{ "3dmet": { "deprecated": true, "description": "3DMET is a database collecting three-dimensional structures of natural metabolites.", "example": "B00162", "homepage": "http://www.3dmet.dna.affrc.go.jp/", "keywords": [ "chemical", "life science", "metabolite", "metabolomics", "structure" ], "mappings": { "biocontext": "3DMET", "edam": "2635", "fairsharing": "FAIRsharing.5ab0n7", "integbio": "nbdc00351", "miriam": "3dmet", "n2t": "3dmet", "prefixcommons": "3dmet", "wikidata": "P2796" }, "name": "3D Metabolites", "pattern": "^B\\d{5}$", "preferred_prefix": "3dmet", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/addgene:$1" } ], "publications": [ { "doi": "10.1093/nar/gku893", "pmc": "PMC4384007", "pubmed": "25392412", "title": "The Addgene repository: an international nonprofit plasmid and data resource", "year": 2014 }, { "doi": "10.1038/505272a", "pubmed": "24429608", "title": "Repositories share key research tools", "year": 2014 }, { "doi": "10.1038/nbt.2177", "pubmed": "22491276", "title": "Addgene provides an open forum for plasmid sharing", "year": 2012 } ], "twitter": "Addgene", "uri_format": "http://addgene.org/$1" }, "adms": { "contact": { "email": "bert.van.nuffelen@tenforce.com", "github": "bertvannuffelen", "name": "Bert Van Nuffelen" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A vocabulary for describing semantic assets, defined as highly reusable metadata (e.g. XML1 schemata, generic data models) and reference data (e.g. code lists, taxonomies, dictionaries, vocabularies).", "example": "Asset", "homepage": "http://www.w3.org/ns/adms", "keywords": [ "metadata" ], "license": "CC-BY-4.0", "mappings": { "lov": "adms" }, "name": "Asset Description Metadata Schema Vocabulary", "preferred_prefix": "adms", "repository": "https://github.com/SEMICeu/ADMS/", "uri_format": "http://www.w3.org/ns/adms#$1" }, "ado": { "contact": { "email": "alpha.tom.kodamullil@scai.fraunhofer.de", "github": "akodamullil", "name": "Alpha Tom Kodamullil", "orcid": "0000-0001-9896-3531" }, "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "depends_on": [ "bfo" ], "description": "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, foundamentally structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelational entities that demonstrate the nextwork of the understanding on Alzheimer's disease and can be readily applied for text mining.", "download_owl": "http://purl.obolibrary.org/obo/ado.owl", "example": "0000001", "homepage": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO", "keywords": [ "alzheimer's disease", "health science", "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "ADO", "bioportal": "ADO", "fairsharing": "FAIRsharing.ckd4rf", "obofoundry": "ado", "ols": "ado", "ontobee": "ADO" }, "name": "Alzheimer's Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "ADO", "publications": [ { "doi": "10.1016/j.jalz.2013.02.009", "pubmed": "23830913", "title": "ADO: a disease ontology representing the domain knowledge specific to Alzheimer's disease", "year": 2013 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/ADO_$1", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1098" ], "repository": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO", "uri_format": "http://purl.obolibrary.org/obo/ADO_$1", "version": "2023-09-20" }, "adw": { "contact": { "email": "adw_geeks@umich.edu", "name": "Animal Diversity Web technical staff" }, "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "deprecated": true, "description": "Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology.", "download_owl": "http://aber-owl.net/media/ontologies/ADW/2/adw.owl", "example": "Lycalopex_vetulus", "homepage": "http://www.animaldiversity.org", "keywords": [ "anatomy", "life science", "obo", "ontology", "taxonomic classification" ], "mappings": { "aberowl": "ADW", "agroportal": "ADW", "biocontext": "ADW", "bioportal": "ADW", "fairsharing": "FAIRsharing.t9fvdn", "miriam": "adw", "n2t": "adw", "obofoundry": "adw" }, "name": "Animal natural history and life history", "pattern": "^[A-Z_a-z]+$", "preferred_prefix": "ADW", "rdf_uri_format": "http://purl.obolibrary.org/obo/ADW_$1", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1098" ], "uri_format": "https://animaldiversity.org/accounts/$1" }, "aeo": { "appears_in": [ "ehdaa2" ], "contact": { "email": "J.Bard@ed.ac.uk", "name": "Jonathan Bard" }, "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "deprecated": true, "description": "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology", "download_obo": "http://purl.obolibrary.org/obo/aeo.obo", "download_owl": "http://purl.obolibrary.org/obo/aeo.owl", "example": "0001017", "homepage": "https://github.com/obophenotype/human-developmental-anatomy-ontology/", "keywords": [ "anatomy", "life science", "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "AEO", "bartoc": "181", "biocontext": "AEO", "bioportal": "AEO", "fairsharing": "FAIRsharing.93ee19", "obofoundry": "aeo", "ols": "aeo", "ontobee": "AEO" }, "name": "Anatomical Entity Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "AEO", "publications": [ { "doi": "10.3389/fgene.2012.00018", "pmc": "PMC3278863", "pubmed": "22347883", "title": "The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues and Organs", "year": 2012 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/AEO_$1", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1098" ], "repository": "https://github.com/obophenotype/human-developmental-anatomy-ontology", "synonyms": [ "AEO_RETIRED" ], "uri_format": "http://purl.obolibrary.org/obo/AEO_$1", "version": "2014-12-05" }, "aeon": { "contact": { "email": "Philip.Stroemert@tib.eu", "github": "StroemPhi", "name": "Philip Strömert", "orcid": "0000-0002-1595-3213" }, "contributor": { "email": "Philip.Stroemert@tib.eu", "github": "StroemPhi", "name": "Philip Strömert", "orcid": "0000-0002-1595-3213" }, "description": "The academic event ontology, currently still in development and thus unstable, is an OBO compliant reference ontology for describing academic events such as conferences, workshops or seminars and their series. It is being developed as part of the [ConfIDent project](https://projects.tib.eu/confident/) to allow RDF representations of the academic events and series stored and curated in the [ConfIDent platform](https://www.confident-conference.org/index.php/main_page).", "download_owl": "https://raw.githubusercontent.com/tibonto/aeon/main/aeon.owl", "example": "0000001", "github_request_issue": 617, "homepage": "https://tibonto.github.io/aeon/", "keywords": [ "ontology" ], "license": "CC-BY-4.0", "name": "Academic Event Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "aeon", "repository": "https://github.com/tibonto/aeon", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://purl.obolibrary.org/obo/AEON_$1" }, "aero": { "contact": { "email": "mcourtot@gmail.com", "name": "Melanie Courtot", "orcid": "0000-0002-9551-6370" }, "contributor_extras": [ { "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "deprecated": true, "description": "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events", "download_owl": "http://purl.obolibrary.org/obo/aero.owl", "example": "0000125", "homepage": "http://purl.obolibrary.org/obo/aero", "keywords": [ "adverse reaction", "biomedical science", "electronic health record", "health science", "medicine", "obo", "ontology", "preclinical studies" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "AERO", "biocontext": "AERO", "bioportal": "AERO", "fairsharing": "FAIRsharing.rycy2x", "obofoundry": "aero", "ols": "aero" }, "name": "Adverse Event Reporting Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "AERO", "rdf_uri_format": "http://purl.obolibrary.org/obo/AERO_$1", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1098" ], "uri_format": "http://purl.obolibrary.org/obo/AERO_$1" }, "affy.probeset": { "description": "An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration.", "example": "243002_at", "homepage": "http://www.affymetrix.com/", "mappings": { "biocontext": "AFFY.PROBESET", "miriam": "affy.probeset", "n2t": "affy.probeset", "togoid": "AffyProbeset" }, "name": "Affymetrix Probeset", "pattern": "^\\d{4,}((_[asx])?_at)$", "preferred_prefix": "affy.probeset", "providers": [ { "code": "CURATOR_REVIEW", "description": "Bio2RDF", "homepage": "http://cu.affymetrix.bio2rdf.org/fct/", "name": "Bio2RDF", "uri_format": "http://cu.affymetrix.bio2rdf.org/describe/?url=http://bio2rdf.org/affymetrix:$1" } ], "uri_format": "https://www.affymetrix.com/LinkServlet?probeset=$1" }, "afo": { "contact": { "email": "more.info@allotrope.org", "name": "Allotrope Foundation" }, "description": "Allotrope Merged Ontology Suite", "download_owl": "http://purl.allotrope.org/voc/afo/merged/REC/2024/06/merged-without-qudt-and-inferred", "homepage": "https://www.allotrope.org/", "keywords": [ "agricultural engineering", "agriculture", "biology", "environmental science", "food", "food chemistry", "forest management", "ontology", "veterinary medicine" ], "mappings": { "aberowl": "AFO", "bioportal": "AFO", "fairsharing": "FAIRsharing.595710", "ols": "afo", "ontobee": "AFO" }, "name": "Allotrope Merged Ontology Suite", "no_own_terms": true, "preferred_prefix": "afo", "version": "2024/06" }, "afpo": { "contact": { "email": "mcmelek@msn.com", "github": "Melek-C", "name": "Melek Chaouch", "orcid": "0000-0001-5868-4204" }, "description": "AfPO is an ontology that can be used in the study of diverse populations across Africa. It brings together publicly available demographic, anthropological and genetic data relating to African people in a standardised and structured format. The AfPO can be employed to classify African study participants comprehensively in prospective research studies. It can also be used to classify past study participants by mapping them using a language or ethnicity identifier or synonyms.", "download_json": "http://purl.obolibrary.org/obo/afpo.json", "download_obo": "http://purl.obolibrary.org/obo/afpo.obo", "download_owl": "http://purl.obolibrary.org/obo/afpo.owl", "example": "0000440", "homepage": "https://github.com/h3abionet/afpo", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "AFPO", "bioportal": "AFPO", "obofoundry": "afpo", "ontobee": "AfPO" }, "name": "African Population Ontology", "preferred_prefix": "AfPO", "rdf_uri_format": "http://purl.obolibrary.org/obo/AfPO_$1", "repository": "https://github.com/h3abionet/afpo", "uri_format": "http://purl.obolibrary.org/obo/AfPO_$1" }, "aftol.category": { "contact": { "email": "davem@umn.edu", "name": "David J. McLaughlin" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Categories in the AFTOL database", "example": "229", "homepage": "https://aftol.umn.edu", "name": "Assembling the Fungal Tree of Life - Category", "preferred_prefix": "aftol.category", "uri_format": "https://aftol.umn.edu/glossary?category=$1" }, "aftol.taxonomy": { "contact": { "email": "davem@umn.edu", "name": "David J. McLaughlin" }, "contributor_extras": [ { "email": "laylamichan@ciencias.unam.mx", "github": "lmichan", "name": "Layla Michán Aguirre", "orcid": "0000-0002-5798-662X" } ], "description": "The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species.", "example": "959", "homepage": "https://aftol.umn.edu", "mappings": { "biocontext": "AFTOL.TAXONOMY", "miriam": "aftol.taxonomy", "n2t": "aftol.taxonomy" }, "name": "Assembling the Fungal Tree of Life - Taxonomy", "pattern": "^\\d+$", "preferred_prefix": "aftol.taxonomy", "uri_format": "http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1" }, "agilent.probe": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This is the Agilent SurePrint G3 Human GE v2 8x60k Microarray, Agilent design ID 039494, GridName 039494_D_F_20120628. Probe layout is 1 x 1 x 384 rows x 164 cols, which is different from a similar ADF A-GEOD-16699 (1 x 1 x 328 rows x 192 cols). Version 2 of this array contains long intergenic non-coding RNA (lincRNA) probes designed to the human catalog of lincRNAs from the Broad Institute, along with an update of mRNA content when compared to version 1. Probes were designed using GRCh37 assembly of the human genome. Annotation of probes came from the following database: RefSeq Build 50, Ensembl Release 52, Unigene Build 216, GenBank (April 2009), Broad Institute Human lincRNA catalog (Nov 2011), Broad Institute TUCP transcripts catalog (Nov 2011). Probe annotation was taken from A-GEOD-16699.", "example": "A_24_P98555", "homepage": "https://www.ebi.ac.uk/arrayexpress/files/A-MEXP-2320/A-MEXP-2320.adf.txt", "keywords": [ "transcriptomics" ], "name": "Agilent Probe", "pattern": "^A_\\d+_.