/CL_0000839 myeloid lineage restricted progenitor cell A cell involved in the formation of a granulocyte. 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_0002194 monopoietic cell http://purl.obolibrary.org/obo/CL_0000839 myeloid lineage restricted progenitor cell A cell involved in the formation of a monocyte (monopoiesis). http://purl.obolibrary.org/obo/CL_0002202 epithelial cell of tracheobronchial tree http://purl.obolibrary.org/obo/CL_0002632 epithelial cell of lower respiratory tract An epithelial cell of the tracheobronchial tree. http://purl.obolibrary.org/obo/CL_0002242 nucleate cell http://purl.obolibrary.org/obo/CL_0000003 native cell A cell containing at least one nucleus. http://purl.obolibrary.org/obo/CL_0002275 pancreatic PP cell http://purl.obolibrary.org/obo/CL_0008024 pancreatic endocrine cell A PP cell located in the islets of the pancreas. http://purl.obolibrary.org/obo/CL_0002293 epithelial cell of thymus http://purl.obolibrary.org/obo/CL_0002076 endo-epithelial cell An epithelial cell of the thymus. Epithelial reticular cells are pleomorphic, stellate, non-phagocytic cells which seem to be supportive in function and are held together by desmosomes. They replace the fibroblastoid reticular cells found in other lymphoid organs. Other epithelial cells in the medulla have the ultrastructure of secretory cells. Although different epithelial cells throughout the thymus appear alike by light microscopy their ultrastructure and function varies. http://purl.obolibrary.org/obo/CL_0002320 connective tissue cell http://purl.obolibrary.org/obo/CL_0002371 somatic cell A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone. http://purl.obolibrary.org/obo/CL_0002321 embryonic cell http://purl.obolibrary.org/obo/CL_0000548 animal cell A cell of the embryo. http://purl.obolibrary.org/obo/CL_0002322 embryonic stem cell http://purl.obolibrary.org/obo/CL_0002321 embryonic cell A stem cell of embryonic origin. http://purl.obolibrary.org/obo/CL_0002328 bronchial epithelial cell http://purl.obolibrary.org/obo/CL_0002202 epithelial cell of tracheobronchial tree An epithelial cell of the bronchus. http://purl.obolibrary.org/obo/CL_0002334 preadipocyte http://purl.obolibrary.org/obo/CL_0000057 fibroblast An undifferentiated fibroblast that can be stimulated to form a fat cell. http://purl.obolibrary.org/obo/CL_0002351 progenitor cell of endocrine pancreas http://purl.obolibrary.org/obo/CL_0000048 multi fate stem cell 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_0002365 medullary thymic epithelial cell http://purl.obolibrary.org/obo/CL_0002293 epithelial cell of thymus 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_0002076 endo-epithelial cell An endo-epithelial cell of the respiratory tract. http://purl.obolibrary.org/obo/CL_0002371 somatic cell http://purl.obolibrary.org/obo/CL_0000003 native cell A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). http://purl.obolibrary.org/obo/CL_0002494 cardiocyte http://purl.obolibrary.org/obo/CL_0002371 somatic cell A cell located in the heart, including both muscle and non muscle cells. http://purl.obolibrary.org/obo/CL_0002544 aortic endothelial cell http://purl.obolibrary.org/obo/CL_1000413 endothelial cell of artery An arterial endothelial cell that is part of the aorta endothelium. http://purl.obolibrary.org/obo/CL_0002546 embryonic blood vessel endothelial progenitor cell http://purl.obolibrary.org/obo/CL_0002371 somatic cell An endothelial progenitor cell that participates in angiogenesis during development. http://purl.obolibrary.org/obo/CL_0005018 ghrelin secreting cell http://purl.obolibrary.org/obo/CL_0000167 peptide hormone secreting cell A cell that secretes ghrelin, the peptide hormone that stimulates hunger. http://purl.obolibrary.org/obo/CL_0005019 pancreatic epsilon cell http://purl.obolibrary.org/obo/CL_0005018 ghrelin secreting cell Ghrelin secreting cells found in the found in the exocrine pancreas. http://purl.obolibrary.org/obo/CL_0005026 hepatoblast http://purl.obolibrary.org/obo/CL_0000048 multi fate stem cell Multi fate stem cell that gives rise to to both hepatocytes and cholangiocytes as descendants. http://purl.obolibrary.org/obo/CL_0007004 premigratory neural crest cell http://purl.obolibrary.org/obo/CL_0000003 native cell Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells. http://purl.obolibrary.org/obo/CL_0008001 hematopoietic precursor cell http://purl.obolibrary.org/obo/CL_0000988 hematopoietic cell Any hematopoietic cell that is a precursor of some other hematopoietic cell type. http://purl.obolibrary.org/obo/CL_1000413 endothelial cell of artery http://purl.obolibrary.org/obo/CL_0000071 blood vessel endothelial cell A blood vessel endothelial cell that is part of an arterial endothelium. http://purl.obolibrary.org/obo/CL_1000415 epithelial cell of gall bladder http://purl.obolibrary.org/obo/CL_0002371 somatic cell An epithelial cell that is part of the gallbladder. http://purl.obolibrary.org/obo/CL_1000488 cholangiocyte http://purl.obolibrary.org/obo/CL_0000069 branched duct 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. http://purl.obolibrary.org/obo/CL_1001433 epithelial cell of exocrine pancreas http://purl.obolibrary.org/obo/CL_0000083 epithelial cell of pancreas An epithelial cell of the exocrine pancreas. http://purl.obolibrary.org/obo/CL_1001599 pancreas exocrine glandular cell http://purl.obolibrary.org/obo/CL_1001433 epithelial cell of exocrine pancreas Glandular cell of exocrine pancreas epithelium. Example: pancreatic acinar cell, glandular cells in pancreatic canaliculi, glandular cells in pancreatic ducts. http://purl.obolibrary.org/obo/CL_1001610 bone marrow hematopoietic cell http://purl.obolibrary.org/obo/CL_0002092 bone marrow cell Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes. http://purl.obolibrary.org/obo/UBERON_0000007 pituitary gland http://purl.obolibrary.org/obo/UBERON_0010314 structure with developmental contribution from neural crest The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN]. http://purl.obolibrary.org/obo/UBERON_0000014 zone of skin http://purl.obolibrary.org/obo/UBERON_0004121 ectoderm-derived structure Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis. http://purl.obolibrary.org/obo/UBERON_0000016 endocrine pancreas http://purl.obolibrary.org/obo/UBERON_0004119 endoderm-derived structure The part of the pancreas that is part of the endocrine system and is made up of islet cells, which produce insulin, glucagon and somatostatin. http://purl.obolibrary.org/obo/UBERON_0000020 sense organ http://purl.obolibrary.org/obo/UBERON_0000062 organ An organ that is capable of transducing sensory stimulus to the nervous system. http://purl.obolibrary.org/obo/UBERON_0000029 lymph node http://purl.obolibrary.org/obo/UBERON_0005057 immune organ Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph. http://purl.obolibrary.org/obo/UBERON_0000059 large intestine http://purl.obolibrary.org/obo/UBERON_0013765 digestive system element A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong]. http://purl.obolibrary.org/obo/UBERON_0000065 respiratory tract http://purl.obolibrary.org/obo/UBERON_0004119 endoderm-derived structure Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts http://purl.obolibrary.org/obo/UBERON_0000160 intestine http://purl.obolibrary.org/obo/UBERON_0004921 subdivision of digestive tract Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine. http://purl.obolibrary.org/obo/UBERON_0000178 blood http://purl.obolibrary.org/obo/UBERON_0000463 organism substance Circulating body substance which consists of blood plasma and hemoglobin-carrying red blood cells. Excludes blood analogues (see UBERON:0000179 haemolymphatic fluid). http://purl.obolibrary.org/obo/UBERON_0000945 stomach http://purl.obolibrary.org/obo/UBERON_0013765 digestive system element An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. http://purl.obolibrary.org/obo/UBERON_0000948 heart http://purl.obolibrary.org/obo/UBERON_0010314 structure with developmental contribution from neural crest A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. http://purl.obolibrary.org/obo/UBERON_0000955 brain http://purl.obolibrary.org/obo/UBERON_0004121 ectoderm-derived structure The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. http://purl.obolibrary.org/obo/UBERON_0000966 retina http://purl.obolibrary.org/obo/UBERON_0004923 organ component layer The retina is 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/UBERON_0000970 eye http://purl.obolibrary.org/obo/UBERON_0000020 sense organ An organ that detects light. http://purl.obolibrary.org/obo/UBERON_0000992 female gonad http://purl.obolibrary.org/obo/UBERON_0003133 reproductive organ the gonad of a female organism which contains germ cells http://purl.obolibrary.org/obo/UBERON_0000995 uterus http://purl.obolibrary.org/obo/UBERON_0013515 subdivision of uterine tube the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth http://purl.obolibrary.org/obo/UBERON_0000996 vagina http://purl.obolibrary.org/obo/UBERON_0013515 subdivision of uterine tube A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]. http://purl.obolibrary.org/obo/UBERON_0000998 seminal vesicle http://purl.obolibrary.org/obo/UBERON_0005399 male reproductive gland Either of a pair of glandular pouches that lie one on either side of the male reproductive tract and in the human male secrete a sugar- and protein-containing fluid into the ejaculatory duct. http://purl.obolibrary.org/obo/UBERON_0001044 saliva-secreting gland http://purl.obolibrary.org/obo/UBERON_0010047 oral gland saliva-secreting exocrine glands of the oral cavity[GO] http://purl.obolibrary.org/obo/UBERON_0001091 calcareous tooth http://purl.obolibrary.org/obo/UBERON_0010314 structure with developmental contribution from neural crest Organ with a cavity which consist of dentine surrounded by enamel. Examples: incisor, molar. http://purl.obolibrary.org/obo/UBERON_0001103 diaphragm http://purl.obolibrary.org/obo/UBERON_0005181 thoracic segment organ A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control http://purl.obolibrary.org/obo/UBERON_0001132 parathyroid gland http://purl.obolibrary.org/obo/UBERON_0002368 endocrine gland The parathyroid gland is an endocrine gland for secretion of parathyroid hormone, usually found as a pair, embedded in the connective tissue capsule on the posterior surface of the thyroid gland. Parathyroid regulates calcium and phosphorous metabolism. http://purl.obolibrary.org/obo/UBERON_0001134 skeletal muscle tissue http://purl.obolibrary.org/obo/UBERON_0002036 striated muscle tissue Muscle tissue that consists primarily of skeletal muscle fibers. http://purl.obolibrary.org/obo/UBERON_0001153 caecum http://purl.obolibrary.org/obo/UBERON_0009854 digestive tract diverticulum A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction. http://purl.obolibrary.org/obo/UBERON_0001154 vermiform appendix http://purl.obolibrary.org/obo/UBERON_0013765 digestive system element A blind-ended tube connected to the cecum, from which it develops embryologically[WP]. http://purl.obolibrary.org/obo/UBERON_0001155 colon http://purl.obolibrary.org/obo/UBERON_0004921 subdivision of digestive tract Last portion of the large intestine before it becomes the rectum. http://purl.obolibrary.org/obo/UBERON_0001159 sigmoid colon http://purl.obolibrary.org/obo/UBERON_0000168 segment of colon The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity. http://purl.obolibrary.org/obo/UBERON_0001165 pyloric antrum http://purl.obolibrary.org/obo/UBERON_0000064 organ part the area at the bottom of the stomach on the caudal side of the pyloric canal that contains gastrin-producing G cells, which stimulate acid production, and the luminal pH-sensitive population of somatostatin-producing D cells http://purl.obolibrary.org/obo/UBERON_0001255 urinary bladder http://purl.obolibrary.org/obo/UBERON_0004120 mesoderm-derived structure distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]. http://purl.obolibrary.org/obo/UBERON_0001301 epididymis http://purl.obolibrary.org/obo/UBERON_0005904 duct of male reproductive system the elongated structure connected to the posterior surface of the testis that transports, stores, and matures spermatozoa between testis and vas deferens http://purl.obolibrary.org/obo/UBERON_0001558 lower respiratory tract http://purl.obolibrary.org/obo/UBERON_0000072 segment of respiratory tract The segment of respiratory tract from the trachea to the lungs[WP,modified] http://purl.obolibrary.org/obo/UBERON_0001637 artery http://purl.obolibrary.org/obo/UBERON_0003509 arterial blood vessel An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. http://purl.obolibrary.org/obo/UBERON_0001723 tongue http://purl.obolibrary.org/obo/UBERON_0013765 digestive system element A muscular organ in the floor of the mouth. http://purl.obolibrary.org/obo/UBERON_0001736 submandibular gland http://purl.obolibrary.org/obo/UBERON_0010314 structure with developmental contribution from neural crest Either of the paired compound tubuloalveolar (aka tubuloacinar) major salivary glands composed of both serous and mucous secretory cells and situated beneath the mandible. http://purl.obolibrary.org/obo/UBERON_0001831 parotid gland http://purl.obolibrary.org/obo/UBERON_0010314 structure with developmental contribution from neural crest The parotid gland is the largest of the salivary glands. It is found wrapped around the mandibular ramus, and it secretes saliva through Stensen's duct into the oral cavity, to facilitate mastication and swallowing. [WP,unvetted]. http://purl.obolibrary.org/obo/UBERON_0001872 parietal lobe http://purl.obolibrary.org/obo/UBERON_0016526 lobe of cerebral hemisphere Upper central part of the cerebral hemisphere. (MSH) http://purl.obolibrary.org/obo/UBERON_0002046 thyroid gland http://purl.obolibrary.org/obo/UBERON_0010314 structure with developmental contribution from neural crest A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO]. http://purl.obolibrary.org/obo/UBERON_0002048 lung http://purl.obolibrary.org/obo/UBERON_0015212 lateral structure Respiration organ that develops as an oupocketing of the esophagus. http://purl.obolibrary.org/obo/UBERON_0002106 spleen http://purl.obolibrary.org/obo/UBERON_0017672 abdominal viscera the organ that functions to filter blood and to store red corpuscles and platelets http://purl.obolibrary.org/obo/UBERON_0002107 liver http://purl.obolibrary.org/obo/UBERON_0006925 digestive gland An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. http://purl.obolibrary.org/obo/UBERON_0002108 small intestine http://purl.obolibrary.org/obo/UBERON_0013765 digestive system element Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong]. http://purl.obolibrary.org/obo/UBERON_0002110 gall bladder http://purl.obolibrary.org/obo/UBERON_0017672 abdominal viscera An organ that aids digestion and stores bile produced by the liver[WP]. http://purl.obolibrary.org/obo/UBERON_0002113 kidney http://purl.obolibrary.org/obo/UBERON_0015212 lateral structure A paired organ of the urinary tract which has the production of urine as its primary function. http://purl.obolibrary.org/obo/UBERON_0002114 duodenum http://purl.obolibrary.org/obo/UBERON_0004921 subdivision of digestive tract The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one). http://purl.obolibrary.org/obo/UBERON_0002116 ileum http://purl.obolibrary.org/obo/UBERON_0004921 subdivision of digestive tract the portion of the small intestine that extends from the jejunum to the colon http://purl.obolibrary.org/obo/UBERON_0002185 bronchus http://purl.obolibrary.org/obo/UBERON_0000117 respiratory tube the upper conducting airways of the lung; these airways arise from the terminus of the trachea http://purl.obolibrary.org/obo/UBERON_0002240 spinal cord http://purl.obolibrary.org/obo/UBERON_0010314 structure with developmental contribution from neural crest Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO) http://purl.obolibrary.org/obo/UBERON_0002336 corpus callosum http://purl.obolibrary.org/obo/UBERON_0001018 axon tract White matter structure containing massive numbers of commissural fibers connecting cortical areas in the two cerebral hemispheres.it is subdivided into a genu, a rostrum, a body, and a splenium. (MM) http://purl.obolibrary.org/obo/UBERON_0002358 peritoneum http://purl.obolibrary.org/obo/UBERON_0000042 serous membrane A serous membrane that lines the peritoneal cavity[VHOG,modified]. http://purl.obolibrary.org/obo/UBERON_0002367 prostate gland http://purl.obolibrary.org/obo/UBERON_0010147 male accessory sex gland The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid. http://purl.obolibrary.org/obo/UBERON_0002368 endocrine gland http://purl.obolibrary.org/obo/UBERON_0002530 gland Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. http://purl.obolibrary.org/obo/UBERON_0002370 thymus http://purl.obolibrary.org/obo/UBERON_0004177 hemopoietic organ Anatomical structure of largely lymphoid tissue that functions in cell-mediated immunity by being the site where T cells develop. http://purl.obolibrary.org/obo/UBERON_0002372 tonsil http://purl.obolibrary.org/obo/UBERON_0034769 lymphomyeloid tissue either of the two small almond-shaped masses of lymph tissue found on either side of the oropharynx http://purl.obolibrary.org/obo/UBERON_0002384 connective tissue http://purl.obolibrary.org/obo/UBERON_0000479 tissue Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. http://purl.obolibrary.org/obo/UBERON_0002394 bile duct http://purl.obolibrary.org/obo/UBERON_0004119 endoderm-derived structure Any of the ducts that form the biliary tree, carrying bile from the liver to the small intestine. http://purl.obolibrary.org/obo/UBERON_0002405 immune system http://purl.obolibrary.org/obo/UBERON_0000061 anatomical structure Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies. http://purl.obolibrary.org/obo/UBERON_0002407 pericardium http://purl.obolibrary.org/obo/UBERON_0006914 squamous epithelium The combination of pericardial sac (a double-walled sac containing the heart and the roots of the great vessels) plus fibrous pericardium. http://purl.obolibrary.org/obo/UBERON_0003126 trachea http://purl.obolibrary.org/obo/UBERON_0000117 respiratory tube The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. http://purl.obolibrary.org/obo/UBERON_0003133 reproductive organ http://purl.obolibrary.org/obo/UBERON_0005156 reproductive structure An organ involved in reproduction http://purl.obolibrary.org/obo/UBERON_0003889 fallopian tube http://purl.obolibrary.org/obo/UBERON_0015212 lateral structure Initial section of the oviduct through which the ova pass from the ovary to the uterus http://purl.obolibrary.org/obo/UBERON_0005057 immune organ http://purl.obolibrary.org/obo/UBERON_0000062 organ An organ that is part of a immune system [Automatically generated definition]. http://purl.obolibrary.org/obo/CHEBI_16670 peptide http://purl.obolibrary.org/obo/CHEBI_37622 carboxamide Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. http://purl.obolibrary.org/obo/CHEBI_21731 N-glycosyl compound http://purl.obolibrary.org/obo/CHEBI_78616 carbohydrates and carbohydrate derivatives A glycosyl compound arising formally from the elimination of water from a glycosidic hydroxy group and an H atom bound to a nitrogen atom, thus creating a C-N bond. http://purl.obolibrary.org/obo/CHEBI_24828 indoles http://purl.obolibrary.org/obo/CHEBI_22728 benzopyrrole Any compound containing an indole skeleton. http://purl.obolibrary.org/obo/CHEBI_33551 organosulfonic acid http://purl.obolibrary.org/obo/CHEBI_33424 sulfur oxoacid derivative An organic derivative of sulfonic acid in which the sulfo group is linked directly to carbon. http://purl.obolibrary.org/obo/CHEBI_33575 carboxylic acid http://purl.obolibrary.org/obo/CHEBI_35605 carbon oxoacid A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid. http://purl.obolibrary.org/obo/CHEBI_33833 heteroarene http://purl.obolibrary.org/obo/CHEBI_33659 organic aromatic compound A heterocyclic compound formally derived from an arene by replacement of one or more methine (-C=) and/or vinylene (-CH=CH-) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous pi-electron system characteristic of aromatic systems and a number of out-of-plane pi-electrons corresponding to the Hueckel rule (4n+2). http://purl.obolibrary.org/obo/CHEBI_35352 organonitrogen compound http://purl.obolibrary.org/obo/CHEBI_51143 nitrogen molecular entity Any heteroorganic entity containing at least one carbon-nitrogen bond. http://purl.obolibrary.org/obo/CHEBI_36586 carbonyl compound http://purl.obolibrary.org/obo/CHEBI_36963 organooxygen compound Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives. http://purl.obolibrary.org/obo/CHEBI_36963 organooxygen compound http://purl.obolibrary.org/obo/CHEBI_36962 organochalcogen compound An organochalcogen compound containing at least one carbon-oxygen bond. http://purl.obolibrary.org/obo/CHEBI_37622 carboxamide http://purl.obolibrary.org/obo/CHEBI_33256 primary amide An amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom. http://purl.obolibrary.org/obo/CHEBI_38104 oxacycle http://purl.obolibrary.org/obo/CHEBI_36963 organooxygen compound Any organic heterocyclic compound containing at least one ring oxygen atom. http://purl.obolibrary.org/obo/CHEBI_50860 organic molecular entity http://purl.obolibrary.org/obo/CHEBI_33675 p-block molecular entity Any molecular entity that contains carbon. http://purl.obolibrary.org/obo/CHEBI_33256 primary amide http://purl.obolibrary.org/obo/CHEBI_51143 nitrogen molecular entity A derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group. http://purl.obolibrary.org/obo/CHEBI_51570 biotins http://purl.obolibrary.org/obo/CHEBI_38297 thiabicycloalkane Compounds containing a biotin (5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid) skeleton. http://purl.obolibrary.org/obo/CHEBI_78616 carbohydrates and carbohydrate derivatives http://purl.obolibrary.org/obo/CHEBI_36963 organooxygen compound Any organooxygen compound that is a polyhydroxy-aldehyde or -ketone, or a compound derived from one. Carbohydrates contain only carbon, hydrogen and oxygen and usually have an empirical formula Cm(H2O)n; carbohydrate derivatives may contain other elements by substitution or condensation. http://purl.obolibrary.org/obo/CHEBI_33694 biomacromolecule http://purl.obolibrary.org/obo/CHEBI_50860 organic molecular entity A macromolecule formed by a living organism. http://purl.obolibrary.org/obo/CHEBI_33697 ribonucleic acid http://purl.obolibrary.org/obo/CHEBI_33696 nucleic acid High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. http://purl.obolibrary.org/obo/CHEBI_68472 pyrimidine deoxyribonucleoside http://purl.obolibrary.org/obo/CHEBI_26440 pyrimidine nucleoside A deoxyribonucleoside containing a pyrimidine base. http://purl.obolibrary.org/obo/CHEBI_37960 cyanine dye http://purl.obolibrary.org/obo/CHEBI_35352 organonitrogen compound Cyanine dyes are synthetic dyes with the general formula R2N[CH=CH]nCH=N(+)R2 <-> R2N(+)=CH[CH=CH]nNR2 (n is a small number) in which the nitrogen and part of the conjugated chain usually form part of a heterocyclic system, such as imidazole, pyridine, pyrrole, quinoline and thiazole. http://purl.obolibrary.org/obo/CHEBI_33273 polyatomic anion http://purl.obolibrary.org/obo/CHEBI_36358 polyatomic ion An anion consisting of more than one atom. http://purl.obolibrary.org/obo/CHEBI_33579 main group molecular entity http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table. http://purl.obolibrary.org/obo/CHEBI_33595 cyclic compound http://purl.obolibrary.org/obo/CHEBI_25367 molecule Any molecule that consists of a series of atoms joined together to form a ring. http://purl.obolibrary.org/obo/CHEBI_472552 5-bromo-2'-deoxyuridine http://purl.obolibrary.org/obo/CHEBI_19255 pyrimidine 2'-deoxyribonucleoside A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase. http://purl.obolibrary.org/obo/CHEBI_51756 Alexa Fluor 532 http://purl.obolibrary.org/obo/CHEBI_38164 organic heteropentacyclic compound An organosulfonic acid that has formula C34H33N3O11S2. http://purl.obolibrary.org/obo/CHEBI_51760 Alexa Fluor 546 http://purl.obolibrary.org/obo/CHEBI_38164 organic heteropentacyclic compound An organic heteropentacyclic compound that has formula C44H46Cl3N4NaO14S3. http://purl.obolibrary.org/obo/GO_0005575 cellular_component http://purl.obolibrary.org/obo/BFO_0000040 material entity The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. http://purl.obolibrary.org/obo/GO_0005730 nucleolus http://purl.obolibrary.org/obo/GO_0044446 intracellular organelle part A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. http://purl.obolibrary.org/obo/GO_0006139 nucleobase-containing compound metabolic process http://purl.obolibrary.org/obo/GO_1901360 organic cyclic compound metabolic process Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. http://purl.obolibrary.org/obo/GO_0006304 DNA modification http://purl.obolibrary.org/obo/GO_0006259 DNA metabolic process The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties. http://purl.obolibrary.org/obo/GO_0006306 DNA methylation http://purl.obolibrary.org/obo/GO_0060255 regulation of macromolecule metabolic process The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. http://purl.obolibrary.org/obo/GO_0006323 DNA packaging http://purl.obolibrary.org/obo/GO_0051276 chromosome organization Any process in which DNA and associated proteins are formed into a compact, orderly structure. http://purl.obolibrary.org/obo/GO_0006338 chromatin remodeling http://purl.obolibrary.org/obo/GO_0016568 chromatin modification Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation. http://purl.obolibrary.org/obo/GO_0006725 cellular aromatic compound metabolic process http://purl.obolibrary.org/obo/GO_0044237 cellular metabolic process The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells. http://purl.obolibrary.org/obo/GO_0006810 transport http://purl.obolibrary.org/obo/GO_0051234 establishment of localization The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. http://purl.obolibrary.org/obo/GO_0006811 ion transport http://purl.obolibrary.org/obo/GO_0044765 single-organism transport The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. http://purl.obolibrary.org/obo/GO_0006812 cation transport http://purl.obolibrary.org/obo/GO_0006811 ion transport The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. http://purl.obolibrary.org/obo/GO_0006996 organelle organization http://purl.obolibrary.org/obo/GO_0009987 cellular process A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. http://purl.obolibrary.org/obo/GO_0007113 endomitotic cell cycle http://purl.obolibrary.org/obo/GO_0007049 cell cycle A mitotic cell cycle in which chromosomes are replicated and sister chromatids separate, but spindle formation, nuclear membrane breakdown and nuclear division do not occur, resulting in an increased number of chromosomes in the cell. http://purl.obolibrary.org/obo/GO_0007143 female meiotic division http://purl.obolibrary.org/obo/GO_0006996 organelle organization A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the female germline. http://purl.obolibrary.org/obo/GO_0007159 leukocyte cell-cell adhesion http://purl.obolibrary.org/obo/GO_0016337 single organismal cell-cell adhesion The attachment of a leukocyte to another cell via adhesion molecules. http://purl.obolibrary.org/obo/GO_0007276 gamete generation http://purl.obolibrary.org/obo/GO_0044702 single organism reproductive process The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell. http://purl.obolibrary.org/obo/GO_0007281 germ cell development http://purl.obolibrary.org/obo/GO_0048468 cell development The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism. http://purl.obolibrary.org/obo/GO_0007565 female pregnancy http://purl.obolibrary.org/obo/GO_0044703 multi-organism reproductive process The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth. http://purl.obolibrary.org/obo/GO_0007596 blood coagulation http://purl.obolibrary.org/obo/GO_0050878 regulation of body fluid levels The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers. http://purl.obolibrary.org/obo/GO_0008015 blood circulation http://purl.obolibrary.org/obo/GO_0003013 circulatory system process The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products. http://purl.obolibrary.org/obo/GO_0008152 metabolic process http://purl.obolibrary.org/obo/GO_0008150 biological_process The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. http://purl.obolibrary.org/obo/GO_0015031 protein transport http://purl.obolibrary.org/obo/GO_0051179 localization The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. http://purl.obolibrary.org/obo/GO_0015671 oxygen transport http://purl.obolibrary.org/obo/GO_0044765 single-organism transport The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. http://purl.obolibrary.org/obo/GO_0015844 monoamine transport http://purl.obolibrary.org/obo/GO_0071705 nitrogen compound transport The directed movement of monoamines, organic compounds that contain one amino group that is connected to an aromatic ring by an ethylene group (-CH2-CH2-), into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. http://purl.obolibrary.org/obo/GO_0015850 organic hydroxy compound transport http://purl.obolibrary.org/obo/GO_0071702 organic substance transport The directed movement of an organic hydroxy compound (organic alcohol) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. An organic hydroxy compound is an organic compound having at least one hydroxy group attached to a carbon atom. http://purl.obolibrary.org/obo/GO_0016043 cellular component organization http://purl.obolibrary.org/obo/GO_0008150 biological_process A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. http://purl.obolibrary.org/obo/GO_0019219 regulation of nucleobase-containing compound metabolic process http://purl.obolibrary.org/obo/GO_0051171 regulation of nitrogen compound metabolic process Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. http://purl.obolibrary.org/obo/GO_0019538 protein metabolic process http://purl.obolibrary.org/obo/GO_0044238 primary metabolic process The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification. http://purl.obolibrary.org/obo/GO_0022610 biological adhesion http://purl.obolibrary.org/obo/GO_0008150 biological_process The attachment of a cell or organism to a substrate or other organism. http://purl.obolibrary.org/obo/GO_0030017 sarcomere http://purl.obolibrary.org/obo/GO_0044449 contractile fiber part The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs. http://purl.obolibrary.org/obo/GO_0030529 ribonucleoprotein complex http://purl.obolibrary.org/obo/GO_0044424 intracellular part A macromolecular complex containing both protein and RNA molecules. http://purl.obolibrary.org/obo/GO_0034641 cellular nitrogen compound metabolic process http://purl.obolibrary.org/obo/GO_0044237 cellular metabolic process The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells. http://purl.obolibrary.org/obo/GO_0034645 cellular macromolecule biosynthetic process http://purl.obolibrary.org/obo/GO_0009059 macromolecule biosynthetic process The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, carried out by individual cells. http://purl.obolibrary.org/obo/GO_0036211 protein modification process http://purl.obolibrary.org/obo/GO_0043412 macromolecule modification The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification). http://purl.obolibrary.org/obo/GO_0042886 amide transport http://purl.obolibrary.org/obo/GO_0071705 nitrogen compound transport The directed movement of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. http://purl.obolibrary.org/obo/GO_0043170 macromolecule metabolic process http://purl.obolibrary.org/obo/GO_0071704 organic substance metabolic process The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. http://purl.obolibrary.org/obo/GO_0043231 intracellular membrane-bounded organelle http://purl.obolibrary.org/obo/GO_0043229 intracellular organelle Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. http://purl.obolibrary.org/obo/GO_0043412 macromolecule modification http://purl.obolibrary.org/obo/GO_0043170 macromolecule metabolic process The covalent alteration of one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule, resulting in a change in its properties. http://purl.obolibrary.org/obo/GO_0044238 primary metabolic process http://purl.obolibrary.org/obo/GO_0008152 metabolic process The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. http://purl.obolibrary.org/obo/GO_0044249 cellular biosynthetic process http://purl.obolibrary.org/obo/GO_0044237 cellular metabolic process The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. http://purl.obolibrary.org/obo/GO_0044260 cellular macromolecule metabolic process http://purl.obolibrary.org/obo/GO_0044237 cellular metabolic process The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells. http://purl.obolibrary.org/obo/GO_0044267 cellular protein metabolic process http://purl.obolibrary.org/obo/GO_0044260 cellular macromolecule metabolic process The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification. http://purl.obolibrary.org/obo/GO_0044449 contractile fiber part http://purl.obolibrary.org/obo/GO_0044444 cytoplasmic part Any constituent part of a contractile fiber, a fiber composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle. http://purl.obolibrary.org/obo/GO_0044464 cell part http://purl.obolibrary.org/obo/GO_0005575 cellular_component Any constituent part of a cell, the basic structural and functional unit of all organisms. http://purl.obolibrary.org/obo/GO_0044706 multi-multicellular organism process http://purl.obolibrary.org/obo/GO_0051704 multi-organism process A multicellular organism process which involves another multicellular organism of the same or different species. http://purl.obolibrary.org/obo/GO_0044710 single-organism metabolic process http://purl.obolibrary.org/obo/GO_0044699 single-organism process A metabolic process - chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances - which involves a single organism. http://purl.obolibrary.org/obo/GO_0044765 single-organism transport http://purl.obolibrary.org/obo/GO_1902578 single-organism localization The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore, involving a single organism. http://purl.obolibrary.org/obo/GO_0048477 oogenesis http://purl.obolibrary.org/obo/GO_0007281 germ cell development The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster. http://purl.obolibrary.org/obo/GO_0048609 multicellular organismal reproductive process http://purl.obolibrary.org/obo/GO_0022414 reproductive process The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs. http://purl.obolibrary.org/obo/GO_0050896 response to stimulus http://purl.obolibrary.org/obo/GO_0008150 biological_process Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. http://purl.obolibrary.org/obo/GO_0051234 establishment of localization http://purl.obolibrary.org/obo/GO_0051179 localization The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location. http://purl.obolibrary.org/obo/GO_0060047 heart contraction http://purl.obolibrary.org/obo/GO_0003013 circulatory system process The multicellular organismal process in which the heart decreases in volume in a characteristic way to propel blood through the body. http://purl.obolibrary.org/obo/GO_0071702 organic substance transport http://purl.obolibrary.org/obo/GO_0006810 transport The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon. http://purl.obolibrary.org/obo/GO_0071704 organic substance metabolic process http://purl.obolibrary.org/obo/GO_0008152 metabolic process The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. http://purl.obolibrary.org/obo/GO_0071705 nitrogen compound transport http://purl.obolibrary.org/obo/GO_0006810 transport The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. http://purl.obolibrary.org/obo/GO_0080090 regulation of primary metabolic process http://purl.obolibrary.org/obo/GO_0019222 regulation of metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. http://purl.obolibrary.org/obo/GO_0090304 