+$", "preferred_prefix": "agilent.probe", "references": [ "http://www.cs.tau.ac.il/cgi-bin/cgiwrap/click/get.cgi/conversionFiles/conversion_human_14850_agilent2entrez.txt" ] }, "agricola": { "contact": { "email": "judith.blake@jax.org", "github": "judyblake", "name": "Judith A Blake", "orcid": "0000-0001-8522-334X" }, "contributor_extras": [ { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "description": "AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century.", "example": "50018", "homepage": "http://agricola.nal.usda.gov/", "mappings": { "biocontext": "AGRICOLA", "go": "AGRICOLA_ID", "miriam": "agricola", "n2t": "agricola", "uniprot": "DB-0266" }, "name": "Agricultural Online Access", "pattern": "^\\d+$", "preferred_prefix": "agricola", "publications": [ { "doi": "10.1093/nar/gkz813", "pmc": "PMC6943066", "pubmed": "31552413", "title": "Alliance of Genome Resources Portal: unified model organism research platform", "year": 2020 } ], "references": [ "https://github.com/biopragmatics/bioregistry/pull/1098" ], "synonyms": [ "AGR", "AGRICOLA_ID" ], "uri_format": "https://agricola.nal.usda.gov/vwebv/holdingsInfo?bibId=$1" }, "agrkb": { "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "contributor": { "github": "sierra-moxon", "name": "Sierra Moxon", "orcid": "0000-0002-8719-7760" }, "description": "The [Alliance of Genome Resources](https://www.alliancegenome.org/about-us) creates identifiers for several biological entity types including genes, other sequence features, constructs, morpholinos, TALENs, CRISPRs, variants, alleles, genotypes, strains, environments and experiments, phenotype annotations, expression annotations, disease annotations, interactions, and variant annotations.\n\nThe Alliance of Genome Resources was founded by the following Model Organism databases and the Gene Ontology Consortium and distributes high-quality, curated knowledge about several model organisms in a single, unified location:\n\n- [ZFIN](https://zfin.org) - Zebrafish Information Network\n- [WormBase](https://wormbase.org)\n- [MGI](https://www.mgi.org) - Mouse Genome Informatics\n- [RGD](https://rgd.mcw.edu) - Rat Genome Database\n- [SGD](https://www.yeastgenome.org) - Saccharomyces Genome Database\n- [FlyBase](https://flybase.org)\n- [Xenbase](https://www.xenbase.org)", "example": "100000000000001", "github_request_issue": 359, "homepage": "https://www.alliancegenome.org", "keywords": [ "model organism database" ], "mappings": { "biolink": "AGRKB" }, "name": "Alliance of Genome Resources Knowledge Base", "pattern": "^[1-9][0-9]{14}$", "preferred_prefix": "agrkb", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.alliancegenome.org/accession/$1" }, "agro": { "contact": { "email": "m.a.laporte@cgiar.org", "github": "marieALaporte", "name": "Marie-Angélique Laporte", "orcid": "0000-0002-8461-9745" }, "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "depends_on": [ "bfo", "envo", "foodon", "go", "iao", "ncbitaxon", "obi", "pato", "peco", "po", "ro", "to", "uo", "xco" ], "description": "AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities", "download_obo": "https://raw.githubusercontent.com/KrishnaTO/agro/master/agro.obo", "download_owl": "http://purl.obolibrary.org/obo/agro.owl", "example": "00020007", "homepage": "https://github.com/AgriculturalSemantics/agro", "keywords": [ "agriculture", "agronomy", "cropping systems", "farming systems research", "obo", "ontology", "plant breeding" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "AGRO", "agroportal": "AGRO", "biocontext": "AGRO", "bioportal": "AGRO", "fairsharing": "FAIRsharing.m40bhw", "obofoundry": "agro", "ols": "agro", "ontobee": "AGRO" }, "name": "Agronomy Ontology", "pattern": "^\\d{8}$", "preferred_prefix": "AGRO", "rdf_uri_format": "http://purl.obolibrary.org/obo/AGRO_$1", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1098" ], "repository": "https://github.com/AgriculturalSemantics/agro", "uri_format": "http://purl.obolibrary.org/obo/AGRO_$1", "version": "2022-11-02" }, "agrovoc": { "banana": "c_", "contact": { "email": "agrovoc@fao.org", "name": "AGROVOC Team" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is the largest Linked Open Data set about agriculture available for public use and its greatest impact is through providing the access and visibility of data across domains and languages.", "example": "2842", "homepage": "https://data.apps.fao.org/catalog/organization/agrovoc", "keywords": [ "agriculture", "botany", "data management", "environmental science", "fisheries science", "food", "forest management", "nutritional science", "thesaurus" ], "mappings": { "agroportal": "AGROVOC", "bartoc": "305", "ecoportal": "AGROVOC", "fairsharing": "FAIRsharing.anpj91", "wikidata": "P8061" }, "name": "Agronomy Vocabulary", "pattern": "^[a-z0-9]+$", "preferred_prefix": "agrovoc", "publications": [ { "doi": "10.4060/cb2838en", "title": "AGROVOC", "year": 2021 }, { "doi": "10.3390/engproc2021009017", "title": "How Agricultural Digital Innovation Can Benefit from Semantics: The Case of the AGROVOC Multilingual Thesaurus", "year": 2021 }, { "doi": "10.1016/j.compag.2020.105965", "title": "AGROVOC: The linked data concept hub for food and agriculture", "year": 2022 } ], "rdf_uri_format": "http://aims.fao.org/aos/agrovoc/$1", "references": [ "http://agrovoc.uniroma2.it/latestAgrovoc/agrovoc_core.nt.zip", "http://agrovoc.uniroma2.it/latestAgrovoc/agrovoc_lod.nt.zip", "https://en.wikipedia.org/wiki/AGROVOC" ], "twitter": "FAOAIMS", "uri_format": "http://aims.fao.org/aos/agrovoc/c_$1" }, "agsc": { "contact": { "email": "srvoss@uky.edu", "name": "Stephen Randal Voss", "orcid": "0000-0002-8332-3176" }, "description": "The Ambystoma Genetic Stock Center (AGSC) maintains a breeding colony of Mexican axolotls (Ambystoma mexicanum) and distributes axolotl embryos, larvae, and adults to laboratories and classrooms throughout the United States and abroad. [from homepage]", "example": "100E", "homepage": "https://ambystoma.uky.edu/genetic-stock-center/", "keywords": [ "adult", "ambystoma", "embryo", "k-12 teacher", "larvae", "salamander" ], "mappings": { "rrid": "AGSC" }, "name": "Ambystoma Genetic Stock Center", "preferred_prefix": "agsc", "publications": [ { "pubmed": "16359543" } ], "uri_format": "https://scicrunch.org/resolver/RRID:AGSC_$1" }, "agsd": { "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "description": "A comprehensive catalogue of animal genome size data where haploid DNA contents (C-values, in picograms) are currently available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources.", "example": "4779", "homepage": "http://www.genomesize.com", "keywords": [ "dna", "genome", "life science" ], "mappings": { "fairsharing": "FAIRsharing.efp5v2", "prefixcommons": "agsd", "re3data": "r3d100012517" }, "name": "Animal Genome Size Database", "preferred_prefix": "agsd", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/agsd:$1" } ], "references": [ "https://github.com/biopragmatics/bioregistry/pull/1098" ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.genomesize.com/result_species.php?id=$1" }, "aio": { "contact": { "email": "MJoachimiak@lbl.gov", "github": "realmarcin", "name": "Marcin Pawel Joachimiak", "orcid": "0000-0001-8175-045X" }, "contributor": { "email": "lindsey.anderson@pnnl.gov", "github": "lnanderson", "name": "Lindsey N. Anderson", "orcid": "0000-0002-8741-7823" }, "description": "This ontology models classes and relationships describing deep learning networks, their component layers and activation functions, as well as potential biases.", "download_json": "https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/main/aio.json", "download_obo": "https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/main/aio.obo", "download_owl": "https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/main/aio.owl", "example": "Causal_Graphical_Model", "github_request_issue": 884, "homepage": "https://github.com/berkeleybop/artificial-intelligence-ontology", "keywords": [ "artificial intelligence", "computational biology", "hidden markov model", "knowledge representation", "machine learning", "natural language processing", "network model", "ontology" ], "mappings": { "aberowl": "AIO", "bioportal": "AIO", "fairsharing": "FAIRsharing.8d6247" }, "name": "The Artificial Intelligence Ontology", "preferred_prefix": "aio", "publications": [ { "doi": "10.48550/arxiv.2404.03044", "title": "The Artificial Intelligence Ontology: LLM-assisted construction of AI concept hierarchies", "year": 2024 } ], "repository": "https://github.com/berkeleybop", "reviewer": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://w3id.org/aio/$1" }, "aism": { "appears_in": [ "colao", "lepao" ], "contact": { "email": "entiminae@gmail.com", "github": "JCGiron", "name": "Jennifer C. Girón", "orcid": "0000-0002-0851-6883" }, "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "depends_on": [ "bfo", "bspo", "caro", "pato", "ro", "uberon" ], "description": "The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research.", "download_json": "http://purl.obolibrary.org/obo/aism.json", "download_obo": "http://purl.obolibrary.org/obo/aism.obo", "download_owl": "http://purl.obolibrary.org/obo/aism.owl", "example": "0000027", "homepage": "https://github.com/insect-morphology/aism", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "AISM", "bioportal": "AISM", "obofoundry": "aism", "ols": "aism", "ontobee": "AISM" }, "name": "Ontology for the Anatomy of the Insect SkeletoMuscular system", "pattern": "^\\d{7}$", "preferred_prefix": "AISM", "rdf_uri_format": "http://purl.obolibrary.org/obo/AISM_$1", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1098" ], "repository": "https://github.com/insect-morphology/aism", "uri_format": "http://purl.obolibrary.org/obo/AISM_$1", "version": "2024-06-20" }, "alfred": { "comment": "This resource doesn't exist on the web anymore", "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "deprecated": true, "description": "ALFRED has been designed to make allele frequency data on anthropologically defined human population samples readily available to the scientific community and to link these polymorphism data to the molecular genetics-human genome databases.", "example": "LO362836C", "homepage": "http://alfred.med.yale.edu", "keywords": [ "classification", "genome" ], "mappings": { "prefixcommons": "alfred" }, "name": "The ALlele FREquency Database", "preferred_prefix": "alfred", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/alfred:$1" } ], "publications": [ { "doi": "10.1093/nar/gkg043", "pmc": "PMC165490", "pubmed": "12519999", "title": "ALFRED: the ALelle FREquency Database. Update", "year": 2003 } ], "references": [ "https://github.com/biopragmatics/bioregistry/pull/1098" ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://alfred.med.yale.edu/alfred/recordinfo.asp?UNID=$1" }, "allergome": { "contact": { "email": "adriano.mari@allergome.org", "name": "Adriano Mari", "orcid": "0000-0002-9137-1442" }, "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "description": "Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources.", "example": "1948", "homepage": "http://www.allergome.org/", "keywords": [ "allergen", "biomedical science", "health science", "life science", "medicine" ], "mappings": { "biocontext": "ALLERGOME", "fairsharing": "FAIRsharing.w6cxgb", "integbio": "nbdc01708", "miriam": "allergome", "n2t": "allergome", "prefixcommons": "allergome", "uniprot": "DB-0160" }, "name": "Allergome", "pattern": "^\\d+$", "preferred_prefix": "allergome", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/allergome:$1" } ], "publications": [ { "doi": "10.1007/s11882-009-0055-9", "pubmed": "19671381", "title": "Allergen databases: current status and perspectives", "year": 2009 }, { "doi": "10.1016/j.cellimm.2007.02.012", "pubmed": "17434469", "title": "Bioinformatics applied to allergy: allergen databases, from collecting sequence information to data integration. The Allergome platform as a model", "year": 2007 }, { "pubmed": "17393720", "title": "Allergome: a unifying platform", "year": 2006 } ], "references": [ "https://github.com/biopragmatics/bioregistry/pull/1098" ], "uri_format": "http://www.allergome.org/script/dettaglio.php?id_molecule=$1" }, "alzforum.mutation": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "description": "Alzforum mutations is a repository of genes and rare variants associated with Alzheimer's disease.", "example": "app-d678n-tottori", "homepage": "https://www.alzforum.org/mutations", "keywords": [ "alzheimer's disease", "genes", "variants" ], "name": "Alzforum Mutations", "preferred_prefix": "alzforum.mutation", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1098" ], "synonyms": [ "Alzforum_mut" ], "uri_format": "https://www.alzforum.org/mutations/$1" }, "alzgene": { "contact": { "email": "bertram@helix.mgh.harvard.edu", "name": "Lars Bertram", "orcid": "0000-0002-0108-124X" }, "description": "The AlzGene database provides a comprehensive, unbiased and regularly updated field synopsis of genetic association studies performed in Alzheimer’s disease. In addition, hundreds of up-to-date meta-analyses are available for all eligible polymorphisms with sufficient data.", "example": "88", "homepage": "http://www.alzgene.org", "keywords": [ "gene" ], "mappings": { "prefixcommons": "alzgene" }, "name": "Alzheimer Gene Database", "preferred_prefix": "alzgene", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/alzgene:$1" } ], "publications": [ { "doi": "10.1038/ng1934", "pubmed": "17192785", "title": "Systematic meta-analyses of Alzheimer disease genetic association studies: the AlzGene database", "year": 2007 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.alzgene.org/geneoverview.asp?geneid=$1" }, "amoebadb": { "contact": { "email": "oharb@upenn.edu", "github": "ramobrah", "name": "Omar S. Harb", "orcid": "0000-0003-4446-6200" }, "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "description": "AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", "example": "EDI_244000", "homepage": "http://amoebadb.org/amoeba/", "keywords": [ "functional genomics", "genomics", "model organism" ], "mappings": { "biocontext": "AMOEBADB", "fairsharing": "FAIRsharing.swbypy", "integbio": "nbdc01207", "miriam": "amoebadb", "n2t": "amoebadb", "prefixcommons": "amoebadb", "re3data": "r3d100012457" }, "name": "AmoebaDB", "pattern": "^EDI_\\d+$", "preferred_prefix": "amoebadb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/amoebadb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkp941", "pmc": "PMC2808945", "pubmed": "19914931", "title": "EuPathDB: a portal to eukaryotic pathogen databases", "year": 2009 } ], "references": [ "https://github.com/biopragmatics/bioregistry/pull/1098" ], "twitter": "eupathdb", "uri_format": "https://amoebadb.org/amoeba/app/record/gene/$1" }, "amphx": { "contact": { "email": "hescriva@obs-banyuls.fr", "github": "hescriva", "name": "Hector Escriva", "orcid": "0000-0001-7577-5028" }, "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "depends_on": [ "uberon" ], "description": "An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum).", "download_obo": "http://purl.obolibrary.org/obo/amphx.obo", "download_owl": "http://purl.obolibrary.org/obo/amphx.owl", "example": "1000160", "homepage": "https://github.com/EBISPOT/amphx_ontology", "keywords": [ "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "AMPHX", "bioportal": "AMPHX", "obofoundry": "amphx", "ols": "amphx", "ontobee": "AMPHX" }, "name": "The Amphioxus Development and Anatomy Ontology", "pattern": "^\\d+$", "preferred_prefix": "AMPHX", "rdf_uri_format": "http://purl.obolibrary.org/obo/AMPHX_$1", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1098" ], "repository": "https://github.com/EBISPOT/amphx_ontology", "uri_format": "http://purl.obolibrary.org/obo/AMPHX_$1", "version": "2020-12-18" }, "antibodyregistry": { "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "description": "The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information.", "example": "493771", "homepage": "http://antibodyregistry.org/", "keywords": [ "antibody", "reagent", "unique identifiers" ], "mappings": { "biocontext": "ANTIBODYREGISTRY", "integbio": "nbdc01696", "miriam": "antibodyregistry", "n2t": "antibodyregistry", "rrid": "AB" }, "name": "Antibody Registry", "pattern": "^\\d{6}$", "preferred_prefix": "antibodyregistry", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1098" ], "uri_format": "http://antibodyregistry.org/AB_$1" }, "antweb": { "description": "AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures.", "example": "casent0106247", "homepage": "http://www.antweb.org/", "keywords": [ "anatomy", "classification", "life science" ], "mappings": { "biocontext": "ANTWEB", "fairsharing": "FAIRsharing.yk38tw", "integbio": "nbdc01710", "miriam": "antweb", "n2t": "antweb", "ncbi": "AntWeb", "prefixcommons": "antweb", "wikidata": "P5299" }, "name": "AntWeb", "pattern": "^casent\\d+(\\-D\\d+)?$", "preferred_prefix": "antweb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/antweb:$1" } ], "publications": [ { "doi": "10.1038/424242b", "pubmed": "12867945", "title": "Ants join online colony to boost conservation efforts", "year": 2003 } ], "uri_format": "http://www.antweb.org/specimen.do?name=$1" }, "anzctr": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "description": " The Australian New Zealand Clinical Trials Registry (ANZCTR) is an online register of clinical trials being undertaken in Australia, New Zealand and elsewhere. The ANZCTR includes trials from the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle, devices, treatment and rehabilitation strategies and complementary therapies.\n\nIn 2007 the ANZCTR was one of the first three trial registries to be recognised by the World Health Organization International Clinical Trials Registry Platform (WHO ICTRP) as a Primary Registry. WHO recognises registries as Primary Registries if they fulfil certain criteria with respect to data content, quality and validity, accessibility, unique identification, technical capacity and administration. The ANZCTR contributes data to the WHO ICTRP, which was developed in 2007. Trials from all ICTRP Primary Registries can be searched at: www.who.int/trialsearch. (from website)", "example": "ACTRN12623000498695", "homepage": "https://anzctr.org.au", "name": "Australian New Zealand Clinical Trials Registry", "pattern": "^ACTRN\\d+$", "preferred_prefix": "anzctr", "providers": [ { "code": "", "description": "", "homepage": "", "name": "", "uri_format": "https://anzctr.org.au/ACTRN$1.aspx" } ], "references": [ "https://github.com/biopragmatics/bioregistry/pull/1098" ], "synonyms": [ "ACTRN" ], "uri_format": "https://anzctr.org.au/Trial/Registration/TrialReview.aspx?ACTRN=$1" }, "aop": { "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "description": "International repository of Adverse Outcome Pathways.", "example": "98", "homepage": "https://aopwiki.org/", "mappings": { "biocontext": "AOP", "miriam": "aop", "n2t": "aop" }, "name": "AOPWiki", "pattern": "^\\d+$", "preferred_prefix": "aop", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1098" ], "uri_format": "https://aopwiki.org/aops/$1" }, "aop.events": { "description": "International repository of Adverse Outcome Pathways.", "example": "3", "homepage": "https://aopwiki.org/", "mappings": { "biocontext": "AOP.EVENTS", "miriam": "aop.events", "n2t": "aop.events" }, "name": "AOPWiki (Key Event)", "pattern": "^\\d+$", "preferred_prefix": "aop.events", "uri_format": "https://aopwiki.org/events/$1" }, "aop.relationships": { "description": "International repository of Adverse Outcome Pathways.", "example": "5", "homepage": "https://aopwiki.org/", "mappings": { "biocontext": "AOP.RELATIONSHIPS", "miriam": "aop.relationships", "n2t": "aop.relationships" }, "name": "AOPWiki (Key Event Relationship)", "pattern": "^\\d+$", "preferred_prefix": "aop.relationships", "uri_format": "https://aopwiki.org/relationships/$1" }, "aop.stressor": { "description": "International