nucleic acid metabolic process http://purl.obolibrary.org/obo/GO_0043170 macromolecule metabolic process Any cellular metabolic process involving nucleic acids. http://purl.obolibrary.org/obo/GO_1901576 organic substance biosynthetic process http://purl.obolibrary.org/obo/GO_0009058 biosynthetic process The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. http://purl.obolibrary.org/obo/GO_0051594 detection of glucose http://purl.obolibrary.org/obo/GO_0009746 response to hexose The series of events in which a glucose stimulus is received by a cell and converted into a molecular signal. http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/GO_0008150 biological_process Any process that modulates a measurable attribute of any biological process, quality or function. http://purl.obolibrary.org/obo/UBERON_0000006 islet of Langerhans http://purl.obolibrary.org/obo/UBERON_0034922 cell cluster the clusters of hormone-producing cells that are scattered throughout the pancreas http://purl.obolibrary.org/obo/UBERON_0000025 tube http://purl.obolibrary.org/obo/UBERON_0004111 anatomical conduit Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. http://purl.obolibrary.org/obo/UBERON_0000042 serous membrane http://purl.obolibrary.org/obo/UBERON_0004457 cavity lining multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer. http://purl.obolibrary.org/obo/UBERON_0000044 dorsal root ganglion http://purl.obolibrary.org/obo/UBERON_0010313 neural crest-derived structure * Sensory ganglia located on the dorsal spinal roots within the vertebral column. The spinal ganglion cells are pseudounipolar. The single primary branch bifurcates sending a peripheral process to carry sensory information from the periphery and a central branch which relays that information to the spinal cord or brain. (MSH) * ganglion found on the posterior root of each spinal nerve, composed of the unipolar nerve cell bodies of the sensory neurons of the nerve. (CSP) http://purl.obolibrary.org/obo/UBERON_0000045 ganglion http://purl.obolibrary.org/obo/UBERON_0034922 cell cluster A biological tissue mass, most commonly a mass of nerve cell bodies. http://purl.obolibrary.org/obo/UBERON_0000058 duct http://purl.obolibrary.org/obo/UBERON_0000025 tube A tubular structure that transports or secretes substances. http://purl.obolibrary.org/obo/UBERON_0000061 anatomical structure http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. http://purl.obolibrary.org/obo/UBERON_0000062 organ http://purl.obolibrary.org/obo/UBERON_0010000 multicellular anatomical structure Anatomical structure that performs a specific function or group of functions [WP]. http://purl.obolibrary.org/obo/UBERON_0000063 organ segment http://purl.obolibrary.org/obo/UBERON_0000064 organ part Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball[FMA]. http://purl.obolibrary.org/obo/UBERON_0000064 organ part http://purl.obolibrary.org/obo/UBERON_0000061 anatomical structure Anatomical structure which has as its direct parts two or more types of tissue and is continuous with one or more anatomical structures likewise constituted by two or more portions of tissues distinct from those of their complement. Examples: osteon, cortical bone, neck of femur, bronchopulmonary segment, left lobe of liver, anterior right side of heart, interventricular branch of left coronary artery, right atrium, mitral valve, head of pancreas[FMA]. http://purl.obolibrary.org/obo/UBERON_0000068 embryo stage http://purl.obolibrary.org/obo/UBERON_0000105 life cycle stage A life cycle stage that starts with fertilization and ends with the fully formed embryo. http://purl.obolibrary.org/obo/UBERON_0000072 segment of respiratory tract http://purl.obolibrary.org/obo/UBERON_0004119 endoderm-derived structure An organ segment that is part of a respiratory tract [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0000077 mixed endoderm/mesoderm-derived structure http://purl.obolibrary.org/obo/UBERON_0004120 mesoderm-derived structure An anatomical structure that develops from the endoderm and the mesoderm. http://purl.obolibrary.org/obo/UBERON_0000078 mixed ectoderm/mesoderm/endoderm-derived structure http://purl.obolibrary.org/obo/UBERON_0004121 ectoderm-derived structure An anatomical structure that develops from the ectoderm, mesoderm and endoderm. http://purl.obolibrary.org/obo/UBERON_0000092 post-embryonic stage http://purl.obolibrary.org/obo/UBERON_0000105 life cycle stage stage succeeding embryo, including mature structure http://purl.obolibrary.org/obo/UBERON_0000105 life cycle stage http://purl.obolibrary.org/obo/GO_0008150 biological_process A spatiotemporal region encompassing some part of the life cycle of an organism. http://purl.obolibrary.org/obo/UBERON_0000113 post-juvenile adult stage http://purl.obolibrary.org/obo/UBERON_0000105 life cycle stage The stage of being a sexually mature adult animal. http://purl.obolibrary.org/obo/UBERON_0000115 lung epithelium http://purl.obolibrary.org/obo/UBERON_0004815 lower respiratory tract epithelium The epithelial layer of the lung. http://purl.obolibrary.org/obo/UBERON_0000117 respiratory tube http://purl.obolibrary.org/obo/UBERON_0004119 endoderm-derived structure A tube in the respiratory system. Examples: bronchus, bronchiole, trachea. http://purl.obolibrary.org/obo/UBERON_0000122 neuron projection bundle http://purl.obolibrary.org/obo/UBERON_0005162 multi cell part structure A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. http://purl.obolibrary.org/obo/UBERON_0000168 segment of colon http://purl.obolibrary.org/obo/UBERON_0004921 subdivision of digestive tract An organ segment that is part of a colon [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0000200 gyrus http://purl.obolibrary.org/obo/UBERON_0010314 structure with developmental contribution from neural crest A ridge on the cerebral cortex. It is generally surrounded by one or more sulci . http://purl.obolibrary.org/obo/UBERON_0000359 preputial gland http://purl.obolibrary.org/obo/UBERON_0003937 sex gland A aired, lobulated, modified sebaceous glands located in the inguinal region adjacent to the penis and vagina, with pheromonal functions in male rodents; in males, the preputial gland empties into the preputial cavity and in females, the preputial (aka clitoral) gland duct empties into the clitoral fossa. http://purl.obolibrary.org/obo/UBERON_0000451 prefrontal cortex http://purl.obolibrary.org/obo/UBERON_0010314 structure with developmental contribution from neural crest The anterior part of the frontal lobes of the brain, lying in front of the motor and premotor areas.nnThis brain region has been implicated in planning complex cognitive behaviors, personality expression, decision making and moderating correct social behavior. The basic activity of this brain region is considered to be orchestration of thoughts and actions in accordance with internal goals.nnThe most typical psychological term for functions carried out by the pre-frontal cortex area is executive function. Executive function relates to abilities to differentiate among conflicting thoughts, determine good and bad, better and best, same and different, future consequences of current activities, working toward a defined goal, prediction of outcomes, expectation based on actions, and social 'control' (the ability to suppress urges that, if not suppressed, could lead to socially-unacceptable outcomes).nnMany authors have indicated an integral link between a person's personality and the functions of the prefrontal cortex. - definition adapted from Wikipedia http://purl.obolibrary.org/obo/UBERON_0000463 organism substance http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity http://purl.obolibrary.org/obo/UBERON_0001062 anatomical entity Anatomical entity that has mass. http://purl.obolibrary.org/obo/UBERON_0000468 multicellular organism http://purl.obolibrary.org/obo/UBERON_0010000 multicellular anatomical structure Anatomical structure that is an individual member of a species and consists of more than one cell. http://purl.obolibrary.org/obo/UBERON_0000471 compound organ component http://purl.obolibrary.org/obo/UBERON_0000481 multi-tissue structure Multi-tissue structure that is part of a compound organ. http://purl.obolibrary.org/obo/UBERON_0000475 organism subdivision http://purl.obolibrary.org/obo/UBERON_0010000 multicellular anatomical structure Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. http://purl.obolibrary.org/obo/UBERON_0000477 anatomical cluster http://purl.obolibrary.org/obo/UBERON_0001062 anatomical entity Anatomical group that has its parts adjacent to one another. http://purl.obolibrary.org/obo/UBERON_0000478 extraembryonic structure http://purl.obolibrary.org/obo/UBERON_0000061 anatomical structure A multicellular anatomical structure that is 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/UBERON_0000479 tissue http://purl.obolibrary.org/obo/UBERON_0010000 multicellular anatomical structure Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. http://purl.obolibrary.org/obo/UBERON_0000481 multi-tissue structure http://purl.obolibrary.org/obo/UBERON_0010000 multicellular anatomical structure Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. http://purl.obolibrary.org/obo/UBERON_0000483 epithelium http://purl.obolibrary.org/obo/UBERON_0000479 tissue Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. http://purl.obolibrary.org/obo/UBERON_0000485 simple columnar epithelium http://purl.obolibrary.org/obo/UBERON_0000490 unilaminar epithelium Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA] http://purl.obolibrary.org/obo/UBERON_0000487 simple squamous epithelium http://purl.obolibrary.org/obo/UBERON_0006914 squamous epithelium Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA] http://purl.obolibrary.org/obo/UBERON_0000489 cavitated compound organ http://purl.obolibrary.org/obo/UBERON_0003103 compound organ Compound organ that contains one or more macroscopic anatomical spaces. http://purl.obolibrary.org/obo/UBERON_0000490 unilaminar epithelium http://purl.obolibrary.org/obo/UBERON_0000483 epithelium Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA] http://purl.obolibrary.org/obo/UBERON_0000922 embryo http://purl.obolibrary.org/obo/UBERON_0000468 multicellular organism Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. http://purl.obolibrary.org/obo/UBERON_0000923 germ layer http://purl.obolibrary.org/obo/UBERON_0010316 germ layer / neural crest A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm. http://purl.obolibrary.org/obo/UBERON_0000924 ectoderm http://purl.obolibrary.org/obo/UBERON_0000923 germ layer Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. http://purl.obolibrary.org/obo/UBERON_0000925 endoderm http://purl.obolibrary.org/obo/UBERON_0000923 germ layer Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. http://purl.obolibrary.org/obo/UBERON_0000926 mesoderm http://purl.obolibrary.org/obo/UBERON_0000923 germ layer The middle germ layer of the embryo, between the endoderm and ectoderm. http://purl.obolibrary.org/obo/UBERON_0000956 cerebral cortex http://purl.obolibrary.org/obo/UBERON_0011215 central nervous system cell part cluster The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex. http://purl.obolibrary.org/obo/UBERON_0000981 femur http://purl.obolibrary.org/obo/UBERON_0015022 hindlimb endochondral element Endochondral longbone connecting the pelvic girdle with posterior zeugopodium skeleton.[VSAO, modified]. http://purl.obolibrary.org/obo/UBERON_0000982 skeletal joint http://purl.obolibrary.org/obo/UBERON_0034921 multi organ part structure Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. http://purl.obolibrary.org/obo/UBERON_0000988 pons http://purl.obolibrary.org/obo/UBERON_0010314 structure with developmental contribution from neural crest Brainstrem structure that has as its parts the pontine tegmentum and basal part of pons[FMA]. http://purl.obolibrary.org/obo/UBERON_0001013 adipose tissue http://purl.obolibrary.org/obo/UBERON_0002384 connective tissue Portion of connective tissue composed of adipocytes enmeshed in areolar tissue http://purl.obolibrary.org/obo/UBERON_0001018 axon tract http://purl.obolibrary.org/obo/UBERON_0011215 central nervous system cell part cluster A group of axons linking two or more neuropils and having a common origin, termination[FBbt]. http://purl.obolibrary.org/obo/UBERON_0001040 yolk sac http://purl.obolibrary.org/obo/UBERON_0005631 extraembryonic membrane A sac-like expansion of the ventral wall of the intestine, narrowed into a yolk stalk near the body[Hyman's]. Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes[WP]. http://purl.obolibrary.org/obo/UBERON_0001062 anatomical entity http://purl.obolibrary.org/obo/CARO_0001008 gross anatomical part Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. http://purl.obolibrary.org/obo/UBERON_0001064 ventral pancreatic duct http://purl.obolibrary.org/obo/UBERON_0007329 pancreatic duct A duct joining the pancreas to the common bile duct to supply pancreatic juices which aid in digestion provided by the exocrine pancreas. The pancreatic duct joins the common bile duct just prior to the ampulla of Vater, after which both ducts perforate the medial side of the second portion of the duodenum at the major duodenal papilla. http://purl.obolibrary.org/obo/UBERON_0001088 urine http://purl.obolibrary.org/obo/UBERON_0000463 organism substance Excretion that is the output of a kidney http://purl.obolibrary.org/obo/UBERON_0001133 cardiac muscle tissue http://purl.obolibrary.org/obo/UBERON_0010314 structure with developmental contribution from neural crest Muscle composed of cardiac muscle cells that is part of the heart[ZFA]. involuntary striated muscle found in the walls of the heart, specifically the myocardium[Wikipedia]. Tissue which consists of cardiac myocytes surrounded by cardiac endomysium. Examples: Cardiac muscle tissue proper, conducting tissue of heart[FMA]. http://purl.obolibrary.org/obo/UBERON_0001263 pancreatic acinus http://purl.obolibrary.org/obo/UBERON_0009842 glandular acinus The secretory units of the exocrine pancreas, where fluid containing digestive enzymes is produced; consists of a group of secretory cells surrounding a luminal space that connects to the pancreatic duct. http://purl.obolibrary.org/obo/UBERON_0001343 seminiferous tubule of testis http://purl.obolibrary.org/obo/UBERON_0005904 duct of male reproductive system the tubules in the testes where spermatogenesis occurs http://purl.obolibrary.org/obo/UBERON_0001347 white adipose tissue http://purl.obolibrary.org/obo/UBERON_0001013 adipose tissue Connective tissue consisting of fat-storing cells and arranged in lobular groups or along minor blood vessels[MP,modified] http://purl.obolibrary.org/obo/UBERON_0001348 brown adipose tissue http://purl.obolibrary.org/obo/UBERON_0001013 adipose tissue A thermogenic form of adipose tissue that is composed of brown adipocytes[MP,modified] http://purl.obolibrary.org/obo/UBERON_0001388 gastrocnemius http://purl.obolibrary.org/obo/UBERON_0004256 hindlimb zeugopod muscle The most superficial muscle of the triceps surae group, in the posterior portion of the lower hindleg. http://purl.obolibrary.org/obo/UBERON_0001389 soleus muscle http://purl.obolibrary.org/obo/UBERON_0004256 hindlimb zeugopod muscle A deep muscle of the triceps surae group, in the superficial posterior compartment of the leg. http://purl.obolibrary.org/obo/UBERON_0001474 bone element http://purl.obolibrary.org/obo/UBERON_0004765 skeletal element Skeletal element that is composed of bone tissue. http://purl.obolibrary.org/obo/UBERON_0001485 knee joint http://purl.obolibrary.org/obo/UBERON_0011139 synovial limb joint The knee joint joins the thigh with the leg and consists of two articulations: one between the femur and tibia, and one between the femur and patella. It is the largest and most complicated joint in the human body. The knee is a mobile trocho-ginglymus (i.e. a pivotal hinge joint), which permits flexion and extension as well as a slight medial and lateral rotation[WP,unvetted]. http://purl.obolibrary.org/obo/UBERON_0001515 thoracic aorta http://purl.obolibrary.org/obo/UBERON_0005800 segment of aorta the part of the aorta that extends from the origin at the heart to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest http://purl.obolibrary.org/obo/UBERON_0001516 abdominal aorta http://purl.obolibrary.org/obo/UBERON_0005800 segment of aorta Abdominal part of aorta: the distal part of the descending aorta, which is the continuation of the thoracic part and gives rise to the inferior phrenic, lumbar, median sacral, superior and inferior mesenteric, middle suprarenal, renal, and testicular or ovarian arteries, and celiac trunk[BTO]. The abdominal aorta is the largest artery in the abdominal cavity. As part of the aorta, it is a direct continuation of descending aorta(of the thorax). [WP,unvetted]. http://purl.obolibrary.org/obo/UBERON_0001630 muscle organ http://purl.obolibrary.org/obo/UBERON_0000062 organ Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. Nonparenchymatous organ that primarily consists of skeletal muscle tissue aggregated into macroscopic fasciculi by connective tissue; together with other muscles, it constitutes the muscular system. Examples: biceps, diaphragm, masseter, right third external intercostal muscle, external oblique, levator ani, serratus anterior[FMA]. http://purl.obolibrary.org/obo/UBERON_0001805 autonomic ganglion http://purl.obolibrary.org/obo/UBERON_0000045 ganglion ganglion that has dendrites that form a junction between autonomic nerves originating from the central nervous system and autonomic nerves innervating their target organs in the periphery. There are two subtypes, sympathetic ganglion and parasympathetic ganglion. http://purl.obolibrary.org/obo/UBERON_0001806 sympathetic ganglion http://purl.obolibrary.org/obo/UBERON_0010313 neural crest-derived structure A ganglion of the sympathetic nervous system. Examples: paravertebral and the prevertebral ganglia, which include the sympathetic chain ganglia, the superior, middle, and inferior cervical ganglia, and the aorticorenal, celiac, and stellate ganglia http://purl.obolibrary.org/obo/UBERON_0001807 paravertebral ganglion http://purl.obolibrary.org/obo/UBERON_0001806 sympathetic ganglion Trunk ganglion which is part of a bilaterally paired set of sympathetic ganglia located anterior and lateral to the spinal cord. http://purl.obolibrary.org/obo/UBERON_0001808 parasympathetic ganglion http://purl.obolibrary.org/obo/UBERON_0010313 neural crest-derived structure Ganglion containing neurons that receive innervation from parasympathetic neurons in the central nervous system and subserves parasympathetic functions through innervation of smooth muscle, cardiac muscle and glands. http://purl.obolibrary.org/obo/UBERON_0001829 major salivary gland http://purl.obolibrary.org/obo/UBERON_0015212 lateral structure One of the three largest glands of the oral cavity that secrete most of the saliva, including the parotid, submandibular, and sublingual glands. http://purl.obolibrary.org/obo/UBERON_0001870 frontal cortex http://purl.obolibrary.org/obo/UBERON_0005401 cerebral hemisphere gray matter Anterior portion of the neocortex, lying anterior to the central sulcus in humans. It is bounded by the parietal cortex posteriorly and the temporal cortex laterally[NIFSTD,modified]. http://purl.obolibrary.org/obo/UBERON_0001873 caudate nucleus http://purl.obolibrary.org/obo/UBERON_0009663 telencephalic nucleus Subcortical nucleus of telecephalic origin consisting of an elongated gray mass lying lateral to and bordering the lateral ventricle. It is divided into a head, body and tail in some species. http://purl.obolibrary.org/obo/UBERON_0001875 globus pallidus http://purl.obolibrary.org/obo/UBERON_0009663 telencephalic nucleus Subcortical nucleus, functionally part of the basal ganglia, which consists of two segments the external (or lateral) and internal (or medial) separated by the medial medullary lamina in primates. In rodents, The globus pallidus lateral is separated from the medial segment by the fibers of the internal capsule/cerebral peduncle. http://purl.obolibrary.org/obo/UBERON_0001876 amygdala http://purl.obolibrary.org/obo/UBERON_0005401 cerebral hemisphere gray matter Subcortical brain region lying anterior to the hippocampal formation in the temporal lobe and anterior to the temporal horn of the lateral ventricle in some species. It is usually subdivided into several groups. Functionally, it is not considered a unitary structure (MM). http://purl.obolibrary.org/obo/UBERON_0001891 midbrain http://purl.obolibrary.org/obo/UBERON_0010314 structure with developmental contribution from neural crest Organ component of neuraxis that has as its parts the tectum, cerebral peduncle, midbrain tegmentum and cerebral aqueduct[FMA]. The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally[ZFA]. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. http://purl.obolibrary.org/obo/UBERON_0001896 medulla oblongata http://purl.obolibrary.org/obo/UBERON_0010314 structure with developmental contribution from neural crest Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO]. http://purl.obolibrary.org/obo/UBERON_0001897 dorsal plus ventral thalamus http://purl.obolibrary.org/obo/UBERON_0015212 lateral structure Subcortical brain region consisting of paired gray matter bodies in the dorsal diencephalon and forming part of the lateral wall of the third ventricle of the brain. The thalamus represents the major portion of the diencephalon and is commonly divided into cellular aggregates known as nuclear groups.(MeSH). The dorsal topographic division of the interbrain. The macrodissected adult human thalamus was clearly illustrated by Vesalius in 1543 and the term as defined here was introduced by His in 1893. It includes the traditional epithalamus, dorsal thalamus, and ventral thalamus of Herrick (1910, pp. 494, 498). Also see Kuhlenbeck (1927, Ch. 9) and Jones (1985, p. 87). http://purl.obolibrary.org/obo/UBERON_0001898 hypothalamus http://purl.obolibrary.org/obo/UBERON_0002616 regional part of brain A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. [ZFA]. One of the most important functions of the hypothalamus is to link the nervous system to the endocrine system via the pituitary gland (hypophysis).[Wikipedia]. http://purl.obolibrary.org/obo/UBERON_0001906 subthalamic nucleus http://purl.obolibrary.org/obo/UBERON_0002308 nucleus of brain The subthalamic nucleus is the lens-shaped nucleus located in the ventral part of the subthalamus on the inner aspect of the internal capsule that is concerned with the integration of somatic motor function[GO]. http://purl.obolibrary.org/obo/UBERON_0001911 mammary gland http://purl.obolibrary.org/obo/UBERON_0019319 exocrine gland of integumental system A specialized accessory gland of the skin of mammals that secretes milk. The gland is typically only developed in females, and regresses in males. http://purl.obolibrary.org/obo/UBERON_0001917 endothelium of artery http://purl.obolibrary.org/obo/UBERON_0004700 arterial system endothelium An endothelium that is part of an artery [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0001928 preoptic area http://purl.obolibrary.org/obo/UBERON_0002616 regional part of brain Area of the forebrain anterior to the posterior tuberculum and the hypothalamus and ventral to the ventral thalamus[ZFA]. http://purl.obolibrary.org/obo/UBERON_0001954 Ammon's horn http://purl.obolibrary.org/obo/UBERON_0010314 structure with developmental contribution from neural crest A part of the brain consisting of a three layered cortex located in the forebrain bordering the medial surface of the lateral ventricle. The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum. http://purl.obolibrary.org/obo/UBERON_0001981 blood vessel http://purl.obolibrary.org/obo/UBERON_0004120 mesoderm-derived structure A vessel through which blood circulates in the body. http://purl.obolibrary.org/obo/UBERON_0001986 endothelium http://purl.obolibrary.org/obo/UBERON_0012275 meso-epithelium A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA] http://purl.obolibrary.org/obo/UBERON_0001989 superior cervical ganglion http://purl.obolibrary.org/obo/UBERON_0001807 paravertebral ganglion Trunk ganglion which is bilaterally paired and located at the anterior end of the sympathetic ganglion chain. http://purl.obolibrary.org/obo/UBERON_0001997 olfactory epithelium http://purl.obolibrary.org/obo/UBERON_0010499 pseudostratified ciliated columnar epithelium A sensory epithelium inside the nasal cavity that is responsible for detecting odors[WP]. http://purl.obolibrary.org/obo/UBERON_0002020 gray matter http://purl.obolibrary.org/obo/UBERON_0011215 central nervous system cell part cluster A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons. http://purl.obolibrary.org/obo/UBERON_0002028 hindbrain http://purl.obolibrary.org/obo/UBERON_0010314 structure with developmental contribution from neural crest The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. http://purl.obolibrary.org/obo/UBERON_0002031 epithelium of bronchus http://purl.obolibrary.org/obo/UBERON_0004815 lower respiratory tract epithelium An epithelium that is part of a bronchus [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0002036 striated muscle tissue http://purl.obolibrary.org/obo/UBERON_0002385 muscle tissue Tissue which consists of striated muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue, Cardiac muscle tissue[FMA]. http://purl.obolibrary.org/obo/UBERON_0002050 embryonic structure http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity Anatomical structure that is part of an embryo. http://purl.obolibrary.org/obo/UBERON_0002058 ciliary ganglion http://purl.obolibrary.org/obo/UBERON_0001808 parasympathetic ganglion The ciliary ganglion is a parasympathetic ganglion located in the posterior orbit. It measures 1P2 millimeters in diameter and contains approximately 2,500 neurons (adapted from Wikipedia) http://purl.obolibrary.org/obo/UBERON_0002066 umbilical vein http://purl.obolibrary.org/obo/UBERON_0001981 blood vessel The umbilical vein is a blood vessel present during fetal development that carries oxygenated blood from the placenta to the growing fetus. [WP,unvetted]. http://purl.obolibrary.org/obo/UBERON_0002072 hypodermis http://purl.obolibrary.org/obo/UBERON_0004923 organ component layer Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. http://purl.obolibrary.org/obo/UBERON_0002075 viscus http://purl.obolibrary.org/obo/UBERON_0005177 trunk region element An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. http://purl.obolibrary.org/obo/UBERON_0002124 medulla of thymus http://purl.obolibrary.org/obo/UBERON_0000471 compound organ component Medullary portion of thymus. The reticulum is coarser than in the cortex, the lymphoid cells are relatively fewer in number, and there are found peculiar nest-like bodies, the concentric corpuscles of Hassall. These concentric corpuscles are composed of a central mass, consisting of one or more granular cells, and of a capsule formed of epithelioid cells. They are the remains of the epithelial tubes, which grow out from the third branchial pouches of the embryo to form the thymus. Each follicle is surrounded by a vascular plexus, from which vessels pass into the interior, and radiate from the periphery toward the center, forming a second zone just within the margin of the medullary portion. In the center of the medullary portion there are very few vessels, and they are of minute size. http://purl.obolibrary.org/obo/UBERON_0002255 vomeronasal organ http://purl.obolibrary.org/obo/UBERON_0004121 ectoderm-derived structure An organ thought to supplement the olfactory system in receiving pheromonic communication. The sensory part of the organ is in two long, thin sacs, situated on either side of the nasal septum at its base. http://purl.obolibrary.org/obo/UBERON_0002264 olfactory bulb http://purl.obolibrary.org/obo/UBERON_0015212 lateral structure A bulbous anterior projection of the olfactory lobe that is the place of termination of the olfactory nerves and is especially well developed in lower vertebrates (as fishes)[BTO]. http://purl.obolibrary.org/obo/UBERON_0002308 nucleus of brain http://purl.obolibrary.org/obo/UBERON_0011215 central nervous system cell part cluster A neural nucleus that is part of the brain. http://purl.obolibrary.org/obo/UBERON_0002331 umbilical cord http://purl.obolibrary.org/obo/UBERON_0004120 mesoderm-derived structure The connecting cord from the developing embryo to the placenta. http://purl.obolibrary.org/obo/UBERON_0002342 neural crest http://purl.obolibrary.org/obo/UBERON_0010316 germ layer / neural crest A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. http://purl.obolibrary.org/obo/UBERON_0002352 atrioventricular node http://purl.obolibrary.org/obo/UBERON_0001133 cardiac muscle tissue Subdivision of conducting system of heart which is located in the muscular part of the interatrial septum that is continuous with the atrioventricular bundle.[FMA] http://purl.obolibrary.org/obo/UBERON_0002365 exocrine gland http://purl.obolibrary.org/obo/UBERON_0002530 gland A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas http://purl.obolibrary.org/obo/UBERON_0002419 skin gland http://purl.obolibrary.org/obo/UBERON_0006003 integumentary adnexa A gland that is part of a skin of body [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0002428 limb bone http://purl.obolibrary.org/obo/UBERON_0015061 limb endochondral element A bone that is part of a limb [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0002435 striatum http://purl.obolibrary.org/obo/UBERON_0011300 gray matter of telencephalon A region of the forebrain consisting of the caudate nucleus, putamen and fundus striati.[GO]. http://purl.obolibrary.org/obo/UBERON_0002513 endochondral bone http://purl.obolibrary.org/obo/UBERON_0010363 endochondral element Replacement bone that forms within cartilage. http://purl.obolibrary.org/obo/UBERON_0002530 gland http://purl.obolibrary.org/obo/UBERON_0000062 organ an organ that functions as a secretory or excretory organ http://purl.obolibrary.org/obo/UBERON_0002544 digit http://purl.obolibrary.org/obo/UBERON_0000475 organism subdivision A subdivision of the autopod that has as part a series of phalanges together with associated vasculature, musculature, integument and nerves. It is continuous with the metapodial subdivision of the autopod, but does not include the metapodials. In species such as humans, fully formed digits are distinct, whereas in other species the digits may be connected by interdigital webbing, or may be completely unseparated (for example, in cetaceans). http://purl.obolibrary.org/obo/UBERON_0002616 regional part of brain http://purl.obolibrary.org/obo/UBERON_0004121 ectoderm-derived structure Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia. Regions of brain across multiple species are contained within this category. http://purl.obolibrary.org/obo/UBERON_0002623 cerebral peduncle http://purl.obolibrary.org/obo/UBERON_0011215 central nervous system cell part cluster Synonym for macrodissected adult human tegmentum (Vicq d'Azyr, 1784; Swanson, 2000); pp. 555-556. Later used thus by for example His (1893b, p. 178), Herrick (1915, p. 160), Strong & Elwyn (1943, p. 17), Carpenter (1976, p. 367), Williams & Warwick (1980, p. 935). http://purl.obolibrary.org/obo/UBERON_0002691 ventral tegmental area http://purl.obolibrary.org/obo/UBERON_0002616 regional part of brain Unpaired midbrain region situated in the ventromedial portion of the reticular formation. The VTA is medial to the substantia nigra and ventral to the red nucleus, and extends caudally from the posterior hypothalamus in the diencephalon. The VTA contains dopamine neurons that project to various limbic and cortical areas and is a critical component of the brain's reward circuitry. http://purl.obolibrary.org/obo/UBERON_0002967 cingulate gyrus http://purl.obolibrary.org/obo/UBERON_0000200 gyrus One of the convolutions on the medial surface of the cerebral hemisphere. It surrounds the rostral part of the brain and interhemispheric commissure and forms part of the limbic system. (MSH) One of three essential structures comprising the limbic lobe, the other two being the hippocampus and parahippocampal gyrus. (CSP) http://purl.obolibrary.org/obo/UBERON_0003102 surface structure http://purl.obolibrary.org/obo/UBERON_0000061 anatomical structure Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism. http://purl.obolibrary.org/obo/UBERON_0003103 compound organ http://purl.obolibrary.org/obo/UBERON_0000062 organ Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. http://purl.obolibrary.org/obo/UBERON_0003258 endoderm of foregut http://purl.obolibrary.org/obo/UBERON_0005911 endo-epithelium An endoderm that is part of a foregut [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0003283 mesentery of oesophagus http://purl.obolibrary.org/obo/UBERON_0000042 serous membrane A mesentery that is part of a esophagus [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0003296 gland of diencephalon http://purl.obolibrary.org/obo/UBERON_0004121 ectoderm-derived structure Any gland that is part of the diencephalon. Examples: pineal gland, neurohypophysis. http://purl.obolibrary.org/obo/UBERON_0003297 gland of integumental system http://purl.obolibrary.org/obo/UBERON_0002530 gland A gland that is part of a integumental system [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0003408 gland of gut http://purl.obolibrary.org/obo/UBERON_0013765 digestive system element A gland that is part of a digestive tract [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0003457 head bone http://purl.obolibrary.org/obo/UBERON_0001474 bone element A bone that is part of a head [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0003462 facial bone http://purl.obolibrary.org/obo/UBERON_0010313 neural crest-derived structure A bone that is part of a facial skeleton [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0003464 hindlimb bone http://purl.obolibrary.org/obo/UBERON_0015022 hindlimb endochondral element A bone that is part of a hindlimb region. Examples: any pes phalanx, femur. Counter-examples: ischium, pubis (they are part of the pelvic girdle) http://purl.obolibrary.org/obo/UBERON_0003469 respiratory system artery http://purl.obolibrary.org/obo/UBERON_0003643 respiratory system arterial blood vessel An artery that is part of a respiratory system [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0003509 arterial blood vessel http://purl.obolibrary.org/obo/UBERON_0001981 blood vessel A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta. http://purl.obolibrary.org/obo/UBERON_0003528 brain gray matter http://purl.obolibrary.org/obo/UBERON_0002020 gray matter A gray matter that is part of a brain [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0003606 limb long bone http://purl.obolibrary.org/obo/UBERON_0002428 limb bone A long bone that is part of a limb [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0003608 hindlimb long bone http://purl.obolibrary.org/obo/UBERON_0003606 limb long bone A long bone that is part of a hindlimb [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0003643 respiratory system arterial blood vessel http://purl.obolibrary.org/obo/UBERON_0003509 arterial blood vessel An arterial blood vessel that is part of a respiratory system [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0003657 limb joint http://purl.obolibrary.org/obo/UBERON_0000982 skeletal joint Any joint that is part of a (free) limb. http://purl.obolibrary.org/obo/UBERON_0003729 mouth mucosa http://purl.obolibrary.org/obo/UBERON_0004923 organ component layer A mucous membrane that lines the mouth. http://purl.obolibrary.org/obo/UBERON_0003913 tooth-like structure http://purl.obolibrary.org/obo/UBERON_0004765 skeletal element hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food. http://purl.obolibrary.org/obo/UBERON_0003914 epithelial tube http://purl.obolibrary.org/obo/UBERON_0000483 epithelium Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. http://purl.obolibrary.org/obo/UBERON_0003915 