repository of Adverse Outcome Pathways.", "example": "9", "homepage": "https://aopwiki.org/", "mappings": { "biocontext": "AOP.STRESSOR", "miriam": "aop.stressor", "n2t": "aop.stressor" }, "name": "AOPWiki (Stressor)", "pattern": "^\\d+$", "preferred_prefix": "aop.stressor", "uri_format": "https://aopwiki.org/stressors/$1" }, "apaonto": { "contact": { "email": "awalker@apa.org", "name": "Alvin Walker", "orcid": "0000-0003-1082-8760" }, "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "description": "An ontology developed by the American Psychological Association (APA). Note that URIs in this ontology appear to have been generated with erroneous settings in Protege.", "download_owl": "http://aber-owl.net/media/ontologies/APAONTO/4/apaonto.owl", "example": "Abdomen", "homepage": "https://bioportal.bioontology.org/ontologies/APAONTO", "keywords": [ "behavior", "ontology", "psychology" ], "mappings": { "aberowl": "APAONTO", "bioportal": "APAONTO", "fairsharing": "FAIRsharing.gkw1w8" }, "name": "Psychology Ontology", "preferred_prefix": "apaonto", "references": [ "https://github.com/biopragmatics/bioregistry/issues/528", "https://github.com/biopragmatics/bioregistry/pull/1098" ], "uri_format": "http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1" }, "apd": { "contact": { "email": "gwang@unmc.edu", "name": "Guangshun Wang", "orcid": "0000-0002-4841-7927" }, "description": "The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides.", "example": "01001", "homepage": "http://aps.unmc.edu/AP/", "keywords": [ "biology", "protein" ], "mappings": { "biocontext": "APD", "fairsharing": "FAIRsharing.ctwd7b", "miriam": "apd", "n2t": "apd", "prefixcommons": "apd", "re3data": "r3d100012901" }, "name": "Antimicrobial Peptide Database", "pattern": "^\\d{5}$", "preferred_prefix": "apd", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/apd:$1" } ], "publications": [ { "doi": "10.1093/nar/gkv1278", "pmc": "PMC4702905", "pubmed": "26602694", "title": "APD3: the antimicrobial peptide database as a tool for research and education", "year": 2015 }, { "doi": "10.1093/nar/gkn823", "pmc": "PMC2686604", "pubmed": "18957441", "title": "APD2: the updated antimicrobial peptide database and its application in peptide design", "year": 2008 }, { "doi": "10.1093/nar/gkh025", "pmc": "PMC308759", "pubmed": "14681488", "title": "APD: the Antimicrobial Peptide Database", "year": 2004 } ], "uri_format": "http://aps.unmc.edu/AP/database/query_output.php?ID=$1" }, "aphidbase.transcript": { "contact": { "email": "fabrice.legeai@rennes.inra.fr", "name": "Fabrice Legeai", "orcid": "0000-0002-6472-4839" }, "description": "AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information.", "example": "ACYPI000159", "homepage": "http://www.aphidbase.com/aphidbase", "keywords": [ "genome" ], "mappings": { "biocontext": "APHIDBASE.TRANSCRIPT", "miriam": "aphidbase.transcript", "n2t": "aphidbase.transcript", "prefixcommons": "aphidbase" }, "name": "AphidBase Transcript", "pattern": "^ACYPI\\d{6}(-RA)?$", "preferred_prefix": "aphidbase.transcript", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/aphidbase:$1" } ], "publications": [ { "doi": "10.1111/j.1365-2583.2009.00930.x", "pmc": "PMC4372297", "pubmed": "20482635", "title": "AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome", "year": 2010 } ], "uri_format": "http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1" }, "apid.interactions": { "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "description": "APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. 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It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information.", "example": "AS000060", "homepage": "http://www.arachnoserver.org/", "keywords": [ "drug", "life science", "protein" ], "mappings": { "biocontext": "ARACHNOSERVER", "edam": "2578", "fairsharing": "FAIRsharing.c54ywe", "integbio": "nbdc01221", "miriam": "arachnoserver", "n2t": "arachnoserver", "prefixcommons": "arachnoserver", "re3data": "r3d100012902", "uniprot": "DB-0145" }, "name": "ArachnoServer", "pattern": "^AS\\d{6}$", "preferred_prefix": "arachnoserver", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/arachnoserver:$1" } ], "publications": [ { "doi": "10.1093/bioinformatics/btx661", "pubmed": "29069336", "title": "ArachnoServer 3.0: an online resource for automated discovery, analysis and annotation of spider toxins", "year": 2018 }, { "doi": "10.1093/nar/gkq1058", "pmc": "PMC3013666", "pubmed": "21036864", "title": "ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures", "year": 2010 } ], "references": [ "https://github.com/biopragmatics/bioregistry/pull/1141" ], "uri_format": "http://www.arachnoserver.org/toxincard.html?id=$1" }, "araport": { "contact": { "email": "hello@vivekkrish.com", "github": "vivekkrish", "name": "Vivek Krishnakuma", "orcid": "0000-0002-5227-0200" }, "description": "Website with general information about Arabidopsis and functionalities such as a genomic viewer", "example": "AT5G05330", "homepage": "https://www.araport.org/", "mappings": { "integbio": "nbdc02433", "miriam": "tair.name", "ncbi": "Araport", "pathguide": "768", "uniprot": "DB-0221" }, "name": "Arabidopsis Information Portal", "pattern": "^AT.G[0-9]{5}$", "preferred_prefix": "araport", "publications": [ { "doi": "10.1093/nar/gku1200", "pmc": "PMC4383980", "pubmed": "25414324", "title": "Araport: the Arabidopsis information portal", "year": 2014 } ], "uri_format": "https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1" }, "archdb": { "contact": { "email": "narcis.fernandez@gmail.com", "name": "Narcis Fernandez-Fuentes", "orcid": "0000-0002-6421-1080" }, "description": "ArchDB is a compilation of structural classifications of loops extracted from known protein structures. The structural classification is based on the geometry and conformation of the loop. The geometry is defined by four internal variables and the type of regular flanking secondary structures, resulting in 10 different loop types. Loops in ArchDB have been classified using an improved version (Espadaler et al.) of the original ArchType program published in 1997 by Oliva et al.", "example": "39421", "homepage": "http://sbi.imim.es/archdb", "keywords": [ "classification", "life science", "protein" ], "mappings": { "fairsharing": "FAIRsharing.tp9z4q", "integbio": "nbdc01795", "prefixcommons": "archdb" }, "name": "ArchDB", "preferred_prefix": "archdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/archdb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkt1189", "pmc": "PMC3964960", "pubmed": "24265221", "title": "ArchDB 2014: structural classification of loops in proteins", "year": 2013 }, { "doi": "10.1093/nar/gkh002", "pmc": "PMC308737", "pubmed": "14681390", "title": "ArchDB: automated protein loop classification as a tool for structural genomics", "year": 2004 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://sbi.imim.es/cgi-bin/archdb//loops.pl?loop=$1" }, "ardb": { "description": "The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes.", "example": "CAE46076", "homepage": "http://ardb.cbcb.umd.edu/", "mappings": { "biocontext": "ARDB", "miriam": "ardb", "n2t": "ardb" }, "name": "Antibiotic Resistance Genes Database", "pattern": "^[A-Z_]{3}[0-9]{4,}$", "preferred_prefix": "ardb", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1141" ], "uri_format": "http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=$1" }, "ark": { "banana": "ark", "contact": { "email": "jakkbl@gmail.com", "github": "jkunze", "name": "John Kunze", "orcid": "0000-0001-7604-8041" }, "contributor_extras": [ { "email": "jakkbl@gmail.com", "github": "jkunze", "name": "John Kunze", "orcid": "0000-0001-7604-8041" }, { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "description": "Archival Resource Keys (ARKs) serve as persistent identifiers, or stable, trusted references for information objects. Among other things, they aim to be web addresses (URLs) that don’t return 404 Page Not Found errors. The ARK Alliance is an open global community supporting the ARK infrastructure on behalf of research and scholarship. End users, especially researchers, rely on ARKs for long term access to the global scientific and cultural record. Since 2001 some 8.2 billion ARKs have been created by over 1000 organizations — libraries, data centers, archives, museums, publishers, government agencies, and vendors. They identify anything digital, physical, or abstract. ARKs are open, mainstream, non-paywalled, decentralized persistent identifiers that can be created by an organization as soon as it is registered with a NAAN (Name Assigning Authority Number). Once registered, an ARK organization can create unlimited numbers of ARKs and publicize them via the n2t.net global resolver or via their own local resolver.", "example": "/53355/cl010066723", "homepage": "https://arks.org", "keywords": [ "centrally registered identifier", "data management", "data retrieval", "subject agnostic" ], "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaThDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--c69281eac0647c6b7a664f0932bee0d5fd27781d/gold_boat_arka.png?disposition=inline", "mappings": { "biocontext": "ARK", "fairsharing": "FAIRsharing.f928f1", "miriam": "ark", "n2t": "ark" }, "mastodon": "arks_org@fosstodon.org", "name": "Archival Resource Key", "namespace_in_lui": true, "pattern": "^/*[0-9A-Za-z]+(?:/[\\w/.=*+@\\$-]*)?(?:\\?.*)?$", "preferred_prefix": "ark", "references": [ "https://n2t.net/e/about.html", "https://github.com/biopragmatics/bioregistry/pull/1141" ], "twitter": "ARKsInTheOpen", "uri_format": "http://n2t.net/ark:$1" }, "aro": { "appears_in": [ "scdo" ], "contact": { "email": "mcarthua@mcmaster.ca", "github": "agmcarthur", "name": "Andrew G. 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CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome.", "example": "icdom:8500_3", "homepage": "https://www.arraymap.org", "keywords": [ "bioinformatics", "biomedical science", "genomics", "life science" ], "mappings": { "biocontext": "ARRAYMAP", "fairsharing": "FAIRsharing.1fbc5y", "miriam": "arraymap", "n2t": "arraymap", "re3data": "r3d100012630" }, "name": "ArrayMap", "pattern": "^[\\w\\-:,]{3,64}$", "preferred_prefix": "arraymap", "publications": [ { "doi": "10.1093/nar/gkv1310", "pmc": "PMC4702916", "pubmed": "26615188", "title": "The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases", "year": 2015 }, { "doi": "10.1093/nar/gku1123", "pmc": "PMC4383937", "pubmed": "25428357", "title": "arrayMap 2014: an updated cancer genome resource", "year": 2014 }, { "doi": "10.1186/1471-2164-15-82", "pmc": "PMC3909908", "pubmed": "24476156", "title": "Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens", "year": 2014 }, { "doi": "10.1371/journal.pone.0036944", "pmc": "PMC3356349", "pubmed": "22629346", "title": "arrayMap: a reference resource for genomic copy number imbalances in human malignancies", "year": 2012 } ], "twitter": "progenetix", "uri_format": "https://www.arraymap.org/pgx:$1" }, "arxiv": { "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "description": "arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology.", "example": "0807.4956v1", "homepage": "https://arxiv.org/", "keywords": [ "bibliography", "preprints", "publishing" ], "mappings": { "bartoc": "20434", "biocontext": "ARXIV", "miriam": "arxiv", "n2t": "arxiv", "prefixcommons": "arxiv", "wikidata": "P818" }, "name": "arXiv", "pattern": "^(\\w+(\\-\\w+)?(\\.\\w+)?)?\\d{4,7}(\\.\\d+(v\\d+)?)?$", "preferred_prefix": "arxiv", "providers": [ { "code": "ar5iv", "description": "Articles from arXiv.org as responsive HTML5 web pages.", "homepage": "https://ar5iv.labs.arxiv.org/", "name": "ar5iv", "uri_format": "https://ar5iv.org/abs/$1" }, { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/asap:$1" } ], "publications": [ { "doi": "10.1093/nar/gkj164", "pmc": "PMC1347526", "pubmed": "16381899", "title": "ASAP: a resource for annotating, curating, comparing, and disseminating genomic data", "year": 2006 }, { "doi": "10.1093/nar/gkg125", "pmc": "PMC165572", "pubmed": "12519969", "title": "ASAP, a systematic annotation package for community analysis of genomes", "year": 2003 } ], "uri_format": "http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$1" }, "ascl": { "contact": { "email": "aallen@ascl.net", "name": "Alice Allen", "orcid": "0000-0003-3477-2845" }, "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "description": "The Astrophysics Source Code Library (ASCL) is a free online registry for software that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001).", "example": "1801.012", "homepage": "http://ascl.net/", "keywords": [ "astrophysics and astronomy" ], "mappings": { "biocontext": "ASCL", "fairsharing": "FAIRsharing.wb0txg", "miriam": "ascl", "n2t": "ascl", "re3data": "r3d100011865" }, "name": "Astrophysics Source Code Library", "pattern": "^[0-9\\.]