endothelial tube http://purl.obolibrary.org/obo/UBERON_0003914 epithelial tube Any endothelium that has the quality of being cylindrical [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0003922 pancreatic epithelial bud http://purl.obolibrary.org/obo/UBERON_0007499 epithelial sac The embryonic pancreas develops from two separate anlagen in the foregut epithelium, one dorsal and two ventral pancreatic buds[PMID]. http://purl.obolibrary.org/obo/UBERON_0003924 ventral pancreatic bud http://purl.obolibrary.org/obo/UBERON_0003922 pancreatic epithelial bud pancreatic bud that gives rise to the major pancreatic duct. http://purl.obolibrary.org/obo/UBERON_0003928 digestive system duct http://purl.obolibrary.org/obo/UBERON_0000058 duct A duct that is part of a digestive system [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0003937 sex gland http://purl.obolibrary.org/obo/UBERON_0005156 reproductive structure Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction. http://purl.obolibrary.org/obo/UBERON_0003947 brain ventricle/choroid plexus http://purl.obolibrary.org/obo/UBERON_0010000 multicellular anatomical structure The brain ventricles or their associated choroid plexuses http://purl.obolibrary.org/obo/UBERON_0004111 anatomical conduit http://purl.obolibrary.org/obo/UBERON_0010000 multicellular anatomical structure Any tube, opening or passage that connects two distinct anatomical spaces. http://purl.obolibrary.org/obo/UBERON_0004119 endoderm-derived structure http://purl.obolibrary.org/obo/UBERON_0000061 anatomical structure An anatomical structure that develops (entirely or partially) from the endoderm. http://purl.obolibrary.org/obo/UBERON_0004120 mesoderm-derived structure http://purl.obolibrary.org/obo/UBERON_0000061 anatomical structure An anatomical structure that develops (entirely or partially) from the mesoderm. http://purl.obolibrary.org/obo/UBERON_0004121 ectoderm-derived structure http://purl.obolibrary.org/obo/UBERON_0000061 anatomical structure An anatomical structure that develops (entirely or partially) from the ectoderm. http://purl.obolibrary.org/obo/UBERON_0004177 hemopoietic organ http://purl.obolibrary.org/obo/UBERON_0004120 mesoderm-derived structure Organ that is part of the hematopoietic system. http://purl.obolibrary.org/obo/UBERON_0004256 hindlimb zeugopod muscle http://purl.obolibrary.org/obo/UBERON_0014892 skeletal muscle organ A muscle organ that is part of a hindlimb zeugopod (lower leg) [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0004375 bone of free limb or fin http://purl.obolibrary.org/obo/UBERON_0010740 bone of appendage girdle complex A bone that is part of an appendage [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0004638 blood vessel endothelium http://purl.obolibrary.org/obo/UBERON_0004852 cardiovascular system endothelium An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart http://purl.obolibrary.org/obo/UBERON_0004700 arterial system endothelium http://purl.obolibrary.org/obo/UBERON_0004852 cardiovascular system endothelium An endothelium that is part of an arterial system [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0004742 dentary http://purl.obolibrary.org/obo/UBERON_0008907 dermal bone The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians, extending to the whole lower jaw in mammals[VHOG,modified]. http://purl.obolibrary.org/obo/UBERON_0004756 dermal skeletal element http://purl.obolibrary.org/obo/UBERON_0010314 structure with developmental contribution from neural crest dermis-derived entity that is made of skeletal tissue. http://purl.obolibrary.org/obo/UBERON_0004765 skeletal element http://purl.obolibrary.org/obo/UBERON_0000062 organ Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. http://purl.obolibrary.org/obo/UBERON_0004768 bone of lower jaw http://purl.obolibrary.org/obo/UBERON_0012360 bone of jaw Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular http://purl.obolibrary.org/obo/UBERON_0004802 respiratory tract epithelium http://purl.obolibrary.org/obo/UBERON_0005911 endo-epithelium the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi http://purl.obolibrary.org/obo/UBERON_0004807 respiratory system epithelium http://purl.obolibrary.org/obo/UBERON_0000483 epithelium An epithelium that is part of a respiratory system [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0004815 lower respiratory tract epithelium http://purl.obolibrary.org/obo/UBERON_0004802 respiratory tract epithelium An epithelium that is part of a lower respiratory tract [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0004851 aorta endothelium http://purl.obolibrary.org/obo/UBERON_0004700 arterial system endothelium the thin layer of flat cells that line the aorta and form a barrier between circulating blood in the lumen and the rest of the vessel wall http://purl.obolibrary.org/obo/UBERON_0004852 cardiovascular system endothelium http://purl.obolibrary.org/obo/UBERON_0001986 endothelium An endothelium that is part of the cardiovascular system. http://purl.obolibrary.org/obo/UBERON_0004921 subdivision of digestive tract http://purl.obolibrary.org/obo/UBERON_0013522 subdivision of tube A proximal-distal subdivision of the digestive tract. http://purl.obolibrary.org/obo/UBERON_0004923 organ component layer http://purl.obolibrary.org/obo/UBERON_0000064 organ part A part of a wall of an organ that forms a layer. http://purl.obolibrary.org/obo/UBERON_0005020 mucosa of tongue http://purl.obolibrary.org/obo/UBERON_0004119 endoderm-derived structure A mucosa that is part of a tongue [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0005156 reproductive structure http://purl.obolibrary.org/obo/UBERON_0004120 mesoderm-derived structure An anatomical structure that is part of the reproductive system. http://purl.obolibrary.org/obo/UBERON_0005162 multi cell part structure http://purl.obolibrary.org/obo/UBERON_0000477 anatomical cluster A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. http://purl.obolibrary.org/obo/UBERON_0005172 abdomen element http://purl.obolibrary.org/obo/UBERON_0005177 trunk region element An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland. http://purl.obolibrary.org/obo/UBERON_0005177 trunk region element http://purl.obolibrary.org/obo/UBERON_0000062 organ An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions. http://purl.obolibrary.org/obo/UBERON_0005181 thoracic segment organ http://purl.obolibrary.org/obo/UBERON_0005177 trunk region element An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. http://purl.obolibrary.org/obo/UBERON_0005291 embryonic tissue http://purl.obolibrary.org/obo/UBERON_0002050 embryonic structure A portion of tissue that is part of an embryo. http://purl.obolibrary.org/obo/UBERON_0005301 male preputial gland http://purl.obolibrary.org/obo/UBERON_0010147 male accessory sex gland One of the sebaceous glands of the corona and neck of the glans penis. http://purl.obolibrary.org/obo/UBERON_0005384 nasal cavity epithelium http://purl.obolibrary.org/obo/UBERON_0019306 nose epithelium An epithelium that lines the nasal cavity. http://purl.obolibrary.org/obo/UBERON_0005399 male reproductive gland http://purl.obolibrary.org/obo/UBERON_0003937 sex gland A sex gland that is part of a male reproductive system. http://purl.obolibrary.org/obo/UBERON_0005401 cerebral hemisphere gray matter http://purl.obolibrary.org/obo/UBERON_0011300 gray matter of telencephalon A gray matter that is part of a cerebral hemisphere. http://purl.obolibrary.org/obo/UBERON_0005631 extraembryonic membrane http://purl.obolibrary.org/obo/UBERON_0004923 organ component layer Intrinsic membrane that arises from embryonic germ layers and grow to surround the developing embryo. http://purl.obolibrary.org/obo/UBERON_0005800 segment of aorta http://purl.obolibrary.org/obo/UBERON_0004120 mesoderm-derived structure Any portion of the aorta including the ascending and descending aorta, and aortic arch or a portion of the aortic orifice of the left ventricle. http://purl.obolibrary.org/obo/UBERON_0005902 occipital region http://purl.obolibrary.org/obo/UBERON_0034921 multi organ part structure Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occipital condyles. http://purl.obolibrary.org/obo/UBERON_0005904 duct of male reproductive system http://purl.obolibrary.org/obo/UBERON_0005156 reproductive structure Any of the ducts that are part of a male reproductive system. http://purl.obolibrary.org/obo/UBERON_0005911 endo-epithelium http://purl.obolibrary.org/obo/UBERON_0004119 endoderm-derived structure Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA] http://purl.obolibrary.org/obo/UBERON_0006003 integumentary adnexa http://purl.obolibrary.org/obo/UBERON_0000064 organ part Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers. http://purl.obolibrary.org/obo/UBERON_0006799 glandular epithelium http://purl.obolibrary.org/obo/UBERON_0000483 epithelium An epithelium that is composed primarily of secretory cells. http://purl.obolibrary.org/obo/UBERON_0006858 adrenal/interrenal gland http://purl.obolibrary.org/obo/UBERON_0010314 structure with developmental contribution from neural crest This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO] http://purl.obolibrary.org/obo/UBERON_0006914 squamous epithelium http://purl.obolibrary.org/obo/UBERON_0000483 epithelium An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. http://purl.obolibrary.org/obo/UBERON_0006925 digestive gland http://purl.obolibrary.org/obo/UBERON_0013765 digestive system element A gland, such as the liver or pancreas, that secretes into the alimentary canal substances necessary for digestion. http://purl.obolibrary.org/obo/UBERON_0007100 primary circulatory organ http://purl.obolibrary.org/obo/UBERON_0003103 compound organ A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. http://purl.obolibrary.org/obo/UBERON_0007196 tracheobronchial tree http://purl.obolibrary.org/obo/UBERON_0004119 endoderm-derived structure The structure from the trachea, bronchi, and bronchioles that forms the airways that supply air to the lungs. The lining of the tracheobronchial tree consists of ciliated columnar epithelial cells. http://purl.obolibrary.org/obo/UBERON_0007376 outer epithelium http://purl.obolibrary.org/obo/UBERON_0010371 ecto-epithelium The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO]. http://purl.obolibrary.org/obo/UBERON_0007499 epithelial sac http://purl.obolibrary.org/obo/UBERON_0009856 sac An epithelial tube that is open at one end only. http://purl.obolibrary.org/obo/UBERON_0007592 ciliated columnar epithelium http://purl.obolibrary.org/obo/UBERON_0000485 simple columnar epithelium Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA] http://purl.obolibrary.org/obo/UBERON_0007827 external nose http://purl.obolibrary.org/obo/UBERON_0004121 ectoderm-derived structure External part of the olfactory apparatus. http://purl.obolibrary.org/obo/UBERON_0008907 dermal bone http://purl.obolibrary.org/obo/UBERON_0004756 dermal skeletal element Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO]. http://purl.obolibrary.org/obo/UBERON_0009663 telencephalic nucleus http://purl.obolibrary.org/obo/UBERON_0002308 nucleus of brain A nucleus of brain that is part of a telencephalon. http://purl.obolibrary.org/obo/UBERON_0009842 glandular acinus http://purl.obolibrary.org/obo/UBERON_0034922 cell cluster The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form. http://purl.obolibrary.org/obo/UBERON_0009854 digestive tract diverticulum http://purl.obolibrary.org/obo/UBERON_0009856 sac Branch or outpocketing of the digestive tract. http://purl.obolibrary.org/obo/UBERON_0010000 multicellular anatomical structure http://purl.obolibrary.org/obo/UBERON_0000061 anatomical structure An anatomical structure that has more than one cell as a part. http://purl.obolibrary.org/obo/UBERON_0010047 oral gland http://purl.obolibrary.org/obo/UBERON_0004121 ectoderm-derived structure Gland of the epithelium lining the oral cavity. The most common are the salivary glands. http://purl.obolibrary.org/obo/UBERON_0010147 male accessory sex gland http://purl.obolibrary.org/obo/UBERON_0005399 male reproductive gland Any gland, other than the gonad, associated with the genital tract, such as the ampulla of the ductus deferens and the bulbourethral, prostate and vesicular glands of the male. http://purl.obolibrary.org/obo/UBERON_0010313 neural crest-derived structure http://purl.obolibrary.org/obo/UBERON_0010314 structure with developmental contribution from neural crest An anatomical structure that develops from the neural crest. http://purl.obolibrary.org/obo/UBERON_0010314 structure with developmental contribution from neural crest http://purl.obolibrary.org/obo/UBERON_0000061 anatomical structure An anatomical structure that has some part that develops from the neural crest. http://purl.obolibrary.org/obo/UBERON_0010363 endochondral element http://purl.obolibrary.org/obo/UBERON_0004765 skeletal element A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification. http://purl.obolibrary.org/obo/UBERON_0010371 ecto-epithelium http://purl.obolibrary.org/obo/UBERON_0004121 ectoderm-derived structure Epithelium that derives from the ectoderm. Examples: epithelium of acinus of lactiferous duct, subscapular lens epithelium, epithelium of posterior surface of cornea. http://purl.obolibrary.org/obo/UBERON_0010499 pseudostratified ciliated columnar epithelium http://purl.obolibrary.org/obo/UBERON_0007592 ciliated columnar epithelium Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile. http://purl.obolibrary.org/obo/UBERON_0010740 bone of appendage girdle complex http://purl.obolibrary.org/obo/UBERON_0001474 bone element A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle). http://purl.obolibrary.org/obo/UBERON_0011139 synovial limb joint http://purl.obolibrary.org/obo/UBERON_0003657 limb joint Any synovial joint that is part of a (free) limb. http://purl.obolibrary.org/obo/UBERON_0011215 central nervous system cell part cluster http://purl.obolibrary.org/obo/UBERON_0005162 multi cell part structure A multi cell part structure that is part of a central nervous system. http://purl.obolibrary.org/obo/UBERON_0011300 gray matter of telencephalon http://purl.obolibrary.org/obo/UBERON_0003528 brain gray matter A portion of gray matter that is part of a telencephalon. http://purl.obolibrary.org/obo/UBERON_0012275 meso-epithelium http://purl.obolibrary.org/obo/UBERON_0004120 mesoderm-derived structure Epithelium that derives from the mesoderm. [Automatically generated definition]. http://purl.obolibrary.org/obo/UBERON_0012360 bone of jaw http://purl.obolibrary.org/obo/UBERON_0013765 digestive system element A bone element that is part of a jaw region. http://purl.obolibrary.org/obo/UBERON_0012429 hemopoietic tissue http://purl.obolibrary.org/obo/UBERON_0034769 lymphomyeloid tissue Blood-forming tissue, consisting of reticular fibers and cells. Also known as hemopoietic tissue http://purl.obolibrary.org/obo/UBERON_0013697 exocrine pancreas epithelium http://purl.obolibrary.org/obo/UBERON_0005911 endo-epithelium Epithelium lining the exocrine pancreas. http://purl.obolibrary.org/obo/UBERON_0013765 digestive system element http://purl.obolibrary.org/obo/UBERON_0000062 organ Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. http://purl.obolibrary.org/obo/UBERON_0014374 embryoid body http://purl.obolibrary.org/obo/UBERON_0002050 embryonic structure Embryoid bodies (EBs) are three-dimensional aggregates of pluripotent stem cells. http://purl.obolibrary.org/obo/UBERON_0014892 skeletal muscle organ http://purl.obolibrary.org/obo/UBERON_0004120 mesoderm-derived structure A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles). http://purl.obolibrary.org/obo/UBERON_0015022 hindlimb endochondral element http://purl.obolibrary.org/obo/UBERON_0015061 limb endochondral element A hindlimb bone or its cartilage or pre-cartilage precursor. http://purl.obolibrary.org/obo/UBERON_0015061 limb endochondral element http://purl.obolibrary.org/obo/UBERON_0010363 endochondral element A limb bone or its cartilage or pre-cartilage precursor. http://purl.obolibrary.org/obo/UBERON_0015212 lateral structure http://purl.obolibrary.org/obo/UBERON_0000061 anatomical structure Any structure that is placed on one side of the left-right axis of a bilaterian. http://purl.obolibrary.org/obo/UBERON_0015787 upper respiratory conduit http://purl.obolibrary.org/obo/UBERON_0004119 endoderm-derived structure Any anatomical conduit which is part of the upper respiratory tract http://purl.obolibrary.org/obo/UBERON_0016526 lobe of cerebral hemisphere http://purl.obolibrary.org/obo/UBERON_0010314 structure with developmental contribution from neural crest Subdivision of telencephalon which is one of a number of subdivisions of each hemisphere separated by both real landmarks (sulci and fissures) and arbitrary boundaries[FMA,modified]. http://purl.obolibrary.org/obo/UBERON_0017672 abdominal viscera http://purl.obolibrary.org/obo/UBERON_0005172 abdomen element A viscus that is part of a abdomen. http://purl.obolibrary.org/obo/UBERON_0019319 exocrine gland of integumental system http://purl.obolibrary.org/obo/UBERON_0003297 gland of integumental system An exocrine gland that is part of a integumental system. http://purl.obolibrary.org/obo/UBERON_0034921 multi organ part structure http://purl.obolibrary.org/obo/UBERON_0010000 multicellular anatomical structure An multicellular anatomical structure that has subparts of multiple organs as a part. http://purl.obolibrary.org/obo/UBERON_0034922 cell cluster http://purl.obolibrary.org/obo/UBERON_0010000 multicellular anatomical structure A cluster of cells, largely surrounded by a morphological boundary. http://purl.obolibrary.org/obo/PR_000005178 CD9 molecule http://purl.obolibrary.org/obo/PR_000000001 protein A tetraspanin that is a translation product of the human CD9 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000005307 CCAAT/enhancer-binding protein alpha http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human CEBPA gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000006611 DNA nucleotidylexotransferase http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human DNTT gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000007431 high affinity immunoglobulin epsilon receptor subunit alpha http://purl.obolibrary.org/obo/PR_000001355 immunoglobulin gamma Fc receptor II/III/IV An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the human FCER1A gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000007602 hepatocyte nuclear factor 3-alpha http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human FOXA1 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000007603 hepatocyte nuclear factor 3-beta http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human FOXA2 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000007857 erythroid transcription factor http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human GATA1 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000007858 endothelial transcription factor GATA-2 http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human GATA2 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000007891 glucagon http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human GCG gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000008652 hepatocyte nuclear factor 1-alpha http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human HNF1A gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000008654 hepatocyte nuclear factor 4-alpha http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human HNF4A gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/CHEBI_33672 heterobicyclic compound http://purl.obolibrary.org/obo/CHEBI_33595 cyclic compound A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom. http://purl.obolibrary.org/obo/OBI_0000969 dose specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity a directive information entity that describes the dose that will be administered to a target http://purl.obolibrary.org/obo/GO_0000785 chromatin http://purl.obolibrary.org/obo/GO_0044446 intracellular organelle part The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. http://purl.obolibrary.org/obo/GO_0000791 euchromatin http://purl.obolibrary.org/obo/GO_0000785 chromatin A dispersed and relatively uncompacted form of chromatin. http://purl.obolibrary.org/obo/GO_0000792 heterochromatin http://purl.obolibrary.org/obo/GO_0000785 chromatin A compact and highly condensed form of chromatin. http://purl.obolibrary.org/obo/GO_0001649 osteoblast differentiation http://purl.obolibrary.org/obo/GO_0030154 cell differentiation The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone. http://purl.obolibrary.org/obo/GO_0001667 ameboidal-type cell migration http://purl.obolibrary.org/obo/GO_0016477 cell migration Cell migration that is accomplished by extension and retraction of a pseudopodium. http://purl.obolibrary.org/obo/GO_0001816 cytokine production http://purl.obolibrary.org/obo/GO_0044707 single-multicellular organism process The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0001820 serotonin secretion http://purl.obolibrary.org/obo/GO_0032940 secretion by cell The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesised in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells. http://purl.obolibrary.org/obo/GO_0002200 somatic diversification of immune receptors http://purl.obolibrary.org/obo/GO_0002376 immune system process The somatic process allowing for the production of immune receptors whose specificity is not encoded in the germline genomic sequences. http://purl.obolibrary.org/obo/GO_0002228 natural killer cell mediated immunity http://purl.obolibrary.org/obo/GO_0045087 innate immune response The promotion of an immune response by natural killer cells through direct recognition of target cells or through the release of cytokines. http://purl.obolibrary.org/obo/GO_0002244 hematopoietic progenitor cell differentiation http://purl.obolibrary.org/obo/GO_0030154 cell differentiation The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells. http://purl.obolibrary.org/obo/GO_0002376 immune system process http://purl.obolibrary.org/obo/GO_0008150 biological_process Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats. http://purl.obolibrary.org/obo/GO_0002449 lymphocyte mediated immunity http://purl.obolibrary.org/obo/GO_0002376 immune system process Any process involved in the carrying out of an immune response by a lymphocyte. http://purl.obolibrary.org/obo/GO_0002456 T cell mediated immunity http://purl.obolibrary.org/obo/GO_0002460 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains Any process involved in the carrying out of an immune response by a T cell. http://purl.obolibrary.org/obo/GO_0002460 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains http://purl.obolibrary.org/obo/GO_0006955 immune response An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process that includes somatic recombination of germline gene segments encoding immunoglobulin superfamily domains, and allowing for enhanced responses upon subsequent exposures to the same antigen (immunological memory). Recombined receptors for antigen encoded by immunoglobulin superfamily domains include T cell receptors and immunoglobulins (antibodies). An example of this is the adaptive immune response found in Mus musculus. http://purl.obolibrary.org/obo/GO_0002521 leukocyte differentiation http://purl.obolibrary.org/obo/GO_0030154 cell differentiation The process in which a relatively unspecialized hemopoietic precursor cell acquires the specialized features of a leukocyte. A leukocyte is an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. http://purl.obolibrary.org/obo/GO_0002562 somatic diversification of immune receptors via germline recombination within a single locus http://purl.obolibrary.org/obo/GO_0006259 DNA metabolic process The process in which immune receptor genes are diversified through recombination of the germline genetic elements within a single genetic locus. http://purl.obolibrary.org/obo/GO_0002573 myeloid leukocyte differentiation http://purl.obolibrary.org/obo/GO_0030099 myeloid cell differentiation The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte lineage. http://purl.obolibrary.org/obo/GO_0002682 regulation of immune system process http://purl.obolibrary.org/obo/GO_0050789 regulation of biological process Any process that modulates the frequency, rate, or extent of an immune system process. http://purl.obolibrary.org/obo/GO_0002694 regulation of leukocyte activation http://purl.obolibrary.org/obo/GO_0050794 regulation of cellular process Any process that modulates the frequency, rate, or extent of leukocyte activation. http://purl.obolibrary.org/obo/GO_0002790 peptide secretion http://purl.obolibrary.org/obo/GO_0046903 secretion The controlled release of a peptide from a cell or a tissue. http://purl.obolibrary.org/obo/GO_0003006 developmental process involved in reproduction http://purl.obolibrary.org/obo/GO_0032502 developmental process A developmental process in which a progressive change in the state of some part of an organism specifically contributes to its ability to form offspring. http://purl.obolibrary.org/obo/GO_0003013 circulatory system process http://purl.obolibrary.org/obo/GO_0044707 single-multicellular organism process A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism. http://purl.obolibrary.org/obo/GO_0003674 molecular_function http://purl.obolibrary.org/obo/BFO_0000034 function Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions. http://purl.obolibrary.org/obo/GO_0003824 catalytic activity http://purl.obolibrary.org/obo/GO_0003674 molecular_function Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. http://purl.obolibrary.org/obo/GO_0003964 RNA-directed DNA polymerase activity http://purl.obolibrary.org/obo/GO_0003824 catalytic activity Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time. http://purl.obolibrary.org/obo/GO_0005634 nucleus http://purl.obolibrary.org/obo/GO_0043231 intracellular membrane-bounded organelle A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. http://purl.obolibrary.org/obo/GO_0005737 cytoplasm http://purl.obolibrary.org/obo/GO_0044424 intracellular part All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. http://purl.obolibrary.org/obo/GO_0005773 vacuole http://purl.obolibrary.org/obo/GO_0044444 cytoplasmic part A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. http://purl.obolibrary.org/obo/GO_0005840 ribosome http://purl.obolibrary.org/obo/GO_0044444 cytoplasmic part An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. http://purl.obolibrary.org/obo/GO_0006259 DNA metabolic process http://purl.obolibrary.org/obo/GO_0090304 nucleic acid metabolic process Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. http://purl.obolibrary.org/obo/GO_0006260 DNA replication http://purl.obolibrary.org/obo/GO_0006259 DNA metabolic process The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. http://purl.obolibrary.org/obo/GO_0006464 cellular protein modification process http://purl.obolibrary.org/obo/GO_0044267 cellular protein metabolic process The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification). http://purl.obolibrary.org/obo/GO_0006837 serotonin transport http://purl.obolibrary.org/obo/GO_0015696 ammonium transport The directed movement of serotonin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Serotonin (5-hydroxytryptamine) is a monoamine neurotransmitter occurring in the peripheral and central nervous systems. http://purl.obolibrary.org/obo/GO_0006915 apoptotic process http://purl.obolibrary.org/obo/GO_0008219 cell death A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. http://purl.obolibrary.org/obo/GO_0006950 response to stress http://purl.obolibrary.org/obo/GO_0050896 response to stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). http://purl.obolibrary.org/obo/GO_0006955 immune response http://purl.obolibrary.org/obo/GO_0002376 immune system process Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. http://purl.obolibrary.org/obo/GO_0007049 cell cycle http://purl.obolibrary.org/obo/GO_0044763 single-organism cellular process The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. http://purl.obolibrary.org/obo/GO_0008150 biological_process http://purl.obolibrary.org/obo/BFO_0000015 process Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. http://purl.obolibrary.org/obo/GO_0009058 biosynthetic process http://purl.obolibrary.org/obo/GO_0008152 metabolic process The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. http://purl.obolibrary.org/obo/GO_0009059 macromolecule biosynthetic process http://purl.obolibrary.org/obo/GO_1901576 organic substance biosynthetic process The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. http://purl.obolibrary.org/obo/GO_0009306 protein secretion http://purl.obolibrary.org/obo/GO_0032940 secretion by cell The controlled release of proteins from a cell. http://purl.obolibrary.org/obo/GO_0009914 hormone transport http://purl.obolibrary.org/obo/GO_0010817 regulation of hormone levels The directed movement of hormones into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. http://purl.obolibrary.org/obo/GO_0009987 cellular process http://purl.obolibrary.org/obo/GO_0008150 biological_process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. http://purl.obolibrary.org/obo/GO_0010467 gene expression http://purl.obolibrary.org/obo/GO_0043170 macromolecule metabolic process The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form. http://purl.obolibrary.org/obo/GO_0010817 regulation of hormone levels http://purl.obolibrary.org/obo/GO_0065008 regulation of biological quality Any process that modulates the levels of hormone within an organism or a tissue. A hormone is any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action. http://purl.obolibrary.org/obo/GO_0015696 ammonium transport http://purl.obolibrary.org/obo/GO_0071705 nitrogen compound transport The directed movement of ammonium into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Ammonium is the cation NH4+ which is formed from N2 by root-nodule bacteria in leguminous plants and is an excretory product in ammonotelic animals. http://purl.obolibrary.org/obo/GO_0015833 peptide transport http://purl.obolibrary.org/obo/GO_0071702 organic substance transport The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. http://purl.obolibrary.org/obo/GO_0016337 single organismal cell-cell adhesion http://purl.obolibrary.org/obo/GO_0098602 single organism cell adhesion The attachment of one cell to another cell via adhesion molecules, where both cells are part of the same organism. http://purl.obolibrary.org/obo/GO_0016447 somatic recombination of immunoglobulin gene segments http://purl.obolibrary.org/obo/GO_0002562 somatic diversification of immune receptors via germline recombination within a single locus The process in which immunoglobulin genes are formed through recombination of the germline genetic elements, as known as immunoglobulin gene segments, within a single locus. http://purl.obolibrary.org/obo/GO_0016477 cell migration http://purl.obolibrary.org/obo/GO_0048870 cell motility The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms. http://purl.obolibrary.org/obo/GO_0016570 histone modification http://purl.obolibrary.org/obo/GO_0016568 chromatin modification The covalent alteration of one or more amino acid residues within a histone protein. http://purl.obolibrary.org/obo/GO_0019724 B cell mediated immunity http://purl.obolibrary.org/obo/GO_0002460 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains Any process involved with the carrying out of an immune response by a B cell, through, for instance, the production of antibodies or cytokines, or antigen presentation to T cells. http://purl.obolibrary.org/obo/GO_0019882 antigen processing and presentation http://purl.obolibrary.org/obo/GO_0002376 immune system process The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. http://purl.obolibrary.org/obo/GO_0022414 reproductive process http://purl.obolibrary.org/obo/GO_0008150 biological_process A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. http://purl.obolibrary.org/obo/GO_0030098 lymphocyte differentiation http://purl.obolibrary.org/obo/GO_0046649 lymphocyte activation The process in which a relatively unspecialized precursor cell acquires specialized features of a lymphocyte. A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. http://purl.obolibrary.org/obo/GO_0030099 myeloid cell differentiation http://purl.obolibrary.org/obo/GO_0030154 cell differentiation The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages. http://purl.obolibrary.org/obo/GO_0030141 secretory granule http://purl.obolibrary.org/obo/GO_0016023 cytoplasmic membrane-bounded vesicle A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules. http://purl.obolibrary.org/obo/GO_0030154 cell differentiation http://purl.obolibrary.org/obo/GO_0048869 cellular developmental process The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. http://purl.obolibrary.org/obo/GO_0030182 neuron differentiation http://purl.obolibrary.org/obo/GO_0030154 cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a neuron. http://purl.obolibrary.org/obo/GO_0030217 T cell differentiation http://purl.obolibrary.org/obo/GO_0042110 T cell activation The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex. http://purl.obolibrary.org/obo/GO_0030261 chromosome condensation http://purl.obolibrary.org/obo/GO_1902589 single-organism organelle organization The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells. http://purl.obolibrary.org/obo/GO_0030667 secretory granule membrane http://purl.obolibrary.org/obo/GO_0031090 organelle membrane The lipid bilayer surrounding a secretory granule. http://purl.obolibrary.org/obo/GO_0030855 epithelial cell differentiation http://purl.obolibrary.org/obo/GO_0030154 cell differentiation The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium. http://purl.obolibrary.org/obo/GO_0031018 endocrine pancreas development http://purl.obolibrary.org/obo/GO_0048856 anatomical structure development The process whose specific outcome is the progression of the endocrine pancreas over time, from its formation to the mature structure. The endocrine pancreas is made up of islet cells that produce insulin, glucagon and somatostatin. http://purl.obolibrary.org/obo/GO_0031323 regulation of cellular metabolic process http://purl.obolibrary.org/obo/GO_0019222 regulation of metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. http://purl.obolibrary.org/obo/GO_0031410 cytoplasmic vesicle http://purl.obolibrary.org/obo/GO_0031982 vesicle A vesicle formed of membrane or protein, found in the cytoplasm of a cell. http://purl.obolibrary.org/obo/GO_0032501 multicellular organismal process http://purl.obolibrary.org/obo/GO_0008150 biological_process Any biological process, occurring at the level of a multicellular organism, pertinent to its function. http://purl.obolibrary.org/obo/GO_0032502 developmental process http://purl.obolibrary.org/obo/GO_0008150 biological_process A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. http://purl.obolibrary.org/obo/GO_0032940 secretion by cell http://purl.obolibrary.org/obo/GO_0046903 secretion The controlled release of a substance by a cell. http://purl.obolibrary.org/obo/GO_0032991 macromolecular complex http://purl.obolibrary.org/obo/GO_0005575 cellular_component A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together. http://purl.obolibrary.org/obo/GO_0034109 homotypic cell-cell adhesion http://purl.obolibrary.org/obo/GO_0016337 single organismal cell-cell adhesion The attachment of a cell to a second cell of the identical type via adhesion molecules. http://purl.obolibrary.org/obo/GO_0042110 T cell activation http://purl.obolibrary.org/obo/GO_0070486 leukocyte aggregation The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. http://purl.obolibrary.org/obo/GO_0042575 DNA polymerase complex http://purl.obolibrary.org/obo/GO_1902494 catalytic complex A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA. http://purl.obolibrary.org/obo/GO_0043011 myeloid dendritic cell differentiation http://purl.obolibrary.org/obo/GO_0045321 leukocyte activation The process in which a monocyte acquires the specialized features of a dendritic cell, an immunocompetent cell of the lymphoid and hemopoietic systems and skin. http://purl.obolibrary.org/obo/GO_0043226 organelle http://purl.obolibrary.org/obo/GO_0005575 cellular_component Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. http://purl.obolibrary.org/obo/GO_0043232 intracellular non-membrane-bounded organelle http://purl.obolibrary.org/obo/GO_0043229 intracellular organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. http://purl.obolibrary.org/obo/GO_0043234 protein complex http://purl.obolibrary.org/obo/GO_0032991 macromolecular complex Any macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical. http://purl.obolibrary.org/obo/GO_0043235 receptor complex http://purl.obolibrary.org/obo/GO_0043234 protein complex Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. http://purl.obolibrary.org/obo/GO_0043414 macromolecule methylation http://purl.obolibrary.org/obo/GO_0044260 cellular macromolecule metabolic process The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule. http://purl.obolibrary.org/obo/GO_0044237 cellular metabolic process http://purl.obolibrary.org/obo/GO_0009987 cellular process The chemical reactions and pathways by which individual cells transform chemical substances. http://purl.obolibrary.org/obo/GO_0044422 organelle part http://purl.obolibrary.org/obo/GO_0005575 cellular_component Any constituent part of an organelle, an organized structure of distinctive morphology and function. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, but excludes the plasma membrane. http://purl.obolibrary.org/obo/GO_0044424 intracellular part http://purl.obolibrary.org/obo/GO_0044464 cell part Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. http://purl.obolibrary.org/obo/GO_0044425 membrane part http://purl.obolibrary.org/obo/GO_0005575 cellular_component Any constituent part of a membrane, a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. http://purl.obolibrary.org/obo/GO_0044433 cytoplasmic vesicle part http://purl.obolibrary.org/obo/GO_0044446 intracellular organelle part Any constituent part of cytoplasmic vesicle, a vesicle formed of membrane or protein, found in the cytoplasm of a cell. http://purl.obolibrary.org/obo/GO_0044444 cytoplasmic part http://purl.obolibrary.org/obo/GO_0044424 intracellular part Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. http://purl.obolibrary.org/obo/GO_0044459 plasma membrane part http://purl.obolibrary.org/obo/GO_0044425 membrane part Any constituent part of the plasma membrane, the membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. http://purl.obolibrary.org/obo/GO_0044699 single-organism process http://purl.obolibrary.org/obo/GO_0008150 biological_process A biological process that involves only one organism. http://purl.obolibrary.org/obo/GO_0044702 single organism reproductive process http://purl.obolibrary.org/obo/GO_0044699 single-organism process A biological process that directly contributes to the process of producing new individuals, involving a single organism. http://purl.obolibrary.org/obo/GO_0044703 multi-organism reproductive process http://purl.obolibrary.org/obo/GO_0051704 multi-organism process A biological process that directly contributes to the process of producing new individuals, involving another organism. http://purl.obolibrary.org/obo/GO_0044707 single-multicellular organism process http://purl.obolibrary.org/obo/GO_0044699 single-organism process A biological process occurring within a single, multicellular organism. http://purl.obolibrary.org/obo/GO_0044763 single-organism cellular process http://purl.obolibrary.org/obo/GO_0044699 single-organism process Any process that is carried out at the cellular level, occurring within a single organism. http://purl.obolibrary.org/obo/GO_0044767 single-organism developmental process http://purl.obolibrary.org/obo/GO_0044699 single-organism process A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition, involving only one organism. http://purl.obolibrary.org/obo/GO_0045087 innate immune response http://purl.obolibrary.org/obo/GO_0006955 immune response Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. http://purl.obolibrary.org/obo/GO_0045321 leukocyte activation http://purl.obolibrary.org/obo/GO_0044763 single-organism cellular process A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor. http://purl.obolibrary.org/obo/GO_0046483 heterocycle metabolic process http://purl.obolibrary.org/obo/GO_0044237 cellular metabolic process The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). http://purl.obolibrary.org/obo/GO_0046649 lymphocyte activation http://purl.obolibrary.org/obo/GO_0045321 leukocyte activation A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor. http://purl.obolibrary.org/obo/GO_0046879 hormone secretion http://purl.obolibrary.org/obo/GO_0023061 signal release The regulated release of hormones, substances with a specific regulatory effect on a particular organ or group of cells. http://purl.obolibrary.org/obo/GO_0046903 secretion http://purl.obolibrary.org/obo/GO_0044765 single-organism transport The controlled release of a substance by a cell or a tissue. http://purl.obolibrary.org/obo/GO_0048468 cell development http://purl.obolibrary.org/obo/GO_0048869 cellular developmental process The process whose specific outcome is the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. http://purl.obolibrary.org/obo/GO_0048856 anatomical structure development http://purl.obolibrary.org/obo/GO_0032502 developmental process The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. http://purl.obolibrary.org/obo/GO_0048869 cellular developmental process http://purl.obolibrary.org/obo/GO_0044767 single-organism developmental process A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. http://purl.obolibrary.org/obo/GO_0048870 cell motility http://purl.obolibrary.org/obo/GO_0044763 single-organism cellular process Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another. http://purl.obolibrary.org/obo/GO_0050776 regulation of immune response http://purl.obolibrary.org/obo/GO_0050789 regulation of biological process Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. http://purl.obolibrary.org/obo/GO_0050789 regulation of biological process http://purl.obolibrary.org/obo/GO_0065007 biological regulation Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. http://purl.obolibrary.org/obo/GO_0050794 regulation of cellular process http://purl.obolibrary.org/obo/GO_0050789 regulation of biological process Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. http://purl.obolibrary.org/obo/GO_0050878 regulation of body fluid levels http://purl.obolibrary.org/obo/GO_0065008 regulation of biological quality Any process that modulates the levels of body fluids. http://purl.obolibrary.org/obo/GO_0051052 regulation of DNA metabolic process http://purl.obolibrary.org/obo/GO_0060255 regulation of macromolecule metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA. http://purl.obolibrary.org/obo/GO_0051276 chromosome organization http://purl.obolibrary.org/obo/GO_0006996 organelle organization A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. http://purl.obolibrary.org/obo/GO_0060255 regulation of macromolecule metabolic process http://purl.obolibrary.org/obo/GO_0019222 regulation of metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. http://purl.obolibrary.org/obo/GO_0065008 regulation of biological quality http://purl.obolibrary.org/obo/GO_0065007 biological regulation Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc. http://purl.obolibrary.org/obo/GO_0070925 organelle assembly http://purl.obolibrary.org/obo/GO_0016043 cellular component organization The aggregation, arrangement and bonding together of a set of components to form an organelle. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. http://purl.obolibrary.org/obo/GO_1901360 organic cyclic compound metabolic process http://purl.obolibrary.org/obo/GO_0071704 organic substance metabolic process The chemical reactions and pathways involving organic cyclic compound. http://purl.obolibrary.org/obo/GO_1902105 regulation of leukocyte differentiation http://purl.obolibrary.org/obo/GO_0045595 regulation of cell differentiation Any process that modulates the frequency, rate or extent of leukocyte differentiation. http://purl.obolibrary.org/obo/GO_1902494 catalytic complex http://purl.obolibrary.org/obo/GO_0043234 protein complex A protein complex which is capable of catalytic activity. http://purl.obolibrary.org/obo/GO_1902589 single-organism organelle organization http://purl.obolibrary.org/obo/GO_0044763 single-organism cellular process An organelle organization which involves only one organism. http://purl.obolibrary.org/obo/GO_2000026 regulation of multicellular organismal development http://purl.obolibrary.org/obo/GO_0050793 regulation of developmental process Any process that modulates the frequency, rate or extent of multicellular organismal development. http://purl.obolibrary.org/obo/GO_0019814 immunoglobulin complex http://purl.obolibrary.org/obo/GO_0043234 protein complex A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. http://purl.obolibrary.org/obo/GO_0019815 B cell receptor complex http://purl.obolibrary.org/obo/GO_0019814 immunoglobulin complex An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. http://purl.obolibrary.org/obo/GO_0022407 regulation of cell-cell adhesion http://purl.obolibrary.org/obo/GO_0050794 regulation of cellular process Any process that modulates the frequency, rate or extent of attachment of a cell to another cell. http://purl.obolibrary.org/obo/GO_0023061 signal release http://purl.obolibrary.org/obo/GO_0032940 secretion by cell The process in which a signal is secreted or discharged into the extracellular medium from a cellular source. http://purl.obolibrary.org/obo/GO_0030072 peptide hormone secretion http://purl.obolibrary.org/obo/GO_0046879 hormone secretion The regulated release of a peptide hormone from a cell. http://purl.obolibrary.org/obo/GO_0030073 insulin secretion http://purl.obolibrary.org/obo/GO_0030072 peptide hormone secretion The regulated release of proinsulin from secretory granules (B granules) in the B cells of the pancreas; accompanied by cleavage of proinsulin to form mature insulin. http://purl.obolibrary.org/obo/GO_0030218 erythrocyte differentiation http://purl.obolibrary.org/obo/GO_0030099 myeloid cell differentiation The process in which a myeloid precursor cell acquires specializes features of an erythrocyte. http://purl.obolibrary.org/obo/GO_0030219 megakaryocyte differentiation http://purl.obolibrary.org/obo/GO_0030099 myeloid cell differentiation The process in which a myeloid precursor cell acquires specializes features of a megakaryocyte. http://purl.obolibrary.org/obo/GO_0030224 monocyte differentiation http://purl.obolibrary.org/obo/GO_0002573 myeloid leukocyte differentiation The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a monocyte. http://purl.obolibrary.org/obo/GO_0030263 apoptotic chromosome condensation http://purl.obolibrary.org/obo/GO_0030261 chromosome condensation The compaction of chromatin during apoptosis. http://purl.obolibrary.org/obo/GO_0030316 osteoclast differentiation http://purl.obolibrary.org/obo/GO_0002573 myeloid leukocyte differentiation The process in which a relatively unspecialized monocyte acquires the specialized features of an osteoclast. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue. http://purl.obolibrary.org/obo/GO_0030659 cytoplasmic vesicle membrane http://purl.obolibrary.org/obo/GO_0031090 organelle membrane The lipid bilayer surrounding a cytoplasmic vesicle. http://purl.obolibrary.org/obo/GO_0030851 granulocyte differentiation http://purl.obolibrary.org/obo/GO_0002573 myeloid leukocyte differentiation The process in which a myeloid precursor cell acquires the specialized features of a granulocyte. Granulocytes are a class of leukocytes characterized by the presence of granules in their cytoplasm. These cells are active in allergic immune reactions such as arthritic inflammation and rashes. This class includes basophils, eosinophils and neutrophils. http://purl.obolibrary.org/obo/GO_0031016 pancreas development http://purl.obolibrary.org/obo/GO_0048856 anatomical structure development The process whose specific outcome is the progression of the pancreas over time, from its formation to the mature structure. The pancreas is an endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes. http://purl.obolibrary.org/obo/GO_0031988 membrane-bounded vesicle http://purl.obolibrary.org/obo/GO_0031982 vesicle Any small, fluid-filled, spherical organelle enclosed by a lipid bilayer. http://purl.obolibrary.org/obo/GO_0033152 immunoglobulin V(D)J recombination http://purl.obolibrary.org/obo/GO_0016447 somatic recombination of immunoglobulin gene segments The process in which immunoglobulin gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). For immunoglobulin heavy chains V, D, and J gene segments are joined, and for immunoglobulin light chains V and J gene segments are joined. http://purl.obolibrary.org/obo/GO_0042470 melanosome http://purl.obolibrary.org/obo/GO_0016023 cytoplasmic membrane-bounded vesicle A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells. http://purl.obolibrary.org/obo/GO_0042611 MHC protein complex http://purl.obolibrary.org/obo/GO_0044459 plasma membrane part A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen. http://purl.obolibrary.org/obo/GO_0043227 membrane-bounded organelle http://purl.obolibrary.org/obo/GO_0043226 organelle Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. http://purl.obolibrary.org/obo/GO_0045580 regulation of T cell differentiation http://purl.obolibrary.org/obo/GO_0050863 regulation of T cell activation Any process that modulates the frequency, rate or extent of T cell differentiation. http://purl.obolibrary.org/obo/GO_0045619 regulation of lymphocyte differentiation http://purl.obolibrary.org/obo/GO_0051249 regulation of lymphocyte activation Any process that modulates the frequency, rate or extent of lymphocyte differentiation. http://purl.obolibrary.org/obo/GO_0050793 regulation of developmental process http://purl.obolibrary.org/obo/GO_0050789 regulation of biological process Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). http://purl.obolibrary.org/obo/GO_0051179 localization http://purl.obolibrary.org/obo/GO_0008150 biological_process Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported to or maintained in a specific location. http://purl.obolibrary.org/obo/GO_0051249 regulation of lymphocyte activation http://purl.obolibrary.org/obo/GO_0002694 regulation of leukocyte activation Any process that modulates the frequency, rate or extent of lymphocyte activation. http://purl.obolibrary.org/obo/GO_0060986 endocrine hormone secretion http://purl.obolibrary.org/obo/GO_0046879 hormone secretion The regulated release of a hormone into the circulatory system. http://purl.obolibrary.org/obo/GO_0036321 ghrelin secretion http://purl.obolibrary.org/obo/GO_0030072 peptide hormone secretion The regulated release of ghrelin from a cell. Ghrelin is a 28 amino acid hunger-stimulating peptide hormone. http://purl.obolibrary.org/obo/GO_0040030 regulation of molecular function, epigenetic http://purl.obolibrary.org/obo/GO_0065007 biological regulation Any heritable epigenetic process that modulates the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya. http://purl.obolibrary.org/obo/GO_0042101 T cell receptor complex http://purl.obolibrary.org/obo/GO_0044459 plasma membrane part A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains. http://purl.obolibrary.org/obo/GO_0042571 immunoglobulin complex, circulating http://purl.obolibrary.org/obo/GO_0019814 immunoglobulin complex An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component. http://purl.obolibrary.org/obo/GO_0042582 azurophil granule http://purl.obolibrary.org/obo/GO_0030141 secretory granule Primary lysosomal granule found in neutrophil granulocytes. Contains a wide range of hydrolytic enzymes and is released into the extracellular fluid. http://purl.obolibrary.org/obo/GO_0042589 zymogen granule membrane http://purl.obolibrary.org/obo/GO_0030667 secretory granule membrane The lipid bilayer surrounding a zymogen granule. http://purl.obolibrary.org/obo/GO_0042613 MHC class II protein complex http://purl.obolibrary.org/obo/GO_0042611 MHC protein complex A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen. http://purl.obolibrary.org/obo/GO_0043229 intracellular organelle http://purl.obolibrary.org/obo/GO_0044424 intracellular part Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. http://purl.obolibrary.org/obo/GO_0044030 regulation of DNA methylation http://purl.obolibrary.org/obo/GO_0051052 regulation of DNA metabolic process Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. http://purl.obolibrary.org/obo/GO_0044342 type B pancreatic cell proliferation http://purl.obolibrary.org/obo/GO_0044699 single-organism process The multiplication or reproduction of pancreatic B cells, resulting in the expansion of an pancreatic B cell population. Pancreatic B cell are cells of the pancreas that secrete insulin. http://purl.obolibrary.org/obo/GO_0045444 fat cell differentiation http://purl.obolibrary.org/obo/GO_0030154 cell differentiation The process in which a relatively unspecialized cell acquires specialized features of an adipocyte, an animal connective tissue cell specialized for the synthesis and storage of fat. http://purl.obolibrary.org/obo/GO_0048103 somatic stem cell division http://purl.obolibrary.org/obo/GO_0017145 stem cell division The self-renewing division of a somatic stem 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/GO_0050863 regulation of T cell activation http://purl.obolibrary.org/obo/GO_0051249 regulation of lymphocyte activation Any process that modulates the frequency, rate or extent of T cell activation. http://purl.obolibrary.org/obo/GO_0051704 multi-organism process http://purl.obolibrary.org/obo/GO_0008150 biological_process A biological process which involves another organism of the same or different species. http://purl.obolibrary.org/obo/GO_1902578 single-organism localization http://purl.obolibrary.org/obo/GO_0051179 localization A localization which involves only one organism. http://purl.obolibrary.org/obo/GO_1903706 regulation of hemopoiesis http://purl.obolibrary.org/obo/GO_2000026 regulation of multicellular organismal development Any process that modulates the frequency, rate or extent of hemopoiesis. http://purl.obolibrary.org/obo/PR_000001002 CD19 molecule http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human CD19 gene or a 1:1 ortholog thereof. It is composed of an N-terminal extracellular domain containing two Ig-like C2-type (immunoglobulin-like) domains, followed by a single-pass transmembrane segment and a cytoplasmic C-terminal tail. CD19 expression is restricted to members of the B cell lineage. It functions as a co-receptor for B-cell antigen receptor (BCR), regulating signal transduction. http://purl.obolibrary.org/obo/PR_000001003 CD34 molecule http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human CD34 gene or a 1:1 ortholog thereof. It is a leukocyte membrane protein expressed specifically by lymphohematopoietic progenitor cells. It contains a single-pass transmembrane domain and that show distinct expression on early hematopoietic precursors and vascular-associated tissue. Acts as a scaffold that presents selectin carbohydrate ligands in a clustered, tissue specific manner to allow for higher avidity interactions between leukocytes and endothelial cells during the inflammatory process. In common with related sialomucins (endoglycan and podocalyxin), the extracellular region is dominated by an N-terminal mucin-like domain, which is densely substituted with sialylated O-linked carbohydrates. The mucin-like region is followed by a cysteine-containing and presumably globular domain. This domain may fold into an immunoglobulin-like structure as the positions of 2 of the cysteines are conserved in the C2 set of the immunoglobulin superfamily. The cytoplasmic domain is around 73-76 residues long and highly conserved. http://purl.obolibrary.org/obo/PR_000001006 receptor-type tyrosine-protein phosphatase C http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human PTPRC gene or a 1:1 ortholog thereof. It is composed of an extracellular domain, a single transmembrane segment and two tandem intracytoplasmic protein-tyrosine phosphatase domains. Contains 1 to 3 copies of the Fibronectin type III domain (Pfam:PF00041) followed by two copies of the Protein-tyrosine phosphatase (Pfam:PF00102) domain. Receptor-type tyrosine-protein phosphatase C (CD45) regulates signal transduction and lymphocyte activation by specific association with receptor molecules on T and B cells. Multiple isoforms of CD45 (180-235 kDa) can be generated asa result of alternative splicing of three variable exons 4(A), 5(B) and 6(C), encoding sequences at the N-terminal extracellular domain of the molecule. http://purl.obolibrary.org/obo/PR_000001012 integrin alpha-M http://purl.obolibrary.org/obo/PR_000000001 protein An integrin alpha with A domain that is a translation product of the human ITGAM gene or a 1:1 ortholog thereof. They constitute subunits of the integrin alpha-M/beta-2 receptor. This receptor is implicated in various adhesive interactions of monocytes, macrophages and granulocytes as well as in mediating the uptake of complement-coated particles. It is also a receptor for fibrinogen, factor X and ICAM1. http://purl.obolibrary.org/obo/PR_000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA http://purl.obolibrary.org/obo/PR_000001006 receptor-type tyrosine-protein phosphatase C A receptor-type tyrosine-protein phosphatase C that is a translation product of a mature transcript of the PTPRC gene, that includes the region encoded by the variable exon 4(A), and lacks the region encoded by exons 5(B) and 6(C). http://purl.obolibrary.org/obo/PR_000001020 CD3 epsilon http://purl.obolibrary.org/obo/PR_000000001 protein A CD3 subunit that is a translation product of the human CD3E gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001024 neural cell adhesion molecule 1 http://purl.obolibrary.org/obo/PR_000000001 protein A neural cell adhesion molecule NCAM that is a translation product of the human NCAM1 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001083 CD2 molecule http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human CD2 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001084 T-cell surface glycoprotein CD8 alpha chain http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human CD8A gene or a 1:1 ortholog thereof. CD8 is a transmembrane that is a co-receptor for MHC class-I antigen/T-cell receptor interaction. The most common form of CD8 is composed of a CD8 alpha and a CD8 beta chain. http://purl.obolibrary.org/obo/PR_000001197 chemokine receptor CCR1/3/1L http://purl.obolibrary.org/obo/PR_000000001 protein A rhodopsin-like G-protein coupled receptor that is a translation product of the CCR1, CCR3, or CCR1L1 genes (the last found so far only in mouse). http://purl.obolibrary.org/obo/PR_000001254 C-C chemokine receptor type 1 http://purl.obolibrary.org/obo/PR_000001197 chemokine receptor CCR1/3/1L A chemokine receptor CCR1/3/1L that is a translation product of the human CCR1 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001255 C-C chemokine receptor type 3 http://purl.obolibrary.org/obo/PR_000001197 chemokine receptor CCR1/3/1L A chemokine receptor CCR1/3/1L that is a translation product of the human CCR3 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001289 membrane-spanning 4-domains subfamily A member 1 http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human MS4A1 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001307 CD44 molecule http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human CD44 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001332 carcinoembryonic antigen-related cell adhesion molecule 8 http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human CEACAM8 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001343 CD69 molecule http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human CD69 gene or a 1:1 ortholog thereof. A type II transmembrane protein with a C-type lectin binding domain in the extracellular portion of the molecule. Involved in lymphocyte proliferation and functions as a signal transmitting receptor in lymphocytes, natural killer (NK) cells, and platelets. http://purl.obolibrary.org/obo/PR_000001344 ectonucleotide pyrophosphatase/phosphodiesterase family member 3 http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human ENPP3 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001345 endoglin http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human ENG gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001355 immunoglobulin gamma Fc receptor II/III/IV http://purl.obolibrary.org/obo/PR_000000001 protein A protein with a core domain architecture consisting of an extracellular domain containing two copies of the Immunoglobulin domain (Pfam:PF00047), followed by a single-pass transmembrane region and a small intracellular domain. The active protein is a low affinity receptor for immunoglobulin gamma chain Fc region. Human II-a, II-b, and II-c represent a recent gene expansion and are equally related to mouse II, III, and IV. Human III-A and III-B are closely related and closer to mouse IV than to mouse III. http://purl.obolibrary.org/obo/PR_000001381 interleukin-2 receptor subunit beta http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human IL2RB gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001408 ADP-ribosyl cyclase 1 http://purl.obolibrary.org/obo/PR_000000001 protein An ADP-ribosyl cyclase that is a translation product of the human CD38 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001444 cadherin-5 http://purl.obolibrary.org/obo/PR_000000001 protein A cadherin that is a translation product of the human CDH5 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001456 alpha-(1,3)-fucosyltransferase FUT4 http://purl.obolibrary.org/obo/PR_000000001 protein A fucosyltransferase that is a translation product of the human FUT4 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001479 low affinity immunoglobulin gamma Fc region receptor II http://purl.obolibrary.org/obo/PR_000001355 immunoglobulin gamma Fc receptor II/III/IV An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the mouse Fcgr2 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001483 low affinity immunoglobulin gamma Fc region receptor III http://purl.obolibrary.org/obo/PR_000001355 immunoglobulin gamma Fc receptor II/III/IV An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the mouse Fcgr3 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001559 epithelial cell adhesion molecule http://purl.obolibrary.org/obo/PR_000000001 protein A tumor-associated calcium signal transducer that is a translation product of the human EPCAM gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001786 prominin-1 http://purl.obolibrary.org/obo/PR_000000001 protein A prominin that is a translation product of the human PROM1 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001800 5'-nucleotidase http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human NT5E gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001809 CD59-like glycoprotein http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the CD59 or closely related gene. This gene is present as a single copy in human and has undergone a lineage-specific duplication in mouse. CD59 antigen has a core architecture consisting of one UPAR/Ly-6 domain (Pfam:PF00021), a small domain of about 70 amino acids and containing 5 conserved disulfide bonds. It is both N- and O-glycosylated and is a GPI-anchored protein that releases soluble forms in some tissues. http://purl.obolibrary.org/obo/PR_000001836 CD7 molecule http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human CD7 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001839 T-cell surface glycoprotein CD5 http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human CD5 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001843 Thy-1 membrane glycoprotein http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human THY1 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001865 interleukin-3 receptor class 2 alpha chain http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human IL3RA gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001867 interleukin-5 receptor subunit alpha http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human IL5RA gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001869 interleukin-7 receptor subunit alpha http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human IL7R gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001874 KLRB1-like protein http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the KLRB1 gene or its closely related paralogs (KLRB1A-F). There are lineage-specific expansions in mouse and rat. http://purl.obolibrary.org/obo/PR_000001879 leukosialin http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human SPN gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001889 CD14 molecule http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human CD14 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001892 CD33 molecule http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human CD33 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001898 neprilysin http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human MME gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001903 paired box protein PAX-5 http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human PAX5 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001932 signal transducer CD24 http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human CD24 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001944 transcription factor PU.1 http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human SPI1 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001945 transferrin receptor protein 1 http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human TFRC gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001950 tumor necrosis factor ligand superfamily member 5 http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human CD40LG gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001969 urokinase plasminogen activator surface receptor http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human PLAUR gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000002065 mast/stem cell growth factor receptor http://purl.obolibrary.org/obo/PR_000000001 protein A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human KIT gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000002112 vascular endothelial growth factor receptor 2 http://purl.obolibrary.org/obo/PR_000000001 protein A vascular endothelial growth factor receptor that is a translation product of the human KDR gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000002978 lymphocyte antigen 6G http://purl.obolibrary.org/obo/PR_000000001 protein A ly-6-like protein that is a translation product of the mouse Ly6g gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000002981 lymphocyte antigen 76 http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the mouse Ly76 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain http://purl.obolibrary.org/obo/NCBITaxon_10090 Mus musculus Mus musculus that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organism. http://purl.obolibrary.org/obo/BCGO_0000003 rat strain http://purl.obolibrary.org/obo/NCBITaxon_10116 Rattus norvegicus Rattus norvegicus that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organism. http://purl.obolibrary.org/obo/BCGO_0000004 insulin expressing cell http://purl.obolibrary.org/obo/CL_0000000 cell a cell that expresses a gene for insulin. http://purl.obolibrary.org/obo/BCGO_0000010 sequence feature quantification http://purl.obolibrary.org/obo/OBI_0200000 data transformation A data transformation that attaches quantified values to specific sequence features, e.g. transcript, exon, etc. http://purl.obolibrary.org/obo/BCGO_0000011 high throughput sequence alignment http://purl.obolibrary.org/obo/OBI_0200000 data transformation a data transformation that aligns sequencing reads to reference sequence. http://purl.obolibrary.org/obo/BCGO_0000014 functional beta cell like cell http://purl.obolibrary.org/obo/CL_0000000 cell A cell that has all features and genetic signatures as functional beta cell. It may not be part of pancreas. http://purl.obolibrary.org/obo/BCGO_0000030 C3H mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain A mouse strain that Inbred from F130 to F170 depending on substrain original generated from a cross of a Bagg albino female and a DBA male by Strong in 1920. It has Agouti coat color. Most substrains have a good reproductive performance. It is widely used in a wide variety of research areas including cancer, immunology and inflammation, sensorineural, and cardiovascular biology. http://purl.obolibrary.org/obo/BCGO_0000057 Insm1-expressing Pdx1 high-positive pancreatic endocrine progenitor cell http://purl.obolibrary.org/obo/BCGO_0000053 Insm1-expressing endocrine progenitor cell A Insm1-expressing endocrine progenitor cell that expresses the gene for pancreas/duodenum homeobox protein 1 at a high level. http://purl.obolibrary.org/obo/BCGO_0000058 Insm1-expressing Pdx1 low-positive pancreatic endocrine progenitor cell http://purl.obolibrary.org/obo/BCGO_0000053 Insm1-expressing endocrine progenitor cell A Insm1-expressing endocrine progenitor cell that expresses the gene for pancreas/duodenum homeobox protein 1 at a low level. http://purl.obolibrary.org/obo/BCGO_0000059 Insm1tm2(GFP.Cre)Mgn/Pdx1tm2(CFP)Mgn mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain A mouse strain that is the result of mating between a Insm1GFPCre/+ mouse and a Pdx1CFP/+ mouse both on a CD-1 background http://purl.obolibrary.org/obo/BCGO_0000060 differential expression software http://purl.obolibrary.org/obo/IAO_0000010 software A software implementing a higher level analysis protocol of type differential expresssion. http://purl.obolibrary.org/obo/BCGO_0000061 B6.Cg-Tg(Ins1-EGFP)1Hara/J mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain A mouse strain that is genetically modified expressing Enhanced Green Fluorescent Protein (EGFP) under the control of the mouse insulin 1 promoter. Fluorescence is detected in tissues where insulin I is normally expressed; fluorescent protein expression in pancreatic beta-cells is evident from embryonic day (E)13.5 through adulthood. The fluorescence expression pattern is similar to the patterns seen in two other strains STOCK Tg(Ins1-Cerulean)24Hara/J and STOCK Tg(Ins1-DsRed*T4)32Hara/J. This mutant mouse strain exhits normal glucose tolerance and pancreatic insulin levels and may be useful in studies of diabetes and pancreatic beta islet cell biology. http://purl.obolibrary.org/obo/BCGO_0000068 ArrayExpress ID http://purl.obolibrary.org/obo/IAO_0000577 centrally registered identifier symbol A CRID symbol assigned by ArrayExpress to uniquely identify a study in ArrayExpress http://purl.obolibrary.org/obo/BCGO_0000069 GEO ID http://purl.obolibrary.org/obo/IAO_0000577 centrally registered identifier symbol A CRID symbol assigned by Gene Expression Omnibus (GEO) to uniquely identify a study in GEO. http://purl.obolibrary.org/obo/BCGO_0000070 cellular marker expression http://purl.obolibrary.org/obo/GO_0010467 gene expression A gene expression that produces cellular surface proteins that can be used to identify and isolate specific cells. http://purl.obolibrary.org/obo/BCGO_0000071 pancreatic material http://purl.obolibrary.org/obo/BFO_0000040 material entity A material entity that could be whole pancreas, part of pancreas (including a single cell type (e.g., beta cell), or precursor to pancreas. http://purl.obolibrary.org/obo/BCGO_0000076 characterization of cell differentiation objective http://purl.obolibrary.org/obo/OBI_0000219 cellular feature identification objective A cellular feature identification objective that aims to examine or characterize cell development or differentiation. http://purl.obolibrary.org/obo/BCGO_0000077 characterization of differentiation of insulin-producing cells objective http://purl.obolibrary.org/obo/BCGO_0000076 characterization of cell differentiation objective A characterization of cell differentiation objective that aims to examine the influence of specific protocols with regard to generating insulin-producing cells from putative progenitors or other mechanisms (e.g., transdifferentiation). http://purl.obolibrary.org/obo/BCGO_0000078 characterization of islet/beta-cell stimulation/injury objective http://purl.obolibrary.org/obo/BCGO_0000080 characterization of cell stimulation or injury objective A characterization of cell stimulation or injury objective that aims to address the effects of compounds, hormones, or cell manipulations on the ability of islets and/or beta-cells to secrete insulin or respond to glucose levels. http://purl.obolibrary.org/obo/BCGO_0000079 characterization of pancreas development and growth objective http://purl.obolibrary.org/obo/OBI_0000015 biological feature identification objective A biological feature identification objective that aims to examine changes in gene expression and/or epigenome during pancreas development or regeneration. http://purl.obolibrary.org/obo/BCGO_0000080 characterization of cell stimulation or injury objective http://purl.obolibrary.org/obo/OBI_0000219 cellular feature identification objective A cellular feature identification objective that aims to address the effects of compounds, hormones, or cell manipulations on the ability of tissues or specific cell types to perform their normal functions or respond to insult. http://purl.obolibrary.org/obo/BCGO_0000081 targets and roles of transcriptional regulators objective http://purl.obolibrary.org/obo/OBI_0000131 molecular feature identification objective A molecular feature identification objective that aims to identify genes and processes regulated by transcription factors, co-activators, and other types of transcriptional regulators. http://purl.obolibrary.org/obo/BCGO_0000082 tissue expression survey objective http://purl.obolibrary.org/obo/OBI_0000015 biological feature identification objective A biological feature identification objective that aims to address the question of what genes are expressed in a given tissue or cell type or the expression of genes across multiple cells and tissues. http://purl.obolibrary.org/obo/BCGO_0000083 epigenetic modification process http://purl.obolibrary.org/obo/GO_0008150 biological_process A biological process of generating epigenetic modifications, such as DNA methylation and histone modifications. http://purl.obolibrary.org/obo/BCGO_0000084 islet expansion in vitro http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process that aims to expand islets in culture and redifferentiate them to insulin producing cells. http://purl.obolibrary.org/obo/BCGO_0000085 islets in diabetes http://purl.obolibrary.org/obo/UBERON_0000006 islet of Langerhans islet of Langerhans that is part of a person who has diabetes. http://purl.obolibrary.org/obo/BCGO_0000095 age datum http://purl.obolibrary.org/obo/IAO_0000027 data item A data item of age. It could be measurement datum like 10 weeks, 2 years, or categorical datum like young, adult. http://purl.obolibrary.org/obo/BCGO_0000097 concentration datum http://purl.obolibrary.org/obo/IAO_0000027 data item A data item of how much of a given substance there is mixed with another substance.Annotations. It could be measurement datum like 10 mM, or categorical datum like low, high concentration. http://purl.obolibrary.org/obo/BCGO_9000253 Ptf1a{LCA} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Ptf1a{tm1(LCA)}). This ES cell line contains a loxed cassette acceptor (LCA) allele in which a 4.1 kb region of this gene (including the proximal promoter and both exons 1 and 2) was replaced with a loxP site, an inverted loxP site, and both positive and negative selectable markers. This enables the use of Recombinase-Mediated Cassette Exchange (RMCE) to easily insert various reporter genes or to make other modifications of the Ptf1a gene locus. http://purl.obolibrary.org/obo/BCGO_9000254 Ptf1a{YFP} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{LCA} using the Loxed Cassette Acceptor allele Ptf1a{tm1.1(YFP)}). This ES cell line contains YFP inserted into a Ptf1a{LCA} allele by recombinase mediated cassette exchange. These cells may be useful for identifying pancreatic progenitor cells in cultures that have been stimulated to differentiate towards endodermal and pancreatic fates. http://purl.obolibrary.org/obo/BCGO_9000255 Gck{LCA} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which the targeted gene, glucokinase (NCBI Gene ID: 19213), has been modified (allele type: Cassette Acceptor) to targeted mutation 4 (MGI ID: gk{tm4(LCA)}). This ES cell line contains a loxed cassette acceptor (LCA) allele that may be utilized for the exchange of DNAs of interest into the glucokinase locus by recombinase mediated cassette exchange (RMCE). This LCA uses a loxP/inverted loxP strategy for RMCE and allows sequences between - 6 kb and + 5 kb (relevative to the hepatic-specific promoter) to be manipulated. This enables a variety of different types of experiments to be performed using a range of cassette designs. http://purl.obolibrary.org/obo/BCGO_9000256 Insm1{LCA} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which the targeted gene, insulinoma-associated 1 (NCBI Gene ID: 53626), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Insm1{tm1(LCA)}). This ES cell line contains a loxed cassette acceptor(LCA)allele that may be utilized for the exchange of DNAs of interest into the Insm1 gene locus by recombinase mediated cassette exchange (RMCE). This LCA uses a lox 66/71 and lox 2272 strategy for RMCE and allows a ~5.2 kb region of this single exon gene to be manipulated. This enables a variety of different types of experiments to be performed using a range of cassette designs. http://purl.obolibrary.org/obo/BCGO_9000257 Nkx2.2{LCA} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Nkx2.2{tm1(LCA)}). This ES cell line contains a loxed cassette acceptor (LCA) allele that may be utilized for the exchange of DNAs of interest into the Nkx2.2 locus by recombinase mediated cassette exchange (RMCE). This LCA uses a Lox71/66 and Lox2272 strategy for RMCE and allows for manipulation of a 5.1 kb region of the gene (contains promoter, exon 1, and exon 2). This leads to a variety of experiments that can be performed using a wide range of cassette designs. http://purl.obolibrary.org/obo/BCGO_9000260 MIP-GFP mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line containing a transgene in which Gfp (transgene) is driven by the Ins1 promoter (NCBI Gene ID: 16333). New ESC line derived from MIP-GFP mice (Hara et al. 2003,Am J Physiol Endocrinol Metab. 284: E177-83). Genetic background is C57Bl6/J. When injected into E3.5 mouse blastocysts this line contributes to chimeras and Insulin+/GFP+ double positive cells are found in E14.5 embryonic pancreas. No GFP+ cells are seen outside the pancreas. http://purl.obolibrary.org/obo/BCGO_9000261 Ngn3-GFP mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line containing a transgene in which Gfp (transgene) is driven by the Neurog3 promoter (NCBI Gene ID: 11925). Mouse ESC line derived from Ngn3-GFP transgenic mice (Gradwohl et al. unpublished). Genetic background is CD1. http://purl.obolibrary.org/obo/BCGO_9000262 Rosa26{LCA} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Rosa26{tm1(LCA)}). This ES cell line contains a loxed cassette acceptor (LCA) allele in which a 5.17 kb region of the gene has been replaced by a Lox66 site, a puromycin-(delta)-thymidine kinase fusion gene driven by the mouse phosphoglycerol kinase promoter, a kanamycin resistance gene driven by the bacterial EM7 promoter, and a Lox2272 site. These features enable use of Recombinase-Mediated Cassette Exchange for the rapid insertion of various DNAs into the Rosa26 gene locus. http://purl.obolibrary.org/obo/BCGO_9000263 Sox17{LCA} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which the targeted gene, SRY-box containing gene 17 (NCBI Gene ID: 20671), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Sox17{tm1(LCA)}). This mouse ES cell line contains a loxed cassette acceptor (LCA) allele that may be utilized for the exchange of DNAs of interest into the Sox17 gene locus by recombinase mediated cassette exchange (RMCE). A 3.79 kb region of the gene (exons 3-5) was replaced by tandemly oriented lox66 and lox2272 sites as well as both positive and negative selectable markers. http://purl.obolibrary.org/obo/BCGO_9000266 Polyclonal rat IAPP raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the rat "IAPP" antigen. http://purl.obolibrary.org/obo/BCGO_9000267 Polyclonal rat C-peptide 2 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the rat "C-peptide 2" antigen. http://purl.obolibrary.org/obo/BCGO_9000268 Polyclonal rat C-peptide 1 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the rat "C-peptide 1" antigen. http://purl.obolibrary.org/obo/BCGO_9000269 Polyclonal mouse C-peptide 1 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the mouse "C-peptide 1" antigen. http://purl.obolibrary.org/obo/BCGO_9000270 Monoclonal human Insulin raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Insulin" antigen. http://purl.obolibrary.org/obo/BCGO_9000271 Polyclonal rat PDX1 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the rat "PDX1" antigen. http://purl.obolibrary.org/obo/BCGO_9000272 Polyclonal rat PDX1 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the rat "PDX1" antigen. http://purl.obolibrary.org/obo/BCGO_9000273 Polyclonal rat Nkx6.1 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the rat "Nkx6.1" antigen. http://purl.obolibrary.org/obo/BCGO_9000274 Polyclonal human Nkx2.2 raised in goat http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in goat that targets the human "Nkx2.2" antigen. http://purl.obolibrary.org/obo/BCGO_9000275 Polyclonal human ghrelin raised in goat http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in goat that targets the human "ghrelin" antigen. http://purl.obolibrary.org/obo/BCGO_9000276 Polyclonal mouse Pax6 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the mouse "Pax6" antigen. http://purl.obolibrary.org/obo/BCGO_9000277 Polyclonal human b-catenin raised in goat http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in goat that targets the human "b-catenin" antigen. http://purl.obolibrary.org/obo/BCGO_9000278 Monoclonal mouse smooth muscle actin raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the mouse "smooth muscle actin" antigen. http://purl.obolibrary.org/obo/BCGO_9000279 Polyclonal human amylase raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the human "amylase" antigen. http://purl.obolibrary.org/obo/BCGO_9000280 Polyclonal human c-myc raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the human "c-myc" antigen. http://purl.obolibrary.org/obo/BCGO_9000281 Polyclonal rat Glut-2 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the rat "Glut-2" antigen. http://purl.obolibrary.org/obo/BCGO_9000282 Polyclonal bovine Carboxypeptidase A raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the bovine "Carboxypeptidase A" antigen. http://purl.obolibrary.org/obo/BCGO_9000283 Polyclonal human Chromogranin A raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the human "Chromogranin A" antigen. http://purl.obolibrary.org/obo/BCGO_9000284 Monoclonal human Chromogranin A raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Chromogranin A" antigen. http://purl.obolibrary.org/obo/BCGO_9000285 Monoclonal human Cytokeratin 7 raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Cytokeratin 7" antigen. http://purl.obolibrary.org/obo/BCGO_9000286 Monoclonal human PECAM-1 raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "PECAM-1" antigen. http://purl.obolibrary.org/obo/BCGO_9000287 Polyclonal aequorea victoria Green Fluorescent Protein raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the aequorea victoria "Green Fluorescent Protein" antigen. http://purl.obolibrary.org/obo/BCGO_9000288 Monoclonal chicken Nkx2.2 raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the chicken "Nkx2.2" antigen. http://purl.obolibrary.org/obo/BCGO_9000289 Polyclonal rat ghrelin raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the rat "ghrelin" antigen. http://purl.obolibrary.org/obo/BCGO_9000290 Monoclonal chicken Islet-1 raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the chicken "Islet-1" antigen. http://purl.obolibrary.org/obo/BCGO_9000291 Polyclonal human GATA-4 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the human "GATA-4" antigen. http://purl.obolibrary.org/obo/BCGO_9000292 Polyclonal mouse PDX1 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the mouse "PDX1" antigen. http://purl.obolibrary.org/obo/BCGO_9000294 Polyclonal mouse PDX1 raised in chicken http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in chicken that targets the mouse "PDX1" antigen. http://purl.obolibrary.org/obo/BCGO_9000295 Monoclonal human Glucagon raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Glucagon" antigen. http://purl.obolibrary.org/obo/BCGO_9000296 Monoclonal human Somatostatin raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Somatostatin" antigen. http://purl.obolibrary.org/obo/BCGO_9000297 Monoclonal rat Pancreatic Ducts raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the rat "Pancreatic Ducts" antigen. http://purl.obolibrary.org/obo/BCGO_9000298 Monoclonal rat Pancreatic Ducts raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the rat "Pancreatic Ducts" antigen. http://purl.obolibrary.org/obo/BCGO_9000299 Monoclonal rat Islet Delta Cells raised in rat http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in rat that targets the rat "Islet Delta Cells" antigen. http://purl.obolibrary.org/obo/BCGO_9000300 Monoclonal rat Pancreatic Ducts raised in rat http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in rat that targets the rat "Pancreatic Ducts" antigen. http://purl.obolibrary.org/obo/BCGO_9000301 Monoclonal human Pro-Insulin raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Pro-Insulin" antigen. http://purl.obolibrary.org/obo/BCGO_9000302 Polyclonal mouse Ngn3 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the mouse "Ngn3" antigen. http://purl.obolibrary.org/obo/BCGO_9000303 Polyclonal mouse Ngn3 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the mouse "Ngn3" antigen. http://purl.obolibrary.org/obo/BCGO_9000304 Monoclonal mouse Ngn3 raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the mouse "Ngn3" antigen. http://purl.obolibrary.org/obo/BCGO_9000305 Monoclonal mouse Ngn3 raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the mouse "Ngn3" antigen. http://purl.obolibrary.org/obo/BCGO_9000307 Monoclonal rat Nkx6.1 raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the rat "Nkx6.1" antigen. http://purl.obolibrary.org/obo/BCGO_9000308 Monoclonal rat Nkx6.1 raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the rat "Nkx6.1" antigen. http://purl.obolibrary.org/obo/BCGO_9000309 Monoclonal rat Nkx6.1 raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the rat "Nkx6.1" antigen. http://purl.obolibrary.org/obo/BCGO_9000310 Monoclonal rat Nkx6.1 raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the rat "Nkx6.1" antigen. http://purl.obolibrary.org/obo/BCGO_9000311 Polyclonal human HNF6 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the human "HNF6" antigen. http://purl.obolibrary.org/obo/BCGO_9000312 Polyclonal mouse PDX1 raised in goat http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in goat that targets the mouse "PDX1" antigen. http://purl.obolibrary.org/obo/BCGO_9000313 Polyclonal mouse PDX1 raised in guinea pig http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in guinea pig that targets the mouse "PDX1" antigen. http://purl.obolibrary.org/obo/BCGO_9000314 Polyclonal human ghrelin raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the human "ghrelin" antigen. http://purl.obolibrary.org/obo/BCGO_9000315 Polyclonal human ghrelin raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the human "ghrelin" antigen. http://purl.obolibrary.org/obo/BCGO_9000316 Monoclonal rat PDX1 raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the rat "PDX1" antigen. http://purl.obolibrary.org/obo/BCGO_9000317 Monoclonal rat PDX1 raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the rat "PDX1" antigen. http://purl.obolibrary.org/obo/BCGO_9000318 Monoclonal rat PDX1 raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the rat "PDX1" antigen. http://purl.obolibrary.org/obo/BCGO_9000321 Polyclonal human Sox2 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the human "Sox2" antigen. http://purl.obolibrary.org/obo/BCGO_9000322 Polyclonal mouse FoxA2 raised in goat http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in goat that targets the mouse "FoxA2" antigen. http://purl.obolibrary.org/obo/BCGO_9000323 Monoclonal human E-cadherin raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "E-cadherin" antigen. http://purl.obolibrary.org/obo/BCGO_9000324 Polyclonal human Sox17 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the human "Sox17" antigen. http://purl.obolibrary.org/obo/BCGO_9000325 Polyclonal human Sox17 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the human "Sox17" antigen. http://purl.obolibrary.org/obo/BCGO_9000326 Monoclonal human Pancreatic endocrine cells raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Pancreatic endocrine cells" antigen. http://purl.obolibrary.org/obo/BCGO_9000327 Monoclonal human Pancreatic endocrine cells raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Pancreatic endocrine cells" antigen. http://purl.obolibrary.org/obo/BCGO_9000328 Monoclonal human Pancreatic endocrine cells raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Pancreatic endocrine cells" antigen. http://purl.obolibrary.org/obo/BCGO_9000329 Monoclonal human Pancreatic endocrine cells raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Pancreatic endocrine cells" antigen. http://purl.obolibrary.org/obo/BCGO_9000330 Monoclonal human Pancreatic endocrine cells raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Pancreatic endocrine cells" antigen. http://purl.obolibrary.org/obo/BCGO_9000331 Polyclonal human Sox17 raised in goat http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in goat that targets the human "Sox17" antigen. http://purl.obolibrary.org/obo/BCGO_9000332 Polyclonal mouse Shh raised in goat http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in goat that targets the mouse "Shh" antigen. http://purl.obolibrary.org/obo/BCGO_9000333 Polyclonal e. coli beta Galactosidase raised in chicken http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in chicken that targets the e. coli "beta Galactosidase" antigen. http://purl.obolibrary.org/obo/BCGO_9000334 Monoclonal aequorea victoria Green Fluorescent Protein raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the aequorea victoria "Green Fluorescent Protein" antigen. http://purl.obolibrary.org/obo/BCGO_9000335 Polyclonal mouse Ptf1a raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the mouse "Ptf1a" antigen. http://purl.obolibrary.org/obo/BCGO_9000336 Polyclonal mouse IA1 (Insm-1) raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the mouse "IA1 (Insm-1)" antigen. http://purl.obolibrary.org/obo/BCGO_9000337 Monoclonal human Pancreatic duct cells raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Pancreatic duct cells" antigen. http://purl.obolibrary.org/obo/BCGO_9000338 Monoclonal human Pancreatic duct cells raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Pancreatic duct cells" antigen. http://purl.obolibrary.org/obo/BCGO_9000339 Monoclonal human Pancreatic exocrine cells raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Pancreatic exocrine cells" antigen. http://purl.obolibrary.org/obo/BCGO_9000340 Monoclonal human Pancreatic exocrine cells raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Pancreatic exocrine cells" antigen. http://purl.obolibrary.org/obo/BCGO_9000341 Monoclonal human Pancreatic endocrine cells raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Pancreatic endocrine cells" antigen. http://purl.obolibrary.org/obo/BCGO_9000342 Monoclonal human Alpha cells raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Alpha cells" antigen. http://purl.obolibrary.org/obo/BCGO_9000343 Monoclonal human Alpha cells raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Alpha cells" antigen. http://purl.obolibrary.org/obo/BCGO_9000344 Monoclonal mouse Mo ES-Derived Definitive Endoderm raised in rat http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Definitive Endoderm" antigen. http://purl.obolibrary.org/obo/BCGO_9000345 Monoclonal mouse Mo ES-Derived Definitive Endoderm raised in rat http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Definitive Endoderm" antigen. http://purl.obolibrary.org/obo/BCGO_9000346 Polyclonal human T (Brachyury) raised in goat http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in goat that targets the human "T (Brachyury)" antigen. http://purl.obolibrary.org/obo/BCGO_9000347 Polyclonal mouse Laminin raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the mouse "Laminin" antigen. http://purl.obolibrary.org/obo/BCGO_9000348 Monoclonal chicken Pax6 raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the chicken "Pax6" antigen. http://purl.obolibrary.org/obo/BCGO_9000602 Sox17{GFPCre} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, SRY-box containing gene 17 (NCBI Gene ID: 20671) is replaced to create Sox17{Cre-GFP} using the Loxed Cassette Acceptor allele Sox17{tm1(LCA)}). Using an RMCE strategy, we inserted a Cre-GFP (Green fluorescent protein) fusion protein into a Sox17[LCA] allele thereby replacing Sox17 coding sequences. The Sox17-CreGFP ESCs may be used to track Sox17-expressing cells and their progeny, or to conditionally inactivate genes in Sox17-expressing cells. Mark the expression of Sox17 with both Cre and GFP. Cre will enable lineage tracing using reporter alleles that are activated by cre recombination. GFP will enable direct visualization of Sox17 gene expression. http://purl.obolibrary.org/obo/BCGO_9000721 Ghrl{LCA} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which the targeted gene, Ghrelin (NCBI Gene ID: 58991), has been modified (allele type: Cassette Acceptor) to targeted mutation (MGI ID: Ghrl{LCA}). ES cells were modified by homologous recombination to replace a 6.912 kb region of the Ghrelin (GHRL) gene from 2.7 kb upstream of exon 1 to 0.5 kb downstream of exon 5 with tandemly oriented lox71 and lox2272 sites as well as both positive and negative selectable markers. The gene was replaced by tandemly oriented lox71 and lox2272 sitesas well as both positive and negative selectable markers. http://purl.obolibrary.org/obo/BCGO_9000761 Ghrl{Cre-eGFP} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, Ghrelin (NCBI Gene ID: 58991) is replaced to create Ghrl{Cre-eGFP} using the Loxed Cassette Acceptor allele Ghrl{LCA}). Recombinase mediated cassette exchange (RMCE) was used to insert the Cre-eGFP fusion protein into the ghrelin locus using ES cells containing the Ghrl{LCA} allele. The Cre-eGFP protein uses the endogenous AUG start codon and polyadenylation sequence. http://purl.obolibrary.org/obo/BCGO_9000821 Monoclonal mouse BetaTC6 raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the mouse "BetaTC6" antigen. http://purl.obolibrary.org/obo/BCGO_9000861 Polyclonal rat CART raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the rat "CART" antigen. http://purl.obolibrary.org/obo/BCGO_9000901 Monoclonal mouse Mo ES-Derived Early Endoderm raised in rat http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen. http://purl.obolibrary.org/obo/BCGO_9000903 Monoclonal mouse Mo ES-Derived Early Endoderm raised in rat http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen. http://purl.obolibrary.org/obo/BCGO_9000904 Monoclonal mouse Mo ES-Derived Early Endoderm raised in rat http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen. http://purl.obolibrary.org/obo/BCGO_9000905 Monoclonal mouse Mo ES-Derived Early Endoderm raised in rat http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen. http://purl.obolibrary.org/obo/BCGO_9000906 Monoclonal mouse Mo ES-Derived Early Endoderm raised in rat http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen. http://purl.obolibrary.org/obo/BCGO_9000907 Monoclonal mouse Mo ES-Derived Early Endoderm raised in rat http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen. http://purl.obolibrary.org/obo/BCGO_9000908 Monoclonal mouse Mo ES-Derived Early Endoderm raised in rat http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen. http://purl.obolibrary.org/obo/BCGO_9000921 Monoclonal human Hu ES-Derived Early Endoderm raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Hu ES-Derived Early Endoderm" antigen. http://purl.obolibrary.org/obo/BCGO_9000922 Monoclonal human Hu ES-Derived Early Endoderm raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Hu ES-Derived Early Endoderm" antigen. http://purl.obolibrary.org/obo/BCGO_9000941 Monoclonal human Hu ES-Derived Early Endoderm raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Hu ES-Derived Early Endoderm" antigen. http://purl.obolibrary.org/obo/BCGO_9000942 Monoclonal mouse Pancreatic duct cells raised in rat http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in rat that targets the mouse "Pancreatic duct cells" antigen. http://purl.obolibrary.org/obo/BCGO_9000943 Monoclonal mouse Pancreatic duct and acinar cells raised in rat http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in rat that targets the mouse "Pancreatic duct and acinar cells" antigen. http://purl.obolibrary.org/obo/BCGO_9000945 Monoclonal mouse Endothelial cells raised in rat http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in rat that targets the mouse "Endothelial cells" antigen. http://purl.obolibrary.org/obo/BCGO_9000961 Monoclonal mouse BetaTC6 raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the mouse "BetaTC6" antigen. http://purl.obolibrary.org/obo/BCGO_9000962 Monoclonal mouse BetaTC6 raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the mouse "BetaTC6" antigen. http://purl.obolibrary.org/obo/BCGO_9000964 Monoclonal human Disp2 raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Disp2" antigen. http://purl.obolibrary.org/obo/BCGO_9000965 Monoclonal human Disp2 raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Disp2" antigen. http://purl.obolibrary.org/obo/BCGO_9000966 Polyclonal mouse Lrp11 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the mouse "Lrp11" antigen. http://purl.obolibrary.org/obo/BCGO_9000967 Polyclonal mouse Sez6l2 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the mouse "Sez6l2" antigen. http://purl.obolibrary.org/obo/BCGO_9000968 Polyclonal mouse Sez6l2 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the mouse "Sez6l2" antigen. http://purl.obolibrary.org/obo/BCGO_9000969 Polyclonal human DDR1 raised in goat http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in goat that targets the human "DDR1" antigen. http://purl.obolibrary.org/obo/BCGO_9000970 Monoclonal human DDR1 raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "DDR1" antigen. http://purl.obolibrary.org/obo/BCGO_9000971 Polyclonal mouse Gpr39-1a raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the mouse "Gpr39-1a" antigen. http://purl.obolibrary.org/obo/BCGO_9000972 Polyclonal rat CART raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the rat "CART" antigen. http://purl.obolibrary.org/obo/BCGO_9000974 Monoclonal rat CART raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the rat "CART" antigen. http://purl.obolibrary.org/obo/BCGO_9000981 Rosa26{R26-60-DR5-TA-Cerulean} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{R26-60-DR5-TA-Cerulean} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In these cells Rosa26 gene sequences from -60 to +81 were replaced by a retinoic acid response element (DR5) fused to a TATA-Cerulean (CFP) reporter. These ESCs may be useful for assess retinoic acid responsiveness. http://purl.obolibrary.org/obo/BCGO_9000982 Rosa26{R26-228-DR5-TA-Cerulean} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Roas26{R26-228-DR5-TA-Cerulean} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In these cells Rosa26 gene sequences from -228 to +81 were replaced by a retinoic acid response element (DR5) fused to a TATA-Cerulean (CFP) reporter. These ESCs may be useful for assess retinoic acid responsiveness. http://purl.obolibrary.org/obo/BCGO_9001161 Polyclonal mouse Carboxypeptidase A1 (CPA1) raised in goat http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in goat that targets the mouse "Carboxypeptidase A1 (CPA1)" antigen. http://purl.obolibrary.org/obo/BCGO_9001162 Polyclonal human Muc1 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the human "Muc1" antigen. http://purl.obolibrary.org/obo/BCGO_9001163 Polyclonal human Cleaved Notch1 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the human "Cleaved Notch1" antigen. http://purl.obolibrary.org/obo/BCGO_9001164 Polyclonal human Jagged1 raised in goat http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in goat that targets the human "Jagged1" antigen. http://purl.obolibrary.org/obo/BCGO_9001181 Pdx1{CFP} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{CFP} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). This ES cell line contains cyan fluorescent protein (CFP, Cerulean variant) inserted into a Pdx1{LCA} allele by recombinase mediated cassette exchange. These cells may be useful for identifying pancreatic progenitor cells in cultures that have been stimulated to differentiate towards endodermal and pancreatic fates. http://purl.obolibrary.org/obo/BCGO_9001961 Rosa26{tm1(Ccnd1)} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{Ccnd1} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). ES cells express mutant cyclin D1-T286A and a cherry reporter under the regulation of a tetracycline-responsive bi-directional minimal CMV promoter (TRE-Tight; tetO) targeted to the ROSA26 locus. http://purl.obolibrary.org/obo/BCGO_9002001 Rosa26{R26-60-IBRE4-TA-Cerulean} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{R26-60-IBRE4-TA-Cerulean} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In these cells Rosa26 gene sequences from -60 to +81 were replaced by a BMP response element (IBRE4) fused to a TATA-Cerulean (CFP) reporter. http://purl.obolibrary.org/obo/BCGO_9002002 Rosa26{R26-228-IBRE4-TA-Cerulean} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{R26-228-IBRE4-TA-Cerulean} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In these cells Rosa26 gene sequences from -228 to +81 were replaced by a BMP response element (IBRE4) fused to a TATA-Cerulean (CFP) reporter. These ESCs may be useful for assess BMP responsiveness. http://purl.obolibrary.org/obo/BCGO_9002201 Polyclonal mouse DNER raised in goat http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in goat that targets the mouse "DNER" antigen. http://purl.obolibrary.org/obo/BCGO_9002222 Monoclonal rat Shh raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the rat "Shh" antigen. http://purl.obolibrary.org/obo/BCGO_9002223 Monoclonal chicken Chick HNF3Beta raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the chicken "Chick HNF3Beta" antigen. http://purl.obolibrary.org/obo/BCGO_9002241 Pdx1{LCA} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Pdx1{tm1(LCA)}). This mouse ES cell line contains a loxed cassette acceptor (LCA) allele that may be utilized for the exchange of DNAs of interest into the Pdx1 gene locus by recombinase mediated cassette exchange (RMCE). An 8.62 kb region of the gene was replaced by tandemly oriented Lox66 and Lox2272 sites flanking both positive (puromycin) and negative (HSV-TK)selectable markers. http://purl.obolibrary.org/obo/BCGO_9002263 Polyclonal mouse Pax4 raised in guinea pig http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in guinea pig that targets the mouse "Pax4" antigen. http://purl.obolibrary.org/obo/BCGO_9002281 Rosa26{EN-Cherry-Neo} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{EN-Cherry-Neo} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line expresses mCherry, a red fluorescent protein, under control of the endogenous Rosa26gene. A cassette containing mCherry and other sequences to assure efficient expression were inserted into the Rosa26[LCA] allele by recombinase mediated cassette exchange. These cells will be used to identify an optimal combination of regulatory elements for fluorescent protein expression from a single gene copy and as a reference cell line for fluorescent cell sorting. http://purl.obolibrary.org/obo/BCGO_9002401 Rosa26{Non-EN-CFP-Neo} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{LCA} using the Loxed Cassette Acceptor allele Rosa26{tm1.8(Non-EN-CFP)}). This ES cell line contains CFP (Cerulean) inserted into a Rosa26{LCA} allele by recombinase mediated cassette exchange. These cells were used to identifythe optimal arrangement of regulatory elements for fluorescent protein expression from a single genomic copy. http://purl.obolibrary.org/obo/BCGO_9002482 Polyclonal mouse Ngn3 raised in goat http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in goat that targets the mouse "Ngn3" antigen. http://purl.obolibrary.org/obo/BCGO_9002502 Rosa26{EN-CFP-Neo} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{EN.CFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line contains CFP (Cerulean) inserted into a Rosa26 LCA allele by recombinase mediated cassette exchange. These cells were used to identify the optimal arrangement of regulatory elements for fluorescent protein expression from a single genomic copy. http://purl.obolibrary.org/obo/BCGO_9002522 Rosa26{EN.CFP.SV40.Neo} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{CFP.SV40} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line contains CFP (Cerulean) inserted into a Rosa26 LCA allele by recombinase mediated cassette exchange. These cells were used to identify the optimal arrangement of regulatory elements for fluorescent protein expression from a single genomic copy. http://purl.obolibrary.org/obo/BCGO_9002542 Rosa26{EN-GFP-Neo} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{EN.GFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line contains eGFP inserted into the Rosa26 gene locus. These cells were used to identify an optimal combination of regulatory elements for fluorescent protein expression from a single genomic copy and can serve as a reference cell line for fluorescent cell sorting. http://purl.obolibrary.org/obo/BCGO_9002562 Rosa26{EN-CFP-bGpA-Neo} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{CFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line contains CFP (Cerulean) inserted into a Rosa26{LCA} allele by recombinase mediated cassette exchange. These cells were used to identify an optimal combination of regulatory elements for fluorescent protein expression from single a genomic copy. http://purl.obolibrary.org/obo/BCGO_9002742 Rosa26{R26-60-3XCNotch-TA-Cerulean} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{(R26-60-CNotch-TA-Cerulean)} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). The Rosa26 gene sequences from -228 to +81 were replaced with a repeat of alternating 32-bp C-elements and 31-bp Rbpj-binding sites (i.e.,C-R-C-R-C-R). The 31 base-pair region is derived from the CBF1/Rbpj binding region of the C-promoter of EBV (cataaattTTTTCCCACGgcgtgtttacacc; uppercase letters are the consensus Rbpj binding sequence within the 31-bp element) (Hsieh, MCB 16:952, 1996). The 32-bp C-element is from the Ela1 enhancer (Kruse et al., MCB 15:4385, 1995). http://purl.obolibrary.org/obo/BCGO_9002762 Rosa26{R26-60-AR8-TA-mCherry} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{R26-60-AR8-TA-mCherry} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In these cells Rosa26 gene sequences from -60 to +81 were replaced by an Activin response element (AR8) fused to a TATA-mCherry reporter http://purl.obolibrary.org/obo/BCGO_9002782 Rosa26{R26-228-AR8-TA-mCherry} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{tm2.2(R26-228-AR8-TA-mCherry)} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In these cells Rosa26 gene sequences from -228 to +81 were replaced by an Activin response element (AR8) fused to a TATA-mCherry reporter. These ESCs may be usefulto assess Activin, Nodal, and TGFbeta responsiveness. http://purl.obolibrary.org/obo/BCGO_9002802 Rosa26{R26-60-6XNotch-TA-Cerulean} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26(R26-60-6XNotch-TA-Cerulean) using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). The binding site for Rbpj, the transcriptional mediator of Notch signaling was inserted into the Rosa 26 locus replacing nucleotides -60 to -228.The complete insert contains the Rbpj cis element in a series of six repeats. Each repeat includes a 31 base-pair region derived from the CBF1/Rbpj binding region of the C-promoter of EBV (cataaattTTTTCCCACGgcgtgtttacacc). Uppercase letters are the consensus Rbpj binding sequence within the 31-bp element) (Hsieh et al., MCB 16:952, 1996). http://purl.obolibrary.org/obo/BCGO_9002822 Rosa26{-228.3XCNotch.TA.Cerulean} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26(R26-228-3XCNotch-TA-Cerulean) using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). The Rosa26 gene sequences from -60 to -228 were replaced with a repeat of alternating 32-bp C-elements and 31-bp Rbpj-binding sites (i.e.,C-R-C-R-C-R). The 31 base-pair region is derived from the CBF1/Rbpj binding region of the C-promoter of EBV (cataaattTTTTCCCACGgcgtgtttacacc; uppercase letters are the consensus Rbpj binding sequence within the 31-bp element) (Hsieh, MCB 16:952, 1996). The 32-bp C-element is from the Ela1 enhancer (Kruse et al., MCB 15:4385, 1995). http://purl.obolibrary.org/obo/BCGO_9002842 Rosa26{-228.6XNotch.TA.Cerulean} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26(Rbpj(R26-228-6XNotch-TA-Cerulean)) using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). The binding site for Rbpj, the transcriptional mediator of Notch signaling was inserted into the Rosa 26 locus replacing nucleotides -60 to -228.The complete insert contains the Rbpj cis element in a series of six repeats. Each repeat includes a 31 base-pair region derived from the CBF1/Rbpj binding region of the C-promoter of EBV (cataaattTTTTCCCACGgcgtgtttacacc). Uppercase letters are the consensus Rbpj binding sequence within the 31-bp element) (Hsieh et al., MCB 16:952, 1996). http://purl.obolibrary.org/obo/BCGO_9003022 Polyclonal mouse Irx2 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the mouse "Irx2" antigen. http://purl.obolibrary.org/obo/BCGO_9003023 Polyclonal mouse Arx raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the mouse "Arx" antigen. http://purl.obolibrary.org/obo/BCGO_9003102 Polyclonal mouse mArx raised in guinea pig http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in guinea pig that targets the mouse "mArx" antigen. http://purl.obolibrary.org/obo/BCGO_9003185 Monoclonal human C-peptide raised in rat http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in rat that targets the human "C-peptide" antigen. http://purl.obolibrary.org/obo/BCGO_9004015 Ptf1a{rtTA} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{rtTA} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). These mESCs contain the reverse tetracycline transactivator (rtTA) under control of the Ptf1a regulatory sequences. rtTA is a transcriptional activator, which can inducibly (in the presence of the tetracycline analog doxycycline) activate the genes under Tet-O activator/promoter element. The rtTA sequences were introduced in to Ptf1a[LCA] by Recombinase-Mediated Cassette Exchange using standard methods.These cells were made in order togenerate a mouse line that express rtTA under control of the Ptf1a gene locus. http://purl.obolibrary.org/obo/BCGO_9004016 Rosa26{Nepn.Cherry} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Nepn-Cherry using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line was generated by RMCE usingthe Rosa26.LCA allele. To create a Nepn reporter allele, a 9kb promoter region of the Nepn gene is inserted upstream of the red fluorescent protein mCherry-pA sequence. Since Nepn is expressed during endoderm development, this cell line can be used for visualisation and sorting of endodermal cell populations. http://purl.obolibrary.org/obo/BCGO_9004017 Rosa26{EN.YFP.bGsplicepA.Neo} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{YFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). These mESCs contain yellow fluorescent protein (YFP, Citrine) under control of the ROSA26 gene locus. They were made as part of a study to quantify variables that affect fluorescent protein expression levels in mESCs. TheYFP sequences are flanked by a translational enhancer and beta-globin splice/polyA sequences. The cassette containing the YFP was inserted intoa ROSA26 LCA allel using Recombinase-Mediated Cassette Exchange. http://purl.obolibrary.org/obo/BCGO_9004018 Rosa26{Apple.bGsplicepA.Neo} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{EN.Apple.bGspliceA.neo} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). To better quantify protein expression levels via confocal microscopy, flow sorting and western blot analysis this cell line contains a 4kb R26 promoter element, Apple (a red fluorescent protein) with an upstream enhancer element, a splicing beta-globin polyA tail and the neomycin gene as a selection agent. Through Recombinase-Mediated Cassette Exchange this construct was inserted into the Rosa26 locus. http://purl.obolibrary.org/obo/BCGO_9004019 Rosa26{Ngn3.Mafa} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, Gt(ROSA)26Sor gene trap ROSA 26, Philippe Soriano [ Mus musculus ] (NCBI Gene ID: 14910) is replaced to create Rosa26 LCA using the Loxed Cassette Acceptor allele ). Recombinase mediated cassette exchange was performed to introduce a bidirectional tetO-regulated cassette containing coding sequences for transcription factors MafA and Ngn3 into Rosa26 LCA mESCs. ThismESC line can be used to generate mice that will simultaneously overexpress MafA and Ngn3 using tet-inducible activation with rtTA. http://purl.obolibrary.org/obo/BCGO_9004023 Rosa26{mIre1.WT.Cherry} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, Gt(ROSA)26Sor gene trap ROSA 26, Philippe Soriano [ Mus musculus ] (NCBI Gene ID: 14910) is replaced to create Rosa26 LCA using the Loxed Cassette Acceptor allele Rosa26{tm1.1(mlre1.WT.Cherry)FerozPapa}). This mESC line contains a bidirectional Tet0-regulated fusion gene that has been inserted into a disabled Rosa26 loxed cassette acceptor allele by RMCE. In one direction the tetO/CMV promoter drives expression of a red fluorescent protein (Cherry) while in the other direction it drives the wild type form of mlre1. mlre1 is an endoplasmic reticulum (ER) membrane kinase response to unfolded protein response (UPR). Activated mlre1 endonucleases leads to the splicing of XBP-1 (a transcription factor which is upregulated in times of ER stress) which transcriptionally increases the expression of ER chaperones and alleviates UPR. This cell line should be useful for studying the role of mlre1 in the response to ER stress. By generating mice with this allele http://purl.obolibrary.org/obo/BCGO_9004024 Rosa26{mIre1.IG.Cherry} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, Gt(ROSA)26Sor gene trap ROSA 26, Philippe Soriano [ Mus musculus ] (NCBI Gene ID: 14910) is replaced to create Rosa26 LCA using the Loxed Cassette Acceptor allele Rosa26{tm1.1(mlre1.IG.Cherry)FerozPapa}). This mESC line contains a bidirectional Tet0-regulated fusion gene that has been inserted into a disabled Rosa26 loxed cassette acceptor allele by RMCE. In one direction the tetO/CMV promoter drives expression of a red fluorescent protein (Cherry) while in the other direction it drives a mutant version of mlre1. mlre1 is an endoplasmic reticulum (ER) membrane kinase response to unfolded protein response (UPR). Activated mlre1 endonucleases leads to the splicing of XBP-1 (a transcription factor which is upregulated in times of ER stress) which transcriptionally increases the expression of ER chaperones and alleviates UPR. This cell line should be useful for studying the role of mlre1 in the response to ER stress. By generating mice with this allele t http://purl.obolibrary.org/obo/BCGO_9004029 Rosa26{Sox9.Cherry} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Sox9/mCherry using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES line contains bidirectional TetO-regulated genes inserted into the Rosa26.LCA allele by RMCE. In one direction the TetO/CMV promoter drives the expression of transcription factor Sox9. In the other direction it drives the expression of red fluorescent protein mCherry. This ES cell line can be used to simultaneously over-express Sox9 and mCherry upon administration of doxycyline when the effector protein rtTA is expressed. http://purl.obolibrary.org/obo/BCGO_9004031 Rosa26{TetO.NRSF} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create NRSF using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This cell line contains bidirectional TetO-regulated genes inserted into the Rosa26{LCA} allele by RMCE. In one direction, the TetO/CMV promoter drives expression of the transcription factor NRSF/REST. In the other direction, it drives the expression of the red fluorescent protein mCherry. In this cell line, when the effector protein rtTA is expressed, NRSF and mCherry are simultaneously over-expressed upon administration of doxycyline. http://purl.obolibrary.org/obo/BCGO_9004032 Ptf1a{tdTOM} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{td.TOM} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). Recombinase mediated cassette exchange was performed using the Ptf1aLCA. This cell line expresses both tdTOM (a red fluorescent protein) and an N-terminal epitope tagged Strep/Flag (NSF) fusion of ptf1a in the adult pancreas. These cells will be useful in a variety of applications such as FACS sorting of ptf1a expressing cells, chromatin immunoprecipitation and proteomic analyses. http://purl.obolibrary.org/obo/BCGO_9004040 Polyclonal human TSPAN7 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the human "TSPAN7" antigen. http://purl.obolibrary.org/obo/BCGO_9004041 Monoclonal human FXYD2 raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "FXYD2" antigen. http://purl.obolibrary.org/obo/BCGO_9004047 Polyclonal mouse Sez6l2 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the mouse "Sez6l2" antigen. http://purl.obolibrary.org/obo/BCGO_9004048 Polyclonal human Lrp11 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the human "Lrp11" antigen. http://purl.obolibrary.org/obo/BCGO_9004052 Polyclonal mouse Onecut1 raised in guinea pig http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in guinea pig that targets the mouse "Onecut1" antigen. http://purl.obolibrary.org/obo/BCGO_9004056 Rosa26{Setd5.GFP} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Setd5/GFP using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line was generated by RMCE in the Rosa26{LCA} allele. A coding sequence for green fluorescent protein (GFP) was inserted into the first exon of the Setd5 gene. This exon is located upstream of the Rosa26 transcribed sequence and is transcribed in an opposite orientation. The GFP-polyA cassette, transcribed from the Setd5 promoter, knocks out Setd5 transcription and provides a reporter for Setd5 gene expression. The purpose of this cell line is to study the molecular function of the Setd5 gene. http://purl.obolibrary.org/obo/BCGO_9004059 Ngn3{HA.LCA} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Cassette Acceptor) to (MGI ID: ). This ES cell line was made by gene targeting and designed to express an HA-tagged version of the transcription factor Ngn3. The Lox71 and Lox2272 sites were inserted flanking the Ngn3 coding sequence. Within the flanked region an HA-tag was placed at the N-terminus of the Ngn3 protein. This allele can be used to study chromatin and protein-protein interactions of Ngn3. Additionally, the Lox71 and Lox2272 sites allow for manipulations of the flanked region by RMCE. http://purl.obolibrary.org/obo/BCGO_9004060 Foxm1{LCA} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which the targeted gene, Forkhead box M1 (NCBI Gene ID: 14235), has been modified (allele type: Gene Replacement) to (MGI ID: ). This ES cell line was made by gene targeting and is designed to serve as a cassette acceptor allele at the Foxm1 locus. The portion of genomic DNA containing exons 2-4 of Foxm1 was flanked with Lox71 and Lox2272 sites and replaced with a selection marker. This line allows for modification of the flanked sequences through RMCE. http://purl.obolibrary.org/obo/BCGO_9004061 Rosa26{Pdx1.YFP} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Pdx1/YFP using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line contains bidirectional TetO-regulated genes inserted into the Rosa26{LCA} allele by RMCE. In one direction, the tetO/CMV promoter will drive expression of Pdx1. In the other direction, it will drive the expression of yellow fluorescent protein (YFP). In this cell line, when the effector protein rtTA is expressed, Pdx1 and YFP will be over-expressed simultaneously upon administration of doxycyline. http://purl.obolibrary.org/obo/BCGO_9004072 Insm1{Pdx1.YFP} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, insulinoma-associated 1 (NCBI Gene ID: 53626) is replaced to create Pdx1/YFP using the Loxed Cassette Acceptor allele Insm1{tm1(LCA)}). This ES cell line contains bidirectional TetO-regulated genes inserted into the Insm1{LCA} allele by RMCE. In one direction, the TetO/CMV promoter drives the expression of the transcription factor Pdx1. In the other direction, it drives the expression of yellow fluorescent protein (YFP). In this cell line, when the effector protein rtTA is expressed, Pdx1 and YFP will be over-expressed simultaneously upon administration of doxycyline. http://purl.obolibrary.org/obo/BCGO_9004074 Rosa26{3TF.Cherry} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create mCherry/MafA/Pdx1/Ngn3 using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line contains bidirectional TetO-regulated genes inserted into the Rosa26{LCA} allele by RMCE. In one direction, the TetO/CMV promoter drives the expression of a polycistronic mRNA with transcription factors MafA, Pdx1, and Ngn3 linked by 2A peptide cleavage sequences. In the other direction, it drives the expression of the red fluorescent protein mCherry. In this cell line, when the effector protein rtTA is expressed, all three transcription factors and mCherry will be over-expressed simultaneously upon administration of doxycyline. http://purl.obolibrary.org/obo/BCGO_9004076 Pdx1{AIVd} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{aIVd} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this ES cell line, Area IV of the Pdx1 enhancer (-2168/-1913 relative to the primary transcription start site) was deleted using RMCE in the Pdx1{LCA} allele. This cell line allows for assessment of the role of these DNA sequences in the regulation and function of Pdx1. http://purl.obolibrary.org/obo/BCGO_9004078 Nkx2.2{cCre-Knock-in} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{Cre} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this ES cell line, the sequence for one of the two bi-partite Cre molecules (cCre) and the IRES sequence were knocked into a site directly upstream of the Nkx2.2 start codon using RMCE in the Nkx2.2{LCA} allele. The presence of the IRES sequence allows for the transcription of cCre and Nkx2.2 from the native Nkx2.2 locus at the same time. This results in the labeling of pancreatic epithelium cells that co-express high levels of Ngn3 and Nkx2.2 during mouse embryonic development. http://purl.obolibrary.org/obo/BCGO_9004080 Nkx2.2{3XHA.Nkx2.2} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{3XHA-Nkx2.2} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this cell line RMCE in the Nkx2.2.LCA allele was used to introduce a triple HA tag in frame at the N-terminus of the transcription factor Nkx2.2. This allows for efficient immunoprecipitation of HA-tagged Nkx2.2 protein from mouse tissues to perform ChIP and protein-protein interaction studies. http://purl.obolibrary.org/obo/BCGO_9004087 Nkx2.2{Cre.EGFP} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{Cre-EGFP} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this ES cell line, a coding portion of the transcription factor Nkx2.2 was replaced with a Cre-EGFP cassette, in frame to the Nkx2.2 ATG. This allows for sites of Nkx2.2 gene expression to be identified in mice using direct immunofluorescence, FACS purification of Nkx2.2 expressing cells, and lineage tracing using Nkx2.2 driven Cre expression. http://purl.obolibrary.org/obo/BCGO_9004093 Nkx2.2{Cherry} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Cherry using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this ES cell, 1.956 kb of the native Nkx2.2 gene, containing a portion of exon 1 (all but the first 214 bp) and all of exon 2, was replaced by the mCherry cassette in frame to the Nkx2.2 ATG. This allows for sites of Nkx2.2 gene expression in the mouse to be identified using direct immunofluorescence and FACS purification of Nkx2.2 expressing cells. http://purl.obolibrary.org/obo/BCGO_9004113 Polyclonal enterobacteria phage p1 Cre raised in guinea pig http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in guinea pig that targets the enterobacteria phage p1 "Cre" antigen. http://purl.obolibrary.org/obo/BCGO_9004123 Pax4{HA.LCA} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which the targeted gene, paired box 4 (NCBI Gene ID: 18506), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Pax4{tm1(LCA)Ggu}). This ES cell line is made by gene targeting and is designed to express an HA-tagged version of the transcription factor Pax4. Lox71 and Lox2272 sites are inserted, flanking the last coding exon of the Pax4 gene. In the flanked region, an HA-tag was placed at the C-terminus of the PAX4 protein. This allele can be used to study chromatin and protein-protein interactions of PAX4. Additionally, the Lox71 and Lox2272 sites allow for future manipulations of the flanked region by RMCE. http://purl.obolibrary.org/obo/BCGO_9004125 Polyclonal human CDCP1 raised in goat http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in goat that targets the human "CDCP1" antigen. http://purl.obolibrary.org/obo/BCGO_9004126 Polyclonal human CD-200 raised in goat http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in goat that targets the human "CD-200" antigen. http://purl.obolibrary.org/obo/BCGO_9004127 Polyclonal human Coagulation factor 3(rhF3) raised in goat http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in goat that targets the human "Coagulation factor 3(rhF3)" antigen. http://purl.obolibrary.org/obo/BCGO_9004129 Polyclonal human Ngn3 raised in sheep http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in sheep that targets the human "Ngn3" antigen. http://purl.obolibrary.org/obo/BCGO_9004130 Monoclonal mouse Pax4 raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the mouse "Pax4" antigen. http://purl.obolibrary.org/obo/BCGO_9004131 Monoclonal mouse Pax4 raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the mouse "Pax4" antigen. http://purl.obolibrary.org/obo/BCGO_9004132 Monoclonal mouse Pax4 raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the mouse "Pax4" antigen. http://purl.obolibrary.org/obo/BCGO_9004133 Monoclonal human CD142 raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "CD142" antigen. http://purl.obolibrary.org/obo/BCGO_9004134 Monoclonal rat Beta cell, IC2 raised in rat http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in rat that targets the rat "Beta cell, IC2" antigen. http://purl.obolibrary.org/obo/BCGO_9004135 Polyclonal human CD-200 raised in goat http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in goat that targets the human "CD-200" antigen. http://purl.obolibrary.org/obo/BCGO_9004144 Pdx1{Cre.ER} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1/cre-ER using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this cell line, the first exon of the transcription factor Pdx1 was replaced with the coding sequence for a Cre-ER fusion protein using RMCE in the Pdx1{LCA} allele. Pdx1-promoter driven Cre-ER expressing mice enable tamoxifen-inducible Cre-LoxP manipulation of pancreatic lineage cells. http://purl.obolibrary.org/obo/BCGO_9004148 Rosa26{228.TOP.CFP} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create 7xTcf/Lef binding site using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line was generated by RMCE in the Rosa26{LCA} allele. The Rosa26 gene sequence (from -228 to +81) was replaced by a Wnt response element (7xTcf/Lef binding site) fused to a TATA-Cerulean (CFP) reporter. This ES cell line may be useful for assessing canonical Wnt responsiveness. http://purl.obolibrary.org/obo/BCGO_9004154 Nepn{Cherry} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which the targeted gene, Nephrocan (NCBI Gene ID: 66650), has been modified (allele type: Global Null) to (MGI ID: Neph(mCherry)). This ES cell line was made by gene targeting and was designed to express red fluorescent protein (mCherry) from the Nepn promoter thereby disrupting the expression of Nepn. The FP coding sequence was inserted dowstream of the Nepn start codon, in front of the Nepn first exon. This cell line is used to study the function and expression of Nepn. http://purl.obolibrary.org/obo/BCGO_9004156 Ins2{Apple.LCA} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which the targeted gene, Insulin 2 (NCBI Gene ID: 20671), has been modified (allele type: Cassette Acceptor) to (MGI ID: Ins2{(apple.LCA)}). This ES cell line was made by gene targeting and designed to express a H2B-Apple fusion protein (nuclear red fluorescent protein) from the Ins2 promoter. The FP coding sequence is downsteam of the Ins2 start codon (replacing exon 2 of Ins2) and is flanked by Lox66/Lox2272 sites to allow for future manipulations of the flanked region by RMCE. http://purl.obolibrary.org/obo/BCGO_9004157 Pdx1{rTTA} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{rTTA} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this cell line, thefirst exon of Pdx1 was replaced with the coding sequence for rTTA protein, using RMCE in the Pdx1{LCA} allele. Generation of Pdx1-promoter driven rTTA expressing mice will enable tetracycline-inducible manipulation of pancreatic lineage cells. http://purl.obolibrary.org/obo/BCGO_9004158 Pdx1{Cre} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1/cre using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this cell line, thefirst exon of Pdx1 was replaced with the coding sequence for Cre-recombinase using RMCE in the Pdx1{LCA} allele. Generation of Pdx1-promoter driven Cre-expressing cells will enable Cre-LoxP manipulation of pancreatic lineage cells. http://purl.obolibrary.org/obo/BCGO_9004159 Rosa26{228.3TF.GFP.Cre} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create 3TF.GFP-Cre using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This cell line contains TetO-regulated genes inserted into the Rosa26{LCA} allele by RMCE. The TetO/miniCMV promoter was placed (at -228) upstream of the putative ROSA26 transcription start site and drives the expression of a polycistronic mRNA with transcription factors MafA, Pdx1, and Ngn3 together with a GFP-Cre fusion protein. The sequences are linked by 2A peptide cleavage sequences. In this cell line, when the effector protein rtTA is expressed, all three transcription factors and GFP-Cre will be over-expressed simultaneously upon administration of doxycyline. http://purl.obolibrary.org/obo/BCGO_9004160 Rosa26{mIre1.N906A.Cherry} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{mIre1.N906A.Cherry} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES line contains bidirectional TetO-regulated genes inserted into the Rosa26{LCA} allele by RMCE. In one direction the TetO/CMV promoter drives the expression of point mutant(N906A) of IRE1, an ER transmenbrane kinase response to unfolded protein response (UPR). In the other direction it drives the expression of red fluorescent protein mCherry. This ES cell line can be used to simultaneously over-express Ire1(N906A) and mCherry upon administration of doxycyline when the effector protein rtTA is expressed. This line can be used to study the roles of IRE1 in the response to ER stress, diet induced obesity and insulin resistance. http://purl.obolibrary.org/obo/BCGO_9004256 Polyclonal human HIP-14 ZDHHC17 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the human "HIP-14 ZDHHC17" antigen. http://purl.obolibrary.org/obo/BCGO_9004305 Monoclonal human Cd31 (PECAM1) raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Cd31 (PECAM1)" antigen. http://purl.obolibrary.org/obo/BCGO_9004306 Polyclonal cow GFAP raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the cow "GFAP" antigen. http://purl.obolibrary.org/obo/BCGO_9004307 Polyclonal human Glucagon (GCG) raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the human "Glucagon (GCG)" antigen. http://purl.obolibrary.org/obo/BCGO_9004308 Polyclonal human Glucagon (GCG) raised in guinea pig http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in guinea pig that targets the human "Glucagon (GCG)" antigen. http://purl.obolibrary.org/obo/BCGO_9004309 Polyclonal pig Insulin raised in guinea pig http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in guinea pig that targets the pig "Insulin" antigen. http://purl.obolibrary.org/obo/BCGO_9004310 Polyclonal human Ki67 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the human "Ki67" antigen. http://purl.obolibrary.org/obo/BCGO_9004311 Polyclonal human MafA raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the human "MafA" antigen. http://purl.obolibrary.org/obo/BCGO_9004312 Polyclonal human MafB raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the human "MafB" antigen. http://purl.obolibrary.org/obo/BCGO_9004313 Polyclonal human Pancreatic Polypeptide (PPY) raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the human "Pancreatic Polypeptide (PPY)" antigen. http://purl.obolibrary.org/obo/BCGO_9004315 Polyclonal human Somatostatin (Sst) raised in sheep http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in sheep that targets the human "Somatostatin (Sst)" antigen. http://purl.obolibrary.org/obo/BCGO_9004316 Monoclonal rat Tuj1 (TUBB3) raised in rabbit http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in rabbit that targets the rat "Tuj1 (TUBB3)" antigen. http://purl.obolibrary.org/obo/BCGO_9004317 Polyclonal rat VEGFA raised in goat http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in goat that targets the rat "VEGFA" antigen. http://purl.obolibrary.org/obo/BCGO_9004318 Polyclonal mouse Foxa2 (HNF3b) raised in goat http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in goat that targets the mouse "Foxa2 (HNF3b)" antigen. http://purl.obolibrary.org/obo/BCGO_9004319 Monoclonal human Muc1 raised in hamster (armenian) http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in hamster (armenian) that targets the human "Muc1" antigen. http://purl.obolibrary.org/obo/BCGO_9004320 Polyclonal human HNF-1β raised in goat http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in goat that targets the human "HNF-1β" antigen. http://purl.obolibrary.org/obo/BCGO_9004321 Polyclonal human Sox9 raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the human "Sox9" antigen. http://purl.obolibrary.org/obo/BCGO_9004322 Polyclonal human CDCP1 raised in goat http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in goat that targets the human "CDCP1" antigen. http://purl.obolibrary.org/obo/BCGO_9004323 Polyclonal human α-Amylase (AMY2A) raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the human "α-Amylase (AMY2A)" antigen. http://purl.obolibrary.org/obo/BCGO_9004324 Polyclonal cow Insulin raised in guinea pig http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in guinea pig that targets the cow "Insulin" antigen. http://purl.obolibrary.org/obo/BCGO_9004325 Polyclonal human Insulin raised in guinea pig http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in guinea pig that targets the human "Insulin" antigen. http://purl.obolibrary.org/obo/BCGO_9004326 Polyclonal human Insulin raised in goat http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in goat that targets the human "Insulin" antigen. http://purl.obolibrary.org/obo/BCGO_9004327 Polyclonal human Glucagon raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the human "Glucagon" antigen. http://purl.obolibrary.org/obo/BCGO_9004328 Polyclonal human Somatostatin (Sst) raised in goat http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in goat that targets the human "Somatostatin (Sst)" antigen. http://purl.obolibrary.org/obo/BCGO_9004329 Polyclonal rat Synaptophysin (SYP) raised in rabbit http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in rabbit that targets the rat "Synaptophysin (SYP)" antigen. http://purl.obolibrary.org/obo/BCGO_9004489 Ngn3{T2A.nCre} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925) is replaced to create Ngn3{T2A.nCre} using the Loxed Cassette Acceptor allele ). In this mouse ES cell line, one of the two bi-partite Cre molecules, nCre, was knocked in upstream of Ngn3 coding sequence by RMCE in Ngn3.HA.LCA ES cell line. nCre sequence is expressed from policistronic mRNA linked by 2a peptide to Ngn3 coding sequence allowing for simultanious expression of both proteins from Ngn3 promoter. This mouse line, in combination with Nkx2.2-cCre mouse line, allows to label pancreatic epithelium cells that co-express high levels of Ngn3 and Nkx2.2 during mouse embryonic development. http://purl.obolibrary.org/obo/BCGO_9004527 Nkx2.2{T2A.cCre} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{T2A.cCre} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this line, one of the two bi-partite Cre molecules, cCre, is inserted downstream of Nkx2.2 coding sequence fused with 2a peptide using RMCE in the Nkx2.2{LCA}allele. The presence of the T2A sequence allows for transcription of Nkx2.2 and cCre from the native Nkx2.2 locus at the same time. Mouse lines obtained from these ES cells allow the labeling of pancreatic epithelium cells that co-express high levels of Ngn3 and Nkx2.2 during mouse embryonic development. http://purl.obolibrary.org/obo/BCGO_9004529 Neurog3{Cre-ER.BAC} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line containing a transgene in which Cre (transgene) is driven by the Neurog3 promoter (NCBI Gene ID: 11925). This line has a single copy of Neurog3.Cre-ER.LCA BAC transgene inserted in a genome. The transgene is designed to express Cre-ER under control of Neurog 3 promoter and will allow inducible tracking or gene inactivation in the Ngn3-LOW and Ngn3-HIGH populations of pre-endocrine cells. Additionally, the lox66 and lox2272 sites will allow the BAC transgene to serve as a loxed cassette acceptor (LCA) in ES cells for future recombinase-mediated cassette exchange (RMCE). http://purl.obolibrary.org/obo/BCGO_9004536 Neurog3{RG.BAC} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line containing a transgene in which RG (transgene) is driven by the Neurog3 promoter (NCBI Gene ID: 11925). This line has a single copy of Neurog3.RG.LCA BAC transgene inserted in the genome. The transgene is designed to express an H2B-mCherry fusion protein in the nucleus and a membrane anchored EGFP (via GPI), both under the control of the Neurog3 promoter. This will allow for live-cell imaging of mitotic nuclear/chromosome dynamics and membrane protrusive behavior in endocrine progenitors. Additionally, Lox71 and Lox2272 sites flanking the transgene will allow for manipulations by RMCE in the future. http://purl.obolibrary.org/obo/BCGO_9004539 Pdx1{H2B.Neptune} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{H2B.Neptune} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this line, the first exon of Pdx1 is replaced with coding sequence for mNeptune (a far red fluorescent protein) using RMCE in the Pdx1 LCA allele. Generation of a Pdx-promoter driven mNeptune fluorescent allele will enable the isolation of pancreatic lineage cells by FACS and broaden the possibilities for combinatorial sorting with other fluorescent alleles. http://purl.obolibrary.org/obo/BCGO_9004545 Sst.rTTA.LCA mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which the targeted gene, Somatostatin (NCBI Gene ID: 20604), has been modified (allele type: Cassette Acceptor) to Sst.rTTA loxed cassette acceptor (MGI ID: Sst.rTTA{LCA}). This allelle is designed to express a tet-inducible reverse-transactivator under control of the somatostatin promoter. Lox66 and Lox2272 sites are inserted flanking 500bp of Sst promoter region, Sst exons I and II and Sst poly A site. The rTTA-beta-globin poly A cassete replaces Sst coding exons (I and II). The allele can be used to drive tet-inducible expression in somatostatin expressing cells (Delta-cells). Additionally, the Lox66 and Lox2272 sites allow for manipulations of the flanked region by RMCE in the future. http://purl.obolibrary.org/obo/BCGO_9004547 Foxa2{LCA} mouse ESC line http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line A mouse ESC line in which the targeted gene, forkhead box A2 (NCBI Gene ID: 15376), has been modified (allele type: Cassette Acceptor) to Forkhead box A2 loxed cassette acceptor (MGI ID: Foxa2{LCA}). This ES cell line contains a loxed cassette acceptor (LCA) allele that may be utilized for the exchange of DNAs of interest into the Foxa2 locus by recombinase mediated cassette exchange (RMCE). This LCA uses a Lox66/71 and Lox2272 strategy for RMCE and allows for manipulation of a 4.7 kb region of the gene (contains a promoter and all exons: exon 1, 2 and 3). This leads to a variety of experiments that can be performed using a wide range of cassette designs. http://purl.obolibrary.org/obo/BCGO_9004548 Polyclonal mouse Ngn3 raised in chicken http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in chicken that targets the mouse "Ngn3" antigen. http://purl.obolibrary.org/obo/BCGO_9004549 Polyclonal mouse Ngn3 raised in chicken http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in chicken that targets the mouse "Ngn3" antigen. http://purl.obolibrary.org/obo/BCGO_9004550 Polyclonal mouse Nkx6.1 raised in chicken http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in chicken that targets the mouse "Nkx6.1" antigen. http://purl.obolibrary.org/obo/BCGO_9004551 Polyclonal mouse Nkx6.1 raised in chicken http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in chicken that targets the mouse "Nkx6.1" antigen. http://purl.obolibrary.org/obo/BCGO_9004552 Polyclonal mouse PDX1 raised in chicken http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in chicken that targets the mouse "PDX1" antigen. http://purl.obolibrary.org/obo/BCGO_9004553 Polyclonal mouse PDX1 raised in chicken http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in chicken that targets the mouse "PDX1" antigen. http://purl.obolibrary.org/obo/BCGO_9004554 Polyclonal mouse Prox1 raised in chicken http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in chicken that targets the mouse "Prox1" antigen. http://purl.obolibrary.org/obo/BCGO_9004555 Polyclonal mouse Prox1 raised in chicken http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody A polyclonal antibody raised in chicken that targets the mouse "Prox1" antigen. http://purl.obolibrary.org/obo/BCGO_9004563 Monoclonal human ghrelin raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "ghrelin" antigen. http://purl.obolibrary.org/obo/BCGO_9004573 Monoclonal human Gallbladder mucosal epithelium raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Gallbladder mucosal epithelium" antigen. http://purl.obolibrary.org/obo/BCGO_9004574 Monoclonal human Gallbladder mucosal epithelium raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Gallbladder mucosal epithelium" antigen. http://purl.obolibrary.org/obo/BCGO_9004575 Monoclonal human Gallbladder mucosal epithelium raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Gallbladder mucosal epithelium" antigen. http://purl.obolibrary.org/obo/BCGO_9004576 Monoclonal human Gallbladder mucosal epithelium raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Gallbladder mucosal epithelium" antigen. http://purl.obolibrary.org/obo/BCGO_9004597 Monoclonal human Alpha cells raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Alpha cells" antigen. http://purl.obolibrary.org/obo/BCGO_9004598 Monoclonal human Pancreatic duct cells raised in mouse http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody A monoclonal antibody raised in mouse that targets the human "Pancreatic duct cells" antigen. http://purl.obolibrary.org/obo/BTO_0000632 insulinoma cell http://purl.obolibrary.org/obo/REO_0000383 cancer cell A cell of a usually benign tumor of the insulin-secreting cells of the pancreas. http://purl.obolibrary.org/obo/BTO_0000773 lymphoblastoid cell line http://purl.obolibrary.org/obo/CLO_0000019 immortal cell line cell Human cell line from tissue infected with Epstein-Barr virus, resembling a lymphoblast. http://purl.obolibrary.org/obo/BTO_0003560 CCE cell http://purl.obolibrary.org/obo/BTO_0001581 embryonic stem cell line CCE is a mouse embryonic stem cell line derived from 129/Sv mouse strain and has been provided for research use only. http://purl.obolibrary.org/obo/CARO_0001008 gross anatomical part http://purl.obolibrary.org/obo/BFO_0000040 material entity Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells. http://purl.obolibrary.org/obo/CLO_0000044 immortal stem cell line cell http://purl.obolibrary.org/obo/CLO_0000019 immortal cell line cell a cell line that is derived from stem cell http://purl.obolibrary.org/obo/CLO_0000081 immortal neuron cell line cell http://purl.obolibrary.org/obo/CLO_0000156 immortal neural cell line cell a immortal electrically responsive cell line cell that is derived from neuron http://purl.obolibrary.org/obo/CLO_0000128 immortal animal cell line cell http://purl.obolibrary.org/obo/CLO_0000019 immortal cell line cell a immortal eukaryotic cell line that is derived from animal cell http://purl.obolibrary.org/obo/CLO_0000147 immortal hematopoietic cell line cell http://purl.obolibrary.org/obo/CLO_0000166 immortal somatic cell line cell a immortal animal cell line that is derived from hematopoietic cell http://purl.obolibrary.org/obo/CLO_0000156 immortal neural cell line cell http://purl.obolibrary.org/obo/CLO_0000166 immortal somatic cell line cell a immortal animal cell line that is derived from neural cell http://purl.obolibrary.org/obo/CLO_0000166 immortal somatic cell line cell http://purl.obolibrary.org/obo/CLO_0000019 immortal cell line cell a cell line that is derived from somatic cell http://purl.obolibrary.org/obo/CLO_0000503 immortal mouse embryo-derived cell line cell http://purl.obolibrary.org/obo/CLO_0000019 immortal cell line cell An immortal embryo-derived cell line cell that derives from mouse. http://purl.obolibrary.org/obo/CL_0008024 pancreatic endocrine cell http://www.ebi.ac.uk/efo/EFO_0002966 pancreatic cell An endocrine cell that is part of the pancreas. http://purl.obolibrary.org/obo/CL_0011115 precursor cell http://purl.obolibrary.org/obo/CL_0000003 native cell A cell that, by division or terminal differentiation, can give rise to other cell types. http://purl.obolibrary.org/obo/CP_0000000 neutrophillic cytoplasm http://purl.obolibrary.org/obo/GO_0005737 cytoplasm Cytoplasm that exhibits molecular interaction for acidic dyes under specific pH conditions. http://purl.obolibrary.org/obo/CP_0000027 acidophilic cytoplasm http://purl.obolibrary.org/obo/GO_0005737 cytoplasm Cytoplasm that exhibits molecular interaction for acidic dyes under specific pH conditions. http://purl.obolibrary.org/obo/CP_0000028 basophilic cytoplasm http://purl.obolibrary.org/obo/GO_0005737 cytoplasm Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions. http://purl.obolibrary.org/obo/CP_0000035 polychromatophilic cytoplasm http://purl.obolibrary.org/obo/GO_0005737 cytoplasm Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions. http://purl.obolibrary.org/obo/CP_0000037 increased nucleus size http://purl.obolibrary.org/obo/GO_0005634 nucleus A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell. http://purl.obolibrary.org/obo/ERO_0000378 surgery http://purl.obolibrary.org/obo/OBI_0000011 planned process A material processing technique that uses operative manual and instrumental techniques on a patient to investigate and/or treat a pathological condition such as disease or injury or to help improve bodily function or appearance. http://purl.obolibrary.org/obo/ERO_0001211 massively parallel signature sequencing http://purl.obolibrary.org/obo/OBI_0000723 DNA sequencing by ligation A DNA sequencing by ligation technique that involves a bead-based method that uses a complex approach of adapter ligation followed by adapter decoding, reading the sequence in increments of four nucleotides; this method made it susceptible to sequence-specific bias or loss of specific sequences. http://purl.obolibrary.org/obo/ERO_0001334 biopsy http://purl.obolibrary.org/obo/OBI_0600005 collecting specimen from organism Specimen creation of a sample of tissue from a living body for diagnostic purposes. http://purl.obolibrary.org/obo/ERO_0001400 stem cell derived cell line http://purl.obolibrary.org/obo/CLO_0000031 cell line A cell line that is derived from a stem cell. http://purl.obolibrary.org/obo/ERO_0001716 database http://purl.obolibrary.org/obo/IAO_0000030 information content entity A database is an organized collection of data, today typically in digital form. http://purl.obolibrary.org/obo/FMA_63919 Fetus http://purl.obolibrary.org/obo/UBERON_0000468 multicellular organism Fetal structure, which is a developmental form of a vertebrate animal at any given time point from 8 weeks of gestation to birth (or hatching). Examples: There is only one fetus. http://purl.obolibrary.org/obo/MP_0001261 obese http://purl.obolibrary.org/obo/PATO_0001995 organismal quality a status with body weight that is grossly above the average, acceptable or desirable weight, usually due to accumulation of excess fat tissue in the body http://purl.obolibrary.org/obo/NBO_0000073 chewing http://purl.obolibrary.org/obo/GO_0050879 multicellular organismal movement "The process of biting and mashing food with the teeth prior to swallowing." [NBO:GVG] http://purl.obolibrary.org/obo/OBCS_0000167 peak calling http://purl.obolibrary.org/obo/OBI_0200000 data transformation A data transformation to identify protein-binding regions in a genome sequence from the data generated from a ChIP-sequencing or ChIP-chip experiment. When the protein is a transcription factor, the region is a transcription factor binding site (TFBS). http://purl.obolibrary.org/obo/REO_0000383 cancer cell http://purl.obolibrary.org/obo/CL_0000000 cell a cell that is the output of some malignant cell transformation process whereby a cell in vivo becomes capable of causing cancer in an organism. Such cells are typically able to proliferate indefinitely if cultured in vitro. http://purl.obolibrary.org/obo/REO_0000501 monoclonal antibody http://purl.obolibrary.org/obo/REO_0000002 antibody reagent An antibody reagent produced by clonal hybridoma cells deriving from the fusion of a single activasted B-cell with a neoplastic cell, such that antibodies isolated from such cells are monospecific for a single epitope. A collection of such antibodies has specificity for a single epitopes on its target antigen - versus a collection of 'polyclonal antibodies', which recognize various different epitopes. But at the structural level of the individual molecular reagent, there is of course no distinction between mono- and poly-clonal antibodies. http://purl.obolibrary.org/obo/REO_0000502 polyclonal antibody http://purl.obolibrary.org/obo/REO_0000002 antibody reagent an antibody reagent that is output from an antibody production process that yields a heterogenous collection of antibodies that are not mono-specific (ie individual antibodies in the collection may recognize different epitopes becasue they arise from more than one clone of B-lymphocyte cells). Polyclonal antibodies are typically manufactured through an antibody production technique in which a host organism is immunized with a specific immunogen and antibodies purified from serum collected following the induced immune response. A collection of such antibodies has specificity for various different epitopes on its target antigen - versus a collection of 'monoclonal antibodies', which all recognize a single epitope. But at the structural level of the individual molecular reagent, there is of course no distinction between mono- and poly-clonal antibodies. http://purl.obolibrary.org/obo/SO_0000150 read http://purl.obolibrary.org/obo/SO_0000001 region A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine. http://purl.obolibrary.org/obo/SO_0000165 enhancer http://purl.obolibrary.org/obo/SO_0000831 gene_member_region A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter. http://purl.obolibrary.org/obo/SO_0000336 pseudogene http://purl.obolibrary.org/obo/SO_0001411 biological_region A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their "normal" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its "normal" paralog). http://purl.obolibrary.org/obo/SO_0000443 polymer_attribute http://purl.obolibrary.org/obo/PATO_0002182 molecular quality An attribute to describe the kind of biological sequence. http://purl.obolibrary.org/obo/SO_0000462 pseudogenic_region http://purl.obolibrary.org/obo/SO_0001411 biological_region A non-functional descendant of a functional entity. http://purl.obolibrary.org/obo/SO_0000590 SRP_RNA http://purl.obolibrary.org/obo/SO_0000655 ncRNA The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding. http://purl.obolibrary.org/obo/SO_0000655 ncRNA http://purl.obolibrary.org/obo/SO_0000673 transcript An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product. http://purl.obolibrary.org/obo/SO_0000673 transcript http://purl.obolibrary.org/obo/SO_0000831 gene_member_region An RNA synthesized on a DNA or RNA template by an RNA polymerase. http://purl.obolibrary.org/obo/SO_0000771 QTL http://purl.obolibrary.org/obo/SO_0001411 biological_region A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci. http://purl.obolibrary.org/obo/SO_0000831 gene_member_region http://purl.obolibrary.org/obo/SO_0001411 biological_region A region of a gene. http://purl.obolibrary.org/obo/SO_0000902 transgene http://purl.obolibrary.org/obo/SO_0000704 gene A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another. http://purl.obolibrary.org/obo/SO_0000999 BAC_end http://purl.obolibrary.org/obo/SO_0000150 read A region of sequence from the end of a BAC clone that may provide a highly specific marker. http://purl.obolibrary.org/obo/SO_0001411 biological_region http://purl.obolibrary.org/obo/SO_0000001 region A region defined by its disposition to be involved in a biological process. http://purl.obolibrary.org/obo/SO_0001498 YAC_end http://purl.obolibrary.org/obo/SO_0000150 read A region of sequence from the end of a YAC clone that may provide a highly specific marker. http://purl.obolibrary.org/obo/SO_0001500 heritable_phenotypic_marker http://purl.obolibrary.org/obo/SO_0001411 biological_region A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus. http://purl.obolibrary.org/obo/SO_0001637 rRNA_gene http://purl.obolibrary.org/obo/SO_0001263 ncRNA_gene A gene that encodes for ribosomal RNA. http://purl.obolibrary.org/obo/SO_0001639 RNase_P_RNA_gene http://purl.obolibrary.org/obo/SO_0001263 ncRNA_gene A gene that encodes an RNase P RNA. http://purl.obolibrary.org/obo/SO_0001640 RNase_MRP_RNA_gene http://purl.obolibrary.org/obo/SO_0001263 ncRNA_gene A gene that encodes a RNase_MRP_RNA. http://purl.obolibrary.org/obo/SO_0001641 lincRNA_gene http://purl.obolibrary.org/obo/SO_0001263 ncRNA_gene A gene that encodes large intervening non-coding RNA. http://purl.obolibrary.org/obo/SO_0001643 telomerase_RNA_gene http://purl.obolibrary.org/obo/SO_0001263 ncRNA_gene A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase. http://purl.obolibrary.org/obo/SO_0001741 pseudogenic_gene_segment http://purl.obolibrary.org/obo/SO_3000000 gene_segment A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product. http://purl.obolibrary.org/obo/SO_3000000 gene_segment http://purl.obolibrary.org/obo/SO_0001411 biological_region A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination. http://purl.obolibrary.org/obo/UO_0000012 kelvin http://purl.obolibrary.org/obo/UO_0000045 base unit A thermodynamic temperature unit which is equal to the fraction 1/273.16 of the thermodynamic temperature of the triple point of water. http://purl.obolibrary.org/obo/UO_0000013 mole http://purl.obolibrary.org/obo/UO_0000045 base unit A substance unit which is equal to the amount of substance of a molecular system which contains as many elementary entities as there are atoms in 0.012 kilogram of carbon 12. http://purl.obolibrary.org/obo/UO_0000028 millisecond http://purl.obolibrary.org/obo/UO_0000003 time unit A time unit which is equal to one thousandth of a second or 10^[-3] s. http://purl.obolibrary.org/obo/UO_0000029 microsecond http://purl.obolibrary.org/obo/UO_0000003 time unit A time unit which is equal to one millionth of a second or 10^[-6] s. http://purl.obolibrary.org/obo/UO_0000043 femtomole http://purl.obolibrary.org/obo/UO_0000006 substance unit A substance unit equal to 10^[-15] mol. http://purl.obolibrary.org/obo/UO_0000044 attomole http://purl.obolibrary.org/obo/UO_0000006 substance unit A substance unit equal to 10^[-18] mol. http://purl.obolibrary.org/obo/UO_0000045 base unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label A unit which is one of a particular measure to which all measures of that type can be related. http://purl.obolibrary.org/obo/UO_0000052 mass density unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label A density unit which is a standard measure of the mass of a substance in a given volume. http://purl.obolibrary.org/obo/UO_0000061 unit of molarity http://purl.obolibrary.org/obo/UO_0000051 concentration unit A concentration unit which is a standard measure of the number of moles of a given substance per liter of solution. http://purl.obolibrary.org/obo/UO_0000104 femtoliter http://purl.obolibrary.org/obo/UO_0000095 volume unit A volume unit which is equal to 10^[-15] L. http://purl.obolibrary.org/obo/UO_0000127 radiation unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label A unit which is a standard measure of the amount of radiation emitted by a given radiation source as well as the amount of radiation absorbed or deposited in a specific material by a radiation source. http://purl.obolibrary.org/obo/UO_0000128 activity (of a radionuclide) unit http://purl.obolibrary.org/obo/UO_0000127 radiation unit A unit which is a standard measure of the transformation (disintegration) rate of a radioactive substance. http://purl.obolibrary.org/obo/UO_0000133 curie http://purl.obolibrary.org/obo/UO_0000128 activity (of a radionuclide) unit An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which there are 3.7 x 10^[10] atom disintegration per second (dps). http://purl.obolibrary.org/obo/UO_0000136 roentgen http://purl.obolibrary.org/obo/UO_0000127 radiation unit An exposure unit which is equal to the amount of radiation required to liberate positive and negative charges of one electrostatic unit of charge in 1 cm^[3] of air at standard temperature and pressure (STP). This corresponds to the generation of approximately 2.0810^[9] ion pairs. http://purl.obolibrary.org/obo/UO_0000140 Roentgen equivalent man http://purl.obolibrary.org/obo/UO_0000127 radiation unit A dose equivalent unit which when multiplied by hundred is equal to one sievert or 1 Sv. 1 Sv is equal to 100 rem. http://purl.obolibrary.org/obo/UO_0000147 disintegrations per minute http://purl.obolibrary.org/obo/UO_0000128 activity (of a radionuclide) unit An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which one nucleus decays per minute or there is one atom disintegration per minute. http://purl.obolibrary.org/obo/UO_0000148 counts per minute http://purl.obolibrary.org/obo/UO_0000128 activity (of a radionuclide) unit An activity (of a radionuclide) unit which is equal to the number of light emissions produced by ionizing radiation in one minute. http://purl.obolibrary.org/obo/UO_0000157 light unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label A unit which is a standard measure of the intensity of light. http://purl.obolibrary.org/obo/UO_0000186 dimensionless unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label A unit which is a standard measure of physical quantity consisting of only a numerical number without any units. http://purl.obolibrary.org/obo/UO_0000187 percent http://purl.obolibrary.org/obo/UO_0000186 dimensionless unit A dimensionless ratio unit which denotes numbers as fractions of 100. http://purl.obolibrary.org/obo/UO_0000189 count unit http://purl.obolibrary.org/obo/UO_0000186 dimensionless unit A dimensionless unit which denotes a simple count of things. http://purl.obolibrary.org/obo/UO_0000195 degree Fahrenheit http://purl.obolibrary.org/obo/UO_0000005 temperature unit A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius. http://purl.obolibrary.org/obo/UO_0000205 volume per unit volume http://purl.obolibrary.org/obo/UO_0000051 concentration unit A dimensionless concentration unit which denotes the given volume of the solute in the total volume of the resulting solution. http://purl.obolibrary.org/obo/UO_0000209 deciliter http://purl.obolibrary.org/obo/UO_0000095 volume unit A volume unit which is equal to one tenth of a liter or 10^[-1] L. http://purl.obolibrary.org/obo/UO_0000213 colony forming unit per milliliter http://purl.obolibrary.org/obo/UO_0000051 concentration unit A colony forming unit which a measure of viable bacterial numbers in one milliliter. http://purl.obolibrary.org/obo/UO_0000232 bit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label An information unit which refers to a digit in the binary numeral system, which consists of base 2 digits (ie there are only 2 possible values: 0 or 1). http://purl.obolibrary.org/obo/VT_0005215 islet of Langerhans morphology trait http://purl.obolibrary.org/obo/PATO_0000051 morphology Any measurable or observable characteristic related to the shape, structure, color or pattern of the cellular masses consisting of several to several hundred cells in the interstitial tissue of the pancreas; they are composed of five different cell types that make up the endocrine portion of the pancreas. http://www.ebi.ac.uk/efo/EFO_0000220 acute lymphoblastic leukemia http://www.ebi.ac.uk/efo/EFO_0001642 lymphoid neoplasm Leukemia with an acute onset, characterized by the presence of lymphoblasts in the bone marrow and the peripheral blood. It includes the acute B lymphoblastic leukemia and acute T lymphoblastic leukemia. http://www.ebi.ac.uk/efo/EFO_0000222 acute myeloid leukemia http://www.ebi.ac.uk/efo/EFO_0002427 myeloid neoplasm Clonal expansion of myeloid blasts in bone marrow, blood, and other tissue. Myeloid leukemias develop from changes in cells that normally produce NEUTROPHILS; BASOPHILS; EOSINOPHILS; and MONOCYTES. http://www.ebi.ac.uk/efo/EFO_0000224 acute promyelocytic leukemia http://www.ebi.ac.uk/efo/EFO_0000222 acute myeloid leukemia An acute myeloid leukemia (AML) in which abnormal promyelocytes predominate. It is characterized by the t(15;17)(q22;q12) translocation. There are two variants: the typical and micro granular (hypo granular) variant. This AML is particularly sensitive to treatment with all trans-retinoic acid and has a favorable prognosis. (WHO, 2001) -- 2003 http://www.ebi.ac.uk/efo/EFO_0000270 asthma http://purl.obolibrary.org/obo/OGMS_0000031 disease A form of bronchial disorder with three distinct components: airway hyper-responsiveness (RESPIRATORY HYPERSENSITIVITY), airway INFLAMMATION, and intermittent AIRWAY OBSTRUCTION. It is characterized by spasmodic contraction of airway smooth muscle, WHEEZING, and dyspnea (DYSPNEA, PAROXYSMAL). http://www.ebi.ac.uk/efo/EFO_0000309 Burkitts lymphoma http://www.ebi.ac.uk/efo/EFO_0001642 lymphoid neoplasm A form of undifferentiated malignant LYMPHOMA usually found in central Africa, but also reported in other parts of the world. It is commonly manifested as a large osteolytic lesion in the jaw or as an abdominal mass. B-cell antigens are expressed on the immature cells that make up the tumor in virtually all cases of Burkitt lymphoma. The Epstein-Barr virus (HERPESVIRUS 4, HUMAN) has been isolated from Burkitt lymphoma cases in Africa and it is implicated as the causative agent in these cases; however, most non-African cases are EBV-negative. http://www.ebi.ac.uk/efo/EFO_0000311 cancer http://www.ebi.ac.uk/efo/EFO_0000616 neoplasm A malignant neoplasm in which new abnormal tissue grow by excessive cellular division and proliferation more rapidly than normal and continues to grow after the stimuli that initiated the new growth cease. http://www.ebi.ac.uk/efo/EFO_0000339 chronic myelogenous leukemia http://www.ebi.ac.uk/efo/EFO_0002427 myeloid neoplasm Clonal hematopoetic disorder caused by an acquired genetic defect in PLURIPOTENT STEM CELLS. It starts in MYELOID CELLS of the bone marrow, invades the blood and then other organs. The condition progresses from a stable, more indolent, chronic phase (LEUKEMIA, MYELOID, CHRONIC PHASE) lasting up to 7 years, to an advanced phase composed of an accelerated phase (LEUKEMIA, MYELOID, ACCELERATED PHASE) and BLAST CRISIS. http://www.ebi.ac.uk/efo/EFO_0000365 colorectal adenocarcinoma http://www.ebi.ac.uk/efo/EFO_0000311 cancer Tumors or cancer of the COLON or the RECTUM or both. Risk factors for colorectal cancer include chronic ULCERATIVE COLITIS; FAMILIAL POLYPOSIS COLI; exposure to ASBESTOS; and irradiation of the CERVIX UTERI. http://www.ebi.ac.uk/efo/EFO_0000369 compound based treatment http://purl.obolibrary.org/obo/OBI_0000011 planned process A treatment process in which a chemical compound is administered to the subject under investigation. http://www.ebi.ac.uk/efo/EFO_0000400 diabetes mellitus http://purl.obolibrary.org/obo/OGMS_0000031 disease A metabolic disorder characterized by abnormally high blood sugar levels due to diminished production of insulin or insulin resistance/desensitization. http://www.ebi.ac.uk/efo/EFO_0000493 family history http://purl.obolibrary.org/obo/OGMS_0000015 clinical history Family history is a form of clinicaly history specifically about relevant aspects of genetic preconditions or family member's clinical history. http://www.ebi.ac.uk/efo/EFO_0000549 insulinoma http://www.ebi.ac.uk/efo/EFO_0000616 neoplasm A benign tumor of the PANCREATIC BETA CELLS. Insulinoma secretes excess INSULIN resulting in HYPOGLYCEMIA. http://www.ebi.ac.uk/efo/EFO_0000565 leukemia http://www.ebi.ac.uk/efo/EFO_0001642 lymphoid neoplasm A malignant (clonal) hematologic disorder, involving hematopoietic stem cells and characterized by the presence of primitive or atypical myeloid or lymphoid cells in the bone marrow and the blood. Leukemias are classified as acute or chronic based on the degree of cellular differentiation and the predominant cell type present. Leukemia is usually associated with anemia, fever, hemorrhagic episodes, and splenomegaly. Common leukemias include acute myeloid leukemia, chronic myelogenous leukemia, acute lymphoblastic or precursor lymphoblastic leukemia, and chronic lymphocytic leukemia. Treatment is vital to patient survival; untreated, the natural course of acute leukemias is normally measured in weeks or months, while that of chronic leukemias is more often measured in months or years. http://www.ebi.ac.uk/efo/EFO_0000616 neoplasm http://purl.obolibrary.org/obo/OGMS_0000031 disease A benign or malignant tissue growth resulting from uncontrolled cell proliferation. Benign neoplastic cells resemble normal cells without exhibiting significant cytologic atypia, while malignant cells exhibit overt signs such as dysplastic features, atypical mitotic figures, necrosis, nuclear pleomorphism, and anaplasia. Representative examples of benign neoplasms include papillomas, cystadenomas, and lipomas; malignant neoplasms include carcinomas, sarcomas, lymphomas, and leukemias. http://www.ebi.ac.uk/efo/EFO_0000647 experiment performer http://purl.obolibrary.org/obo/OBI_0000202 investigation agent role An individual who does some experimental process. http://www.ebi.ac.uk/efo/EFO_0001359 type I diabetes mellitus http://www.ebi.ac.uk/efo/EFO_0000400 diabetes mellitus An autoimmune disease of endocrine system and is_a diabetes mellitus that results from autoimmune destruction of insulin-producing beta cells of the pancreas. http://www.ebi.ac.uk/efo/EFO_0001360 type II diabetes mellitus http://www.ebi.ac.uk/efo/EFO_0000400 diabetes mellitus A subclass of DIABETES MELLITUS that is not INSULIN-responsive or dependent (NIDDM). It is characterized initially by INSULIN RESISTANCE and HYPERINSULINEMIA; and eventually by GLUCOSE INTOLERANCE; HYPERGLYCEMIA; and overt diabetes. Type II diabetes mellitus is no longer considered a disease exclusively found in adults. Patients seldom develop KETOSIS but often exhibit OBESITY. http://www.ebi.ac.uk/efo/EFO_0001642 lymphoid neoplasm http://www.ebi.ac.uk/efo/EFO_0000311 cancer Malignant lymphoma composed of large B lymphoid cells whose nuclear size can exceed normal macrophage nuclei, or more than twice the size of a normal lymphocyte. The pattern is predominantly diffuse. Most of these lymphomas represent the malignant counterpart of B-lymphocytes at midstage in the process of differentiation. http://www.ebi.ac.uk/efo/EFO_0001799 ethnic group http://purl.obolibrary.org/obo/OBI_0000181 population A group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. (MSH); A social group characterized by a distinctive social and cultural tradition maintained from generation to generation, a common history and origin and a sense of identification with the group; members of the group have distinctive features in their way of life, shared experiences and often a common genetic heritage; these features may be reflected in their experience of health and disease. (NCI); Ethnicity - an arbitrary classification of the social group a person belongs to, and either identifies with or is identified with by others, as a result of a complex of cultural, biological, geographical and other factors such as linguistic, dietary and religion traditions; ancestry, background, allegiance, or association; and physical characteristics traditionally associated with race. Increasingly the concept is used synonymously with race but this use trend has a pragmatic basis rather than scientific. (NCI); The concept of ethnic origin is an attempt to classify people, not according to their current ethnicity, but according to where their ancestors came from. Ethnic origin has become a popular classification in statistics, where the concept of race has been largely discarded. (from Wikipedia) (NCI); a group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. (CSP) http://www.ebi.ac.uk/efo/EFO_0002529 INS-1 http://purl.obolibrary.org/obo/CLO_0000128 immortal animal cell line cell Pancreatic beta -cell line of rat origin. http://www.ebi.ac.uk/efo/EFO_0002588 Theiler stage 28 http://www.ebi.ac.uk/efo/EFO_0004390 mouse postnatal Theiler stage 28 is a mouse postnatal stage characterised by postnatal development after a mouse is newly born. http://www.ebi.ac.uk/efo/EFO_0002756 fasting http://purl.obolibrary.org/obo/GO_0008150 biological_process Abstaining from food. http://www.ebi.ac.uk/efo/EFO_0002829 MIN6 http://purl.obolibrary.org/obo/CLO_0000128 immortal animal cell line cell The murine MIN6 cell line derived from in vivo immortalized insulin-secreting pancreatic beta cells. http://www.ebi.ac.uk/efo/EFO_0004391 Theiler stage 27 http://www.ebi.ac.uk/efo/EFO_0004390 mouse postnatal Theiler stage 27 is a newborn mouse. http://purl.obolibrary.org/obo/GO_0008219 cell death http://purl.obolibrary.org/obo/GO_0044763 single-organism cellular process Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as "apoptotic bodies"); and/or (3) its corpse (or its fragments) have been engulfed by an adjacent cell in vivo. http://purl.obolibrary.org/obo/GO_0009730 detection of carbohydrate stimulus http://purl.obolibrary.org/obo/GO_0009743 response to carbohydrate The series of events in which a carbohydrate stimulus is received by a cell and converted into a molecular signal. http://purl.obolibrary.org/obo/GO_0009732 detection of hexose stimulus http://purl.obolibrary.org/obo/GO_0034287 detection of monosaccharide stimulus The series of events in which a stimulus from a hexose is received and converted into a molecular signal. http://purl.obolibrary.org/obo/GO_0009743 response to carbohydrate http://purl.obolibrary.org/obo/GO_0050896 response to stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a carbohydrate stimulus. http://purl.obolibrary.org/obo/GO_0009746 response to hexose http://purl.obolibrary.org/obo/GO_0034284 response to monosaccharide Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hexose stimulus. http://purl.obolibrary.org/obo/GO_0015106 bicarbonate transmembrane transporter activity http://purl.obolibrary.org/obo/GO_0003674 molecular_function Catalysis of the transfer of bicarbonate from one side of a membrane to the other. Bicarbonate is the hydrogencarbonate ion, HCO3-. http://purl.obolibrary.org/obo/GO_0016023 cytoplasmic membrane-bounded vesicle http://purl.obolibrary.org/obo/GO_0031988 membrane-bounded vesicle A membrane-bounded vesicle found in the cytoplasm of the cell. http://purl.obolibrary.org/obo/GO_0016568 chromatin modification http://purl.obolibrary.org/obo/GO_0016043 cellular component organization The alteration of DNA, protein, or sometimes RNA, in chromatin, which may result in changing the chromatin structure. http://purl.obolibrary.org/obo/GO_0017145 stem cell division http://purl.obolibrary.org/obo/GO_0044763 single-organism cellular process The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types. http://purl.obolibrary.org/obo/GO_0019222 regulation of metabolic process http://purl.obolibrary.org/obo/GO_0050789 regulation of biological process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. http://purl.obolibrary.org/obo/GO_0030225 macrophage differentiation http://purl.obolibrary.org/obo/GO_0002573 myeloid leukocyte differentiation The process in which a relatively unspecialized monocyte acquires the specialized features of a macrophage. http://purl.obolibrary.org/obo/GO_0031090 organelle membrane http://purl.obolibrary.org/obo/GO_0044422 organelle part A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. http://purl.obolibrary.org/obo/GO_0031982 vesicle http://purl.obolibrary.org/obo/GO_0043226 organelle Any small, fluid-filled, spherical organelle enclosed by membrane or protein. http://purl.obolibrary.org/obo/GO_0034284 response to monosaccharide http://purl.obolibrary.org/obo/GO_0009743 response to carbohydrate Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a monosaccharide stimulus. http://purl.obolibrary.org/obo/GO_0034287 detection of monosaccharide stimulus http://purl.obolibrary.org/obo/GO_0034284 response to monosaccharide The series of events in which a stimulus from a monosaccharide is received and converted into a molecular signal. http://purl.obolibrary.org/obo/GO_0043565 sequence-specific DNA binding http://purl.obolibrary.org/obo/GO_0003674 molecular_function Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. http://purl.obolibrary.org/obo/GO_0044446 intracellular organelle part http://purl.obolibrary.org/obo/GO_0044424 intracellular part A constituent part of an intracellular organelle, an organized structure of distinctive morphology and function, occurring within the cell. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton but excludes the plasma membrane. http://purl.obolibrary.org/obo/GO_0045595 regulation of cell differentiation http://purl.obolibrary.org/obo/GO_0050793 regulation of developmental process Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features. http://purl.obolibrary.org/obo/GO_0048863 stem cell differentiation http://purl.obolibrary.org/obo/GO_0030154 cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a stem cell. A stem cell is a 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/GO_0050432 catecholamine secretion http://purl.obolibrary.org/obo/GO_0051937 catecholamine transport The regulated release of catecholamines by a cell. The catecholamines are a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine. http://purl.obolibrary.org/obo/GO_0050879 multicellular organismal movement http://purl.obolibrary.org/obo/GO_0044707 single-multicellular organism process Any physiological process involved in changing the position of a multicellular organism or an anatomical part of a multicellular organism. http://purl.obolibrary.org/obo/GO_0051171 regulation of nitrogen compound metabolic process http://purl.obolibrary.org/obo/GO_0019222 regulation of metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. http://purl.obolibrary.org/obo/GO_0051937 catecholamine transport http://purl.obolibrary.org/obo/GO_0015850 organic hydroxy compound transport The directed movement of catecholamines, a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine. http://purl.obolibrary.org/obo/GO_0098602 single organism cell adhesion http://purl.obolibrary.org/obo/GO_0044699 single-organism process The attachment, via cell adhesion molecules, of a cell to either another cell of the same organism, or to an underlying substrate of the same organism such as the extracellular matrix. http://purl.obolibrary.org/obo/GO_0055007 cardiac muscle cell differentiation http://purl.obolibrary.org/obo/GO_0030154 cell differentiation The process in which a cardiac muscle precursor cell acquires specialized features of a cardiac muscle cell. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. http://purl.obolibrary.org/obo/GO_0060290 transdifferentiation http://purl.obolibrary.org/obo/GO_0030154 cell differentiation The conversion of a differentiated cell of one fate into a differentiated cell of another fate without first undergoing cell division or reversion to a more primitive or stem cell-like fate. http://purl.obolibrary.org/obo/GO_0060591 chondroblast differentiation http://purl.obolibrary.org/obo/GO_0030154 cell differentiation The process in which a mesenchymal cell, acquires specialized structural and/or functional features of a chondroblast. Differentiation includes the processes involved in commitment of a cell to a chondroblast fate. A chondroblast is a precursor cell to chondrocytes. http://purl.obolibrary.org/obo/GO_0070091 glucagon secretion http://purl.obolibrary.org/obo/GO_0030072 peptide hormone secretion The regulated release of glucagon from secretory granules in the A (alpha) cells of the pancreas (islets of Langerhans). http://purl.obolibrary.org/obo/GO_0070253 somatostatin secretion http://purl.obolibrary.org/obo/GO_0030072 peptide hormone secretion The regulated release of somatostatin from secretory granules in the D cells of the pancreas. http://purl.obolibrary.org/obo/GO_0070486 leukocyte aggregation http://purl.obolibrary.org/obo/GO_0034109 homotypic cell-cell adhesion The adhesion of one leukocyte to one or more other leukocytes via adhesion molecules. http://purl.obolibrary.org/obo/GO_0071971 extracellular exosome assembly http://purl.obolibrary.org/obo/GO_0070925 organelle assembly The aggregation, arrangement and bonding together of a set of components to form an extracellular vesicular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. http://purl.obolibrary.org/obo/PR_000009054 insulin http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human INS gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000009062 insulinoma-associated protein 1 http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human INSM1 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000009116 insulin gene enhancer protein ISL-1 http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human ISL1 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000010047 transcription factor MafA http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human MAFA gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000011152 neurogenic differentiation factor 1 http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human NEUROD1 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000011158 neurogenin-3 http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human NEUROG3 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000011242 homeobox protein Nkx-2.2 http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human NKX2-2 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000011250 homeobox protein Nkx-6.1 http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human NKX6-1 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000011639 hepatocyte nuclear factor 6 http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human ONECUT1 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000012523 pancreas/duodenum homeobox protein 1 http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human PDX1 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000013418 pancreas transcription factor 1 subunit alpha http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human PTF1A gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000013824 recombining binding protein suppressor of hairless http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human RBPJ gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000013825 recombining binding protein suppressor of hairless-like protein http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human RBPJL gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/SO_0000110 sequence_feature http://purl.obolibrary.org/obo/BFO_0000031 generically dependent continuant Any extent of continuous biological sequence. http://purl.obolibrary.org/obo/SO_0000704 gene http://purl.obolibrary.org/obo/SO_0001411 biological_region A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. 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/BCGO_0000021 obsolete_STOCK Tg(Tnpo1-EGFP)6729Hara/Mmmh mouse strain http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class RES188 mouse strain http://purl.obolibrary.org/obo/BCGO_0000105 Black and tan, brachyury mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain BTBR http://purl.obolibrary.org/obo/BCGO_0000106 large pancreatic ductal cell http://purl.obolibrary.org/obo/CL_0002079 pancreatic ductal cell large duct cell http://purl.obolibrary.org/obo/BCGO_0000107 small pancreatic ductal cell' http://purl.obolibrary.org/obo/CL_0002079 pancreatic ductal cell small duct cell http://purl.obolibrary.org/obo/BCGO_0000108 Tet-On/Ngn3 embryonic stem cell http://purl.obolibrary.org/obo/BTO_0001581 embryonic stem cell line ES (Tet-On/Ngn3) http://purl.obolibrary.org/obo/BCGO_0000109 GKP2 cell http://purl.obolibrary.org/obo/CLO_0000128 immortal animal cell line cell GKP2 http://purl.obolibrary.org/obo/BCGO_0000110 GKP4 cell http://purl.obolibrary.org/obo/CLO_0000128 immortal animal cell line cell GKP4 http://purl.obolibrary.org/obo/BCGO_0000121 mPAC L20 cell http://purl.obolibrary.org/obo/CLO_0000128 immortal animal cell line cell mPAC L20 http://purl.obolibrary.org/obo/BCGO_0000122 PANC-1 cell http://purl.obolibrary.org/obo/CLO_0000128 immortal animal cell line cell PANC-1 http://purl.obolibrary.org/obo/BCGO_0000123 R7T1 cell http://purl.obolibrary.org/obo/CLO_0000128 immortal animal cell line cell R7T1 http://purl.obolibrary.org/obo/CHEBI_38295 azabicycloalkane http://purl.obolibrary.org/obo/CHEBI_38101 organonitrogen heterocyclic compound http://purl.obolibrary.org/obo/CHEBI_22728 benzopyrrole http://purl.obolibrary.org/obo/CHEBI_33833 heteroarene http://purl.obolibrary.org/obo/CHEBI_38297 thiabicycloalkane http://purl.obolibrary.org/obo/CHEBI_38106 organosulfur heterocyclic compound http://purl.obolibrary.org/obo/CHEBI_38106 organosulfur heterocyclic compound http://purl.obolibrary.org/obo/CHEBI_24532 organic heterocyclic compound http://purl.obolibrary.org/obo/CHEBI_33670 heteromonocyclic compound http://purl.obolibrary.org/obo/CHEBI_33595 cyclic compound http://purl.obolibrary.org/obo/CHEBI_33671 heteropolycyclic compound http://purl.obolibrary.org/obo/CHEBI_33595 cyclic compound http://purl.obolibrary.org/obo/CHEBI_27171 organic heterobicyclic compound http://purl.obolibrary.org/obo/CHEBI_33672 heterobicyclic compound http://purl.obolibrary.org/obo/CHEBI_38164 organic heteropentacyclic compound http://purl.obolibrary.org/obo/CHEBI_38166 organic heteropolycyclic compound http://purl.obolibrary.org/obo/CHEBI_38166 organic heteropolycyclic compound http://purl.obolibrary.org/obo/CHEBI_33671 heteropolycyclic compound http://purl.obolibrary.org/obo/CHEBI_25693 organic heteromonocyclic compound http://purl.obolibrary.org/obo/CHEBI_33670 heteromonocyclic compound http://purl.obolibrary.org/obo/CHEBI_35605 carbon oxoacid http://purl.obolibrary.org/obo/CHEBI_36963 organooxygen compound http://purl.obolibrary.org/obo/CHEBI_25806 oxygen molecular entity http://purl.obolibrary.org/obo/CHEBI_33304 chalcogen molecular entity http://purl.obolibrary.org/obo/CHEBI_26835 sulfur molecular entity http://purl.obolibrary.org/obo/CHEBI_33304 chalcogen molecular entity http://purl.obolibrary.org/obo/CHEBI_51143 nitrogen molecular entity http://purl.obolibrary.org/obo/CHEBI_33675 p-block molecular entity http://purl.obolibrary.org/obo/CHEBI_33659 organic aromatic compound http://purl.obolibrary.org/obo/CHEBI_33595 cyclic compound http://purl.obolibrary.org/obo/CHEBI_33482 sulfur oxoanion http://purl.obolibrary.org/obo/CHEBI_26835 sulfur molecular entity http://purl.obolibrary.org/obo/CHEBI_33424 sulfur oxoacid derivative http://purl.obolibrary.org/obo/CHEBI_26835 sulfur molecular entity http://purl.obolibrary.org/obo/CHEBI_26440 pyrimidine nucleoside http://purl.obolibrary.org/obo/CHEBI_33838 nucleoside http://purl.obolibrary.org/obo/PATO_0000068 qualitative http://purl.obolibrary.org/obo/PATO_0000001 quality http://purl.obolibrary.org/obo/BFO_0000008 temporal region http://purl.obolibrary.org/obo/BFO_0000003 occurrent http://purl.obolibrary.org/obo/BFO_0000011 spatiotemporal region http://purl.obolibrary.org/obo/BFO_0000003 occurrent http://purl.obolibrary.org/obo/BFO_0000141 immaterial entity http://purl.obolibrary.org/obo/BFO_0000004 independent continuant http://purl.obolibrary.org/obo/BFO_0000009 two-dimensional spatial region http://purl.obolibrary.org/obo/BFO_0000006 spatial region http://purl.obolibrary.org/obo/BFO_0000018 zero-dimensional spatial region http://purl.obolibrary.org/obo/BFO_0000006 spatial region http://purl.obolibrary.org/obo/BFO_0000026 one-dimensional spatial region http://purl.obolibrary.org/obo/BFO_0000006 spatial region http://purl.obolibrary.org/obo/BFO_0000028 three-dimensional spatial region http://purl.obolibrary.org/obo/BFO_0000006 spatial region http://purl.obolibrary.org/obo/BFO_0000038 one-dimensional temporal region http://purl.obolibrary.org/obo/BFO_0000008 temporal region http://purl.obolibrary.org/obo/BFO_0000182 history http://purl.obolibrary.org/obo/BFO_0000015 process http://purl.obolibrary.org/obo/BFO_0000034 function http://purl.obolibrary.org/obo/BFO_0000017 realizable entity http://purl.obolibrary.org/obo/BFO_0000016 disposition http://purl.obolibrary.org/obo/BFO_0000017 realizable entity http://purl.obolibrary.org/obo/BFO_0000019 quality http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant http://purl.obolibrary.org/obo/BFO_0000024 fiat object 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/CLO_0001932 BETA-TC-3 cell http://purl.obolibrary.org/obo/CLO_0000019 immortal cell line cell http://purl.obolibrary.org/obo/CLO_0002708 Daudi cell http://purl.obolibrary.org/obo/CLO_0000019 immortal cell line cell http://purl.obolibrary.org/obo/CLO_0003612 H9 cell http://purl.obolibrary.org/obo/CLO_0000019 immortal cell line cell http://purl.obolibrary.org/obo/CLO_0007050 K 562 cell http://purl.obolibrary.org/obo/CLO_0000019 immortal cell line cell http://purl.obolibrary.org/obo/CLO_0008734 Raji cell http://purl.obolibrary.org/obo/CLO_0000019 immortal cell line cell http://purl.obolibrary.org/obo/CLO_0009218 SW480 cell http://purl.obolibrary.org/obo/CLO_0000019 immortal cell line cell http://www.ebi.ac.uk/efo/EFO_0002927 International Unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label http://www.ebi.ac.uk/efo/swo/SWO_0000107 Feature Extraction Software http://purl.obolibrary.org/obo/IAO_0000010 software http://purl.obolibrary.org/obo/IAO_0000429 email address http://purl.obolibrary.org/obo/IAO_0000030 information content entity http://www.ebi.ac.uk/efo/EFO_0001734 data analyst http://purl.obolibrary.org/obo/OBI_0000202 investigation agent role http://www.ebi.ac.uk/efo/EFO_0001739 investigator http://purl.obolibrary.org/obo/OBI_0000202 investigation agent role http://www.ebi.ac.uk/efo/EFO_0001741 submitter http://purl.obolibrary.org/obo/OBI_0000202 investigation agent role http://purl.obolibrary.org/obo/OBI_0000794 transcription factor binding site http://purl.obolibrary.org/obo/OBI_0000905 sequence feature annotation http://purl.obolibrary.org/obo/NCBITaxon_10239 Viruses http://purl.obolibrary.org/obo/OBI_0100026 organism http://purl.obolibrary.org/obo/NCBITaxon_2157 Archaea http://purl.obolibrary.org/obo/OBI_0100026 organism http://purl.obolibrary.org/obo/NCBITaxon_2 Bacteria http://purl.obolibrary.org/obo/OBI_0100026 organism http://purl.obolibrary.org/obo/NCBITaxon_2759 Eukaryota http://purl.obolibrary.org/obo/OBI_0100026 organism http://purl.obolibrary.org/obo/PATO_0001894 phenotypic sex http://purl.obolibrary.org/obo/PATO_0000047 biological sex http://purl.obolibrary.org/obo/CHEBI_19255 pyrimidine 2'-deoxyribonucleoside http://purl.obolibrary.org/obo/CHEBI_68472 pyrimidine deoxyribonucleoside http://purl.obolibrary.org/obo/CHEBI_18274 2'-deoxyribonucleoside http://purl.obolibrary.org/obo/CHEBI_26912 oxolanes http://purl.obolibrary.org/obo/CHEBI_4705 double-stranded DNA http://purl.obolibrary.org/obo/CHEBI_16991 deoxyribonucleic acid http://purl.obolibrary.org/obo/CHEBI_2511 agarose http://purl.obolibrary.org/obo/CHEBI_18154 polysaccharide http://purl.obolibrary.org/obo/CHEBI_23636 deoxyribonucleoside http://purl.obolibrary.org/obo/CHEBI_33838 nucleoside http://www.ebi.ac.uk/efo/EFO_0002966 pancreatic cell http://purl.obolibrary.org/obo/BCGO_0000071 pancreatic material http://purl.obolibrary.org/obo/CL_0000255 eukaryotic cell http://purl.obolibrary.org/obo/CL_0000003 native cell http://purl.obolibrary.org/obo/CL_0000329 oxygen accumulating cell http://purl.obolibrary.org/obo/CL_0000003 native cell http://purl.obolibrary.org/obo/CL_0000680 muscle precursor cell http://purl.obolibrary.org/obo/CL_0002371 somatic cell http://purl.obolibrary.org/obo/CL_0010021 cardiac myoblast http://purl.obolibrary.org/obo/CL_0000056 myoblast http://purl.obolibrary.org/obo/CL_0000068 duct epithelial cell http://purl.obolibrary.org/obo/CL_0002371 somatic cell http://purl.obolibrary.org/obo/CL_0000076 squamous epithelial cell http://purl.obolibrary.org/obo/CL_0000066 epithelial cell http://purl.obolibrary.org/obo/CL_0000069 branched duct epithelial cell http://purl.obolibrary.org/obo/CL_0000068 duct epithelial cell http://purl.obolibrary.org/obo/CL_0000154 protein secreting cell http://purl.obolibrary.org/obo/CL_0000151 secretory cell http://purl.obolibrary.org/obo/CL_0000167 peptide hormone secreting cell http://purl.obolibrary.org/obo/CL_0000151 secretory cell http://purl.obolibrary.org/obo/CL_0000168 insulin secreting cell http://purl.obolibrary.org/obo/BCGO_0000004 insulin expressing cell http://purl.obolibrary.org/obo/CL_0000457 biogenic amine secreting cell http://purl.obolibrary.org/obo/CL_0000163 endocrine cell http://purl.obolibrary.org/obo/CL_0000172 somatostatin secreting cell http://purl.obolibrary.org/obo/CL_0000167 peptide hormone secreting cell http://purl.obolibrary.org/obo/CL_0000548 animal cell http://purl.obolibrary.org/obo/CL_0000255 eukaryotic cell http://purl.obolibrary.org/obo/CL_0000417 endopolyploid cell http://purl.obolibrary.org/obo/CL_0000412 polyploid 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_0011115 precursor cell http://purl.obolibrary.org/obo/CL_0001012 CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor http://purl.obolibrary.org/obo/CL_0011115 precursor cell http://purl.obolibrary.org/obo/CL_0002632 epithelial cell of lower respiratory tract http://purl.obolibrary.org/obo/CL_0002368 respiratory epithelial cell http://purl.obolibrary.org/obo/CHEBI_37987 Cy3 dye http://purl.obolibrary.org/obo/CHEBI_37960 cyanine dye http://purl.obolibrary.org/obo/CHEBI_37989 Cy5 dye http://purl.obolibrary.org/obo/CHEBI_37960 cyanine dye http://purl.obolibrary.org/obo/NCBITaxon_10116 Rattus norvegicus http://purl.obolibrary.org/obo/NCBITaxon_10114 Rattus http://purl.obolibrary.org/obo/NCBITaxon_32443 Teleostei http://purl.obolibrary.org/obo/NCBITaxon_117571 Euteleostomi http://purl.obolibrary.org/obo/NCBITaxon_32524 Amniota http://purl.obolibrary.org/obo/NCBITaxon_117571 Euteleostomi http://purl.obolibrary.org/obo/NCBITaxon_7742 Vertebrata http://purl.obolibrary.org/obo/NCBITaxon_2759 Eukaryota http://purl.obolibrary.org/obo/NCBITaxon_9606 Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_314146 Euarchontoglires http://purl.obolibrary.org/obo/NCBITaxon_39107 Murinae http://purl.obolibrary.org/obo/NCBITaxon_314146 Euarchontoglires http://purl.obolibrary.org/obo/NCBITaxon_7955 Danio rerio http://purl.obolibrary.org/obo/NCBITaxon_32443 Teleostei http://purl.obolibrary.org/obo/NCBITaxon_314146 Euarchontoglires http://purl.obolibrary.org/obo/NCBITaxon_32524 Amniota http://purl.obolibrary.org/obo/NCBITaxon_32561 Sauria http://purl.obolibrary.org/obo/NCBITaxon_32524 Amniota http://purl.obolibrary.org/obo/NCBITaxon_8782 Aves http://purl.obolibrary.org/obo/NCBITaxon_32561 Sauria http://purl.obolibrary.org/obo/NCBITaxon_8570 Serpentes http://purl.obolibrary.org/obo/NCBITaxon_32561 Sauria http://purl.obolibrary.org/obo/NCBITaxon_10090 Mus musculus http://purl.obolibrary.org/obo/NCBITaxon_39107 Murinae http://purl.obolibrary.org/obo/NCBITaxon_10114 Rattus http://purl.obolibrary.org/obo/NCBITaxon_39107 Murinae http://purl.obolibrary.org/obo/NCBITaxon_7776 Gnathostomata http://purl.obolibrary.org/obo/NCBITaxon_7742 Vertebrata http://purl.obolibrary.org/obo/NCBITaxon_117571 Euteleostomi http://purl.obolibrary.org/obo/NCBITaxon_7776 Gnathostomata http://purl.obolibrary.org/obo/UBERON_0009856 sac http://purl.obolibrary.org/obo/UBERON_0000061 anatomical structure http://purl.obolibrary.org/obo/UBERON_0013522 subdivision of tube http://purl.obolibrary.org/obo/UBERON_0000064 organ part http://purl.obolibrary.org/obo/UBERON_0000112 sexually immature stage http://purl.obolibrary.org/obo/UBERON_0000105 life cycle stage http://www.ebi.ac.uk/efo/EFO_0002543 mouse prenatal http://purl.obolibrary.org/obo/UBERON_0000105 life cycle stage http://www.ebi.ac.uk/efo/EFO_0004390 mouse postnatal http://purl.obolibrary.org/obo/UBERON_0000105 life cycle stage http://purl.obolibrary.org/obo/UBERON_0034769 lymphomyeloid tissue http://purl.obolibrary.org/obo/UBERON_0000479 tissue http://purl.obolibrary.org/obo/UBERON_0019306 nose epithelium http://purl.obolibrary.org/obo/UBERON_0010371 ecto-epithelium http://purl.obolibrary.org/obo/UBERON_0004457 cavity lining http://purl.obolibrary.org/obo/UBERON_0004923 organ component layer http://purl.obolibrary.org/obo/UBERON_0005439 definitive endoderm http://purl.obolibrary.org/obo/UBERON_0002050 embryonic structure http://purl.obolibrary.org/obo/UBERON_0013515 subdivision of uterine tube http://purl.obolibrary.org/obo/UBERON_0013522 subdivision of tube http://purl.obolibrary.org/obo/UBERON_0010316 germ layer / neural crest http://purl.obolibrary.org/obo/UBERON_0005291 embryonic tissue http://purl.obolibrary.org/obo/BCGO_0000087 stress and apoptosis in islets or beta cells http://purl.obolibrary.org/obo/GO_0008150 biological_process http://purl.obolibrary.org/obo/REO_0000002 antibody reagent http://purl.obolibrary.org/obo/GO_0042571 immunoglobulin complex, circulating http://purl.obolibrary.org/obo/BCGO_0000031 black swiss mouse strain http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain http://www.ebi.ac.uk/efo/EFO_0002547 NOD mouse http://purl.obolibrary.org/obo/BCGO_0000002 mouse strain http://purl.obolibrary.org/obo/RS_0002307 ICR http://purl.obolibrary.org/obo/BCGO_0000003 rat strain http://purl.obolibrary.org/obo/BTO_0001581 embryonic stem cell line http://purl.obolibrary.org/obo/CLO_0000044 immortal stem cell line cell http://purl.obolibrary.org/obo/CLO_0007043 JURKAT cell http://purl.obolibrary.org/obo/CLO_0000081 immortal neuron cell line cell http://purl.obolibrary.org/obo/CLO_0001690 Ainv15 cell http://purl.obolibrary.org/obo/CLO_0000147 immortal hematopoietic cell line cell http://purl.obolibrary.org/obo/CLO_0001352 3T3-L1 cell http://purl.obolibrary.org/obo/CLO_0000503 immortal mouse embryo-derived cell line cell http://purl.obolibrary.org/obo/CLO_0002405 CGR8 cell http://purl.obolibrary.org/obo/CLO_0000503 immortal mouse embryo-derived cell line cell http://purl.obolibrary.org/obo/BCGO_0000111 Sox17 expressiong H9 cell http://purl.obolibrary.org/obo/CLO_0003612 H9 cell http://purl.obolibrary.org/obo/BTO_0003081 pancreatic ductal adenocarcinoma cell http://purl.obolibrary.org/obo/REO_0000383 cancer cell http://purl.obolibrary.org/obo/SO_0001265 miRNA_gene http://purl.obolibrary.org/obo/SO_0001263 ncRNA_gene http://purl.obolibrary.org/obo/SO_0001266 scRNA_gene http://purl.obolibrary.org/obo/SO_0001263 ncRNA_gene http://purl.obolibrary.org/obo/SO_0001267 snoRNA_gene http://purl.obolibrary.org/obo/SO_0001263 ncRNA_gene http://purl.obolibrary.org/obo/SO_0001268 snRNA_gene http://purl.obolibrary.org/obo/SO_0001263 ncRNA_gene http://purl.obolibrary.org/obo/SO_0001272 tRNA_gene http://purl.obolibrary.org/obo/SO_0001263 ncRNA_gene http://www.ebi.ac.uk/efo/EFO_0002427 myeloid neoplasm http://www.ebi.ac.uk/efo/EFO_0001642 lymphoid neoplasm http://purl.obolibrary.org/obo/BCGO_0000120 INS-1E http://www.ebi.ac.uk/efo/EFO_0002529 INS-1 http://purl.obolibrary.org/obo/BCGO_0000112 INS-1 (832/1 and 832/2) http://www.ebi.ac.uk/efo/EFO_0002529 INS-1 http://purl.obolibrary.org/obo/BCGO_0000113 INS-1 (832/1) cell http://www.ebi.ac.uk/efo/EFO_0002529 INS-1 http://purl.obolibrary.org/obo/BCGO_0000114 INS-1 (832/13 and 833/15) http://www.ebi.ac.uk/efo/EFO_0002529 INS-1 http://purl.obolibrary.org/obo/BCGO_0000115 INS-1 (832/13) cell http://www.ebi.ac.uk/efo/EFO_0002529 INS-1 http://purl.obolibrary.org/obo/BCGO_0000116 INS-1 (832/2) cell http://www.ebi.ac.uk/efo/EFO_0002529 INS-1 http://purl.obolibrary.org/obo/BCGO_0000117 INS-1 (833/117) cell http://www.ebi.ac.uk/efo/EFO_0002529 INS-1 http://purl.obolibrary.org/obo/BCGO_0000118 INS-1 (833/15) cell http://www.ebi.ac.uk/efo/EFO_0002529 INS-1 http://purl.obolibrary.org/obo/BCGO_0000119 INS-1 (834/40) cell http://www.ebi.ac.uk/efo/EFO_0002529 INS-1 http://www.ebi.ac.uk/efo/EFO_0002582 Theiler stage 11 http://www.ebi.ac.uk/efo/EFO_0002543 mouse prenatal http://www.ebi.ac.uk/efo/EFO_0002583 Theiler stage 17 http://www.ebi.ac.uk/efo/EFO_0002543 mouse prenatal http://www.ebi.ac.uk/efo/EFO_0002584 Theiler stage 21 http://www.ebi.ac.uk/efo/EFO_0002543 mouse prenatal http://www.ebi.ac.uk/efo/EFO_0002585 Theiler stage 22 http://www.ebi.ac.uk/efo/EFO_0002543 mouse prenatal http://www.ebi.ac.uk/efo/EFO_0002586 Theiler stage 24 http://www.ebi.ac.uk/efo/EFO_0002543 mouse prenatal http://www.ebi.ac.uk/efo/EFO_0002587 Theiler stage 26 http://www.ebi.ac.uk/efo/EFO_0002543 mouse prenatal http://www.ebi.ac.uk/efo/EFO_0004393 Theiler stage 1 http://www.ebi.ac.uk/efo/EFO_0002543 mouse prenatal http://www.ebi.ac.uk/efo/EFO_0004394 Theiler stage 2 http://www.ebi.ac.uk/efo/EFO_0002543 mouse prenatal http://www.ebi.ac.uk/efo/EFO_0004395 Theiler stage 3 http://www.ebi.ac.uk/efo/EFO_0002543 mouse prenatal http://www.ebi.ac.uk/efo/EFO_0004396 Theiler stage 4 http://www.ebi.ac.uk/efo/EFO_0002543 mouse prenatal http://www.ebi.ac.uk/efo/EFO_0004397 Theiler stage 5 http://www.ebi.ac.uk/efo/EFO_0002543 mouse prenatal http://www.ebi.ac.uk/efo/EFO_0004398 Theiler stage 6 http://www.ebi.ac.uk/efo/EFO_0002543 mouse prenatal http://www.ebi.ac.uk/efo/EFO_0004399 Theiler stage 7 http://www.ebi.ac.uk/efo/EFO_0002543 mouse prenatal http://www.ebi.ac.uk/efo/EFO_0004400 Theiler stage 8 http://www.ebi.ac.uk/efo/EFO_0002543 mouse prenatal http://www.ebi.ac.uk/efo/EFO_0004401 Theiler stage 9 http://www.ebi.ac.uk/efo/EFO_0002543 mouse prenatal http://www.ebi.ac.uk/efo/EFO_0004402 Theiler stage 10 http://www.ebi.ac.uk/efo/EFO_0002543 mouse prenatal http://www.ebi.ac.uk/efo/EFO_0004403 Theiler stage 12 http://www.ebi.ac.uk/efo/EFO_0002543 mouse prenatal http://www.ebi.ac.uk/efo/EFO_0004404 Theiler stage 13 http://www.ebi.ac.uk/efo/EFO_0002543 mouse prenatal http://www.ebi.ac.uk/efo/EFO_0004405 Theiler stage 14 http://www.ebi.ac.uk/efo/EFO_0002543 mouse prenatal http://www.ebi.ac.uk/efo/EFO_0004406 Theiler stage 15 http://www.ebi.ac.uk/efo/EFO_0002543 mouse prenatal http://www.ebi.ac.uk/efo/EFO_0004407 Theiler stage 16 http://www.ebi.ac.uk/efo/EFO_0002543 mouse prenatal http://www.ebi.ac.uk/efo/EFO_0004408 Theiler stage 18 http://www.ebi.ac.uk/efo/EFO_0002543 mouse prenatal http://www.ebi.ac.uk/efo/EFO_0004409 Theiler stage 19 http://www.ebi.ac.uk/efo/EFO_0002543 mouse prenatal http://www.ebi.ac.uk/efo/EFO_0004410 Theiler stage 20 http://www.ebi.ac.uk/efo/EFO_0002543 mouse prenatal http://www.ebi.ac.uk/efo/EFO_0004411 Theiler stage 23 http://www.ebi.ac.uk/efo/EFO_0002543 mouse prenatal http://www.ebi.ac.uk/efo/EFO_0004412 Theiler stage 25 http://www.ebi.ac.uk/efo/EFO_0002543 mouse prenatal http://purl.obolibrary.org/obo/SO_0001217 protein_coding_gene http://purl.obolibrary.org/obo/SO_0000704 gene http://purl.obolibrary.org/obo/SO_0001263 ncRNA_gene http://purl.obolibrary.org/obo/SO_0000704 gene http://purl.obolibrary.org/obo/BFO_0000001 entity http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://purl.obolibrary.org/obo/RO_0000079 function of http://purl.obolibrary.org/obo/RO_0000052 inheres in is function of a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000080 quality of http://purl.obolibrary.org/obo/RO_0000052 inheres in quality_of a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000085 has function http://purl.obolibrary.org/obo/RO_0000053 bearer of has_function a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000086 has quality http://purl.obolibrary.org/obo/RO_0000053 bearer of has_quality a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0002350 member of http://purl.obolibrary.org/obo/BFO_0000050 part of member part of is member of is a mereological relation between a item and a collection. http://purl.obolibrary.org/obo/RO_0002218 has active participant http://purl.obolibrary.org/obo/RO_0000057 has participant has agent x has participant y if and only if x realizes some active role that inheres in y http://purl.obolibrary.org/obo/RO_0000087 has role http://purl.obolibrary.org/obo/RO_0000053 bearer of has_role a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000081 role of http://purl.obolibrary.org/obo/RO_0000052 inheres in role_of a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0002217 actively participates in http://purl.obolibrary.org/obo/RO_0000056 participates in agent in x actively participates in y if and only if x participates in y and x realizes some active role http://purl.obolibrary.org/obo/pato#increased_in_magnitude_relative_to increased_in_magnitude_relative_to http://purl.obolibrary.org/obo/pato#different_in_magnitude_relative_to different_in_magnitude_relative_to q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. 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/OBI_0000293 has_specified_input http://purl.obolibrary.org/obo/RO_0000057 has participant A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. http://purl.obolibrary.org/obo/OBI_0000299 has_specified_output http://purl.obolibrary.org/obo/RO_0000057 has participant A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. http://purl.obolibrary.org/obo/OBI_0000312 is_specified_output_of http://purl.obolibrary.org/obo/RO_0000056 participates in A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. http://purl.obolibrary.org/obo/OBI_0000643 has grain http://purl.obolibrary.org/obo/BFO_0000051 has part the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car. http://purl.obolibrary.org/obo/OBI_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_0002351 has member http://purl.obolibrary.org/obo/BFO_0000051 has part has member is a mereological relation between a collection and an item. http://purl.obolibrary.org/obo/cl#has_high_plasma_membrane_amount has_high_plasma_membrane_amount http://purl.obolibrary.org/obo/RO_0002104 has plasma membrane part A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). http://purl.obolibrary.org/obo/cl#has_low_plasma_membrane_amount has_low_plasma_membrane_amount http://purl.obolibrary.org/obo/RO_0002104 has plasma membrane part A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). http://purl.obolibrary.org/obo/BCGO_0000022 produces_low_amount http://purl.obolibrary.org/obo/RO_0003000 produces a produces b if some process that occurs_in a has_output b and amount of b is low relative to normal cases, where a and b are material entities. Examples: defective beta ccell line produces less amount of insulin http://purl.obolibrary.org/obo/BCGO_0000023 produces_high_amount http://purl.obolibrary.org/obo/RO_0003000 produces a produces b if some process that occurs_in a has_output b and amount of b is high relative to generally cases, where a and b are material entities. http://purl.obolibrary.org/obo/BCGO_0000169 is about organism species http://purl.obolibrary.org/obo/IAO_0000136 is about relates an information artifact to the species of an organism that it is about. http://purl.obolibrary.org/obo/BCGO_0000171 is about genotype http://purl.obolibrary.org/obo/IAO_0000136 is about relates an information artifact to the genotype of an organism that it is about. http://purl.obolibrary.org/obo/BCGO_0000172 is about cell type http://purl.obolibrary.org/obo/IAO_0000136 is about relates an information artifact to the type of a cell that it is about. http://purl.obolibrary.org/obo/BCGO_0000173 is about cell line http://purl.obolibrary.org/obo/IAO_0000136 is about relates an information artifact to the cell line that it is about. http://purl.obolibrary.org/obo/BCGO_0000174 is about tissue http://purl.obolibrary.org/obo/IAO_0000136 is about relates an information artifact to the tissue of an organism that it is about. http://purl.obolibrary.org/obo/BCGO_0000178 is about strain http://purl.obolibrary.org/obo/IAO_0000136 is about relates an information artifact to the strain of an organism that it is about. http://purl.obolibrary.org/obo/BCGO_0000179 is about phenotype http://purl.obolibrary.org/obo/IAO_0000136 is about relates an information artifact to the phenotype born by an organism that it is about. http://purl.obolibrary.org/obo/RO_0002104 has plasma membrane part http://purl.obolibrary.org/obo/BFO_0000051 has part Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. http://purl.obolibrary.org/obo/RO_0002087 immediately preceded by http://purl.obolibrary.org/obo/BFO_0000062 preceded by starts_at_end_of http://purl.obolibrary.org/obo/RO_0002090 immediately precedes http://purl.obolibrary.org/obo/BFO_0000063 precedes meets http://purl.obolibrary.org/obo/BCGO_0000180 is about development stage http://purl.obolibrary.org/obo/IAO_0000136 is about http://purl.obolibrary.org/obo/BCGO_0000181 is about treatment http://purl.obolibrary.org/obo/IAO_0000136 is about 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_0002203 develops into http://purl.obolibrary.org/obo/RO_0002387 has potential to develop into 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 a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000053 bearer of is bearer of a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000056 participates in participates_in a relation between a continuant and a process, in which the continuant is somehow involved in the process http://purl.obolibrary.org/obo/RO_0000057 has participant has_participant a relation between a process and a continuant, in which the continuant is somehow involved in the process http://purl.obolibrary.org/obo/RO_0001000 derives from derives_from a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity http://purl.obolibrary.org/obo/RO_0001001 derives into derives_into a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity http://purl.obolibrary.org/obo/RO_0001015 location of location_of a relation between two independent continuants, the location and the target, in which the target is entirely within the location http://purl.obolibrary.org/obo/RO_0002000 2D boundary of is boundary of a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity http://purl.obolibrary.org/obo/RO_0002002 has 2D boundary has_2D_boundary a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity http://purl.obolibrary.org/obo/RO_0001025 located in located_in a relation between two independent continuants, the target and the location, in which the target is entirely within the location http://purl.obolibrary.org/obo/BFO_0000051 has part has_part a core relation that holds between a whole and its part http://purl.obolibrary.org/obo/BFO_0000050 part of part_of a core relation that holds between a part and its whole http://purl.obolibrary.org/obo/BFO_0000066 occurs in unfolds_in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t http://purl.obolibrary.org/obo/RO_0002215 capable of has function realized in A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. http://purl.obolibrary.org/obo/pato#different_in_magnitude_relative_to different_in_magnitude_relative_to q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. http://purl.obolibrary.org/obo/pato#has_cross_section has_cross_section s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. http://purl.obolibrary.org/obo/BFO_0000067 contains process [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t http://purl.obolibrary.org/obo/IAO_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_0000646 supplies A relation between an organisation or person and a material entity who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner. http://purl.obolibrary.org/obo/OBI_0000647 has_supplier A relation between a material entity and an organisation or person who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner. http://purl.obolibrary.org/obo/OBI_0000833 objective_achieved_by This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. http://purl.obolibrary.org/obo/OBI_0000846 is member of organization Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization. http://purl.obolibrary.org/obo/OBI_0001937 has specified value A relation between a value specification and a number that quantifies it. http://purl.obolibrary.org/obo/RO_0000058 is concretized as A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. http://purl.obolibrary.org/obo/RO_0000059 concretizes A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. http://purl.obolibrary.org/obo/RO_0002202 develops from x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y http://purl.obolibrary.org/obo/RO_0003000 produces a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. http://purl.obolibrary.org/obo/BCGO_0000015 has_genetic_background_of strain a has genetic backgroud as strain b is that strain a is derived from strain b and genetic make-up (all its alleles at all loci) of strain a is same to strain b except the mutated gene of interest and a very small amount of other genetic material, generally from one or two other strains. For example, the genetic background of the mutant strains NOD.129S7(B6)-Rag1tm1Mom/J (003729) and NOD.Cg-Rag1tm1Mom Prf1tm1Sdz/SzJ (004848) is NOD. http://purl.obolibrary.org/obo/BCGO_0000024 not_produce a produces_no b if some process that occurs_in a and has_no_output b, where a and b are material entities. http://purl.obolibrary.org/obo/BCGO_0000066 has email address a instance-level relation between a person or an organization to an email address the person or organization has. http://purl.obolibrary.org/obo/BCGO_0000170 is denoted by is denoted by is an instance-level, relation obtaining between an entity to an information content entity that is created to specifically refer to something. It is the inverse relation of 'denotes'. http://purl.obolibrary.org/obo/BCGO_0000177 has gene member relates the member (a data item) of a gene list (a data set) to the gene that it is about. http://purl.obolibrary.org/obo/BCGO_0000182 has duration relates a process to a time-measurement-datum that represents the duration of the process http://purl.obolibrary.org/obo/BCGO_0000184 binding context relates a gene that has protein binding to the biological context in which that binding was identified. http://purl.obolibrary.org/obo/BCGO_0000185 differential expression context relates a gene that is differentially expressed to the biological context in which that differential expression was identified. http://purl.obolibrary.org/obo/BCGO_0000186 context of differential expression relates a biological context (e.g., cell, developmental stage, etc.) to a gene whose protein binding was identified in this specific context. http://purl.obolibrary.org/obo/BCGO_0000187 context of binding relates the context to a gene that protein binding is identified in this specific context http://purl.obolibrary.org/obo/RO_0002214 has prototype x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation. http://purl.obolibrary.org/obo/RO_0002387 has potential to develop into x has the potential to develop into y iff x develops into y or if x is capable of developing into y http://purl.obolibrary.org/obo/so_translates_to translates_to Inverse of translation _of. http://purl.obolibrary.org/obo/so_translation_of translation_of X is translation of Y if X is translated by ribosome to create Y. http://purl.obolibrary.org/obo/BFO_0000054 realized in realized_in http://purl.obolibrary.org/obo/BFO_0000062 preceded by preceded_by http://purl.obolibrary.org/obo/BFO_0000055 realizes http://purl.obolibrary.org/obo/BFO_0000063 precedes http://purl.obolibrary.org/obo/IAO_0000004 has measurement value http://purl.obolibrary.org/obo/RO_0003001 produced by http://purl.obolibrary.org/obo/RO_0002222 temporal relation http://purl.obolibrary.org/obo/cl#lacks_plasma_membrane_part lacks_plasma_membrane_part http://www.w3.org/2006/vcard/ns#familyName has last name http://purl.obolibrary.org/obo/cl#lacks_part lacks_part http://www.w3.org/2006/vcard/ns#givenName first name http://purl.obolibrary.org/obo/BCGO_0000063 has contact http://purl.obolibrary.org/obo/BCGO_0000064 has external resource http://purl.obolibrary.org/obo/BCGO_0000065 has external identifier http://purl.obolibrary.org/obo/BCGO_0000067 executes http://purl.obolibrary.org/obo/BCGO_0000072 has experimental factor http://purl.obolibrary.org/obo/BCGO_0000073 has experimental factor value http://purl.obolibrary.org/obo/BCGO_0000074 value of experimental factor http://purl.obolibrary.org/obo/BCGO_0000075 examines http://purl.obolibrary.org/obo/BCGO_0000099 associated PubMed ID http://purl.obolibrary.org/obo/BCGO_0000175 has NCBI gene id http://purl.obolibrary.org/obo/BCGO_0000176 differential expression pattern http://purl.obolibrary.org/obo/BCGO_0000183 has concentration http://purl.obolibrary.org/obo/CLO_0000167 has disease