+$", "preferred_prefix": "ascl", "publications": [ { "doi": "10.5334/jors.bv", "title": "Looking before Leaping: Creating a Software Registry", "year": 2015 } ], "twitter": "asclnet", "uri_format": "http://ascl.net/$1" }, "asin": { "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "description": "Almost every product on our site has its own ASIN, a unique code we use to identify it. For books, the ASIN is the same as the ISBN number, but for all other products a new ASIN is created when the item is uploaded to our catalogue.", "example": "0471491039", "homepage": "https://www.amazon.co.uk/gp/help/customer/display.html/277-3416785-8259466?ie=UTF8&nodeId=898182", "mappings": { "biocontext": "ASIN", "miriam": "asin", "n2t": "asin" }, "name": "Amazon Standard Identification Number", "pattern": "^[0-9]{10}$", "preferred_prefix": "asin", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1141" ], "uri_format": "https://amzn.com/$1" }, "aspgd.locus": { "description": "The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references gene information.", "example": "ASPL0000349247", "homepage": "http://www.aspgd.org/", "mappings": { "biocontext": "ASPGD.LOCUS", "biolink": "AspGD", "go": "AspGD_LOCUS", "miriam": "aspgd.locus", "n2t": "aspgd.locus" }, "name": "Aspergillus Genome Database", "pattern": "^[A-Za-z_0-9]+$", "preferred_prefix": "aspgd.locus", "uri_format": "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$1" }, "aspgd.protein": { "description": "The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references protein information.", "example": "ASPL0000349247", "homepage": "http://www.aspgd.org/", "mappings": { "biocontext": "ASPGD.PROTEIN", "miriam": "aspgd.protein", "n2t": "aspgd.protein" }, "name": "AspGD Protein", "pattern": "^[A-Za-z_0-9]+$", "preferred_prefix": "aspgd.protein", "uri_format": "http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=$1" }, "asrp": { "contact": { "email": "kasschau@cgrb.oregonstate.edu", "name": "Kristin D. Kasschau" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Arabidopsis Small RNA Project is a repository of data on Arabidopsis small RNA genes.", "example": "ASRP1423", "homepage": "https://asrp.danforthcenter.org/", "keywords": [ "genome", "regulation", "rna" ], "mappings": { "prefixcommons": "asrp" }, "name": "Arabidopsis Small RNA Project", "preferred_prefix": "asrp", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/asrp:$1" } ], "publications": [ { "doi": "10.1093/nar/gkm997", "pmc": "PMC2238918", "pubmed": "17999994", "title": "Update of ASRP: the Arabidopsis Small RNA Project database", "year": 2007 }, { "doi": "10.1093/nar/gki127", "pmc": "PMC540081", "pubmed": "15608278", "title": "ASRP: the Arabidopsis Small RNA Project Database", "year": 2005 } ], "uri_format": "http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html?ASRP_id=$1" }, "astd": { "comment": "This resource doesn't exist on the web anymore", "deprecated": true, "description": "Identifier of an object from the ASTD database.", "example": "ENSG00000136147", "homepage": "http://www.ebi.ac.uk/astd/", "keywords": [ "alternative splicing", "gene", "transcript" ], "mappings": { "edam": "2367", "prefixcommons": "astd" }, "name": "ASTD", "preferred_prefix": "astd", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/astd:$1" } ], "provides": "ensembl", "publications": [ { "doi": "10.1016/j.ygeno.2008.11.003", "pubmed": "19059335", "title": "ASTD: The Alternative Splicing and Transcript Diversity database", "year": 2008 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.ebi.ac.uk/astd/geneview.html?acc=$1" }, "atc": { "contact": { "email": "whocc@fhi.no", "name": "WHO Collaborating Centre for Drug Statistics Methodology" }, "description": "The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels.", "example": "A10BA02", "homepage": "http://www.whocc.no/atc_ddd_index/", "keywords": [ "anatomical therapeutic chemical code", "approved drug", "biomedical science", "chemical", "chemical biology", "drug", "ontology", "pharmacological family classification", "pharmacology" ], "mappings": { "aberowl": "ATC", "bartoc": "449", "biocontext": "ATC", "bioportal": "ATC", "edam": "3103", "fairsharing": "FAIRsharing.1a27h8", "hl7": "2.16.840.1.113883.6.73", "miriam": "atc", "n2t": "atc", "prefixcommons": "atc", "togoid": "Atc", "wikidata": "P267" }, "name": "Anatomical Therapeutic Chemical Classification System", "pattern": "^[A-Z](\\d+([A-Z]{1,2}(\\d+)?)?)?$", "preferred_prefix": "atc", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/atc:$1" } ], "publications": [ { "pubmed": "7368387", "title": "[New classification of drugs. The Medical list and the Drug catalogue are introduced in Anatomical--Therapeutic--Chemical classification code (ACT-code) in 1981]", "year": 1980 }, { "doi": "10.1007/s002280000200", "pubmed": "11214783", "title": "Different versions of the anatomical therapeutic chemical classification system and the defined daily dose--are drug utilisation data comparable?", "year": 2000 } ], "synonyms": [ "ATC_code", "ATTC" ], "uri_format": "http://www.whocc.no/atc_ddd_index/?code=$1" }, "atcc": { "description": "The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences.", "example": "11303", "example_extras": [ "ccl-1.4", "ccl-1" ], "homepage": "https://www.lgcstandards-atcc.org", "keywords": [ "epidemiology", "life science", "virology" ], "mappings": { "biocontext": "ATCC", "cellosaurus": "ATCC", "fairsharing": "FAIRsharing.j0ezpm", "hl7": "2.16.840.1.113883.6.77", "miriam": "atcc", "n2t": "atcc", "ncbi": "ATCC" }, "name": "American Type Culture Collection", "pattern": "^([a-zA-Z]+-)?\\d+(\\.\\d)?$", "preferred_prefix": "atcc", "synonyms": [ "ATCC", "ATCC number", "ATCC(dna)", "ATCC(in host)" ], "uri_format": "https://www.atcc.org/products/$1" }, "atcvet": { "description": "The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use.", "example": "QJ51RV02", "homepage": "http://www.whocc.no/atcvet/atcvet_index/", "mappings": { "biocontext": "ATCVET", "miriam": "atcvet", "n2t": "atcvet" }, "name": "Anatomical Therapeutic Chemical Vetinary", "pattern": "^Q[A-Z0-9]+$", "preferred_prefix": "atcvet", "uri_format": "http://www.whocc.no/atcvet/atcvet_index/?code=$1" }, "atfdb.family": { "description": "The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found.", "example": "CUT", "homepage": "http://www.bioguo.org/AnimalTFDB/family_index.php", "mappings": { "biocontext": "ATFDB.FAMILY", "miriam": "atfdb.family", "n2t": "atfdb.family" }, "name": "Animal TFDB Family", "pattern": "^\\w+$", "preferred_prefix": "atfdb.family", "uri_format": "http://www.bioguo.org/AnimalTFDB/family.php?fam=$1" }, "ato": { "contact": { "email": "david.c.blackburn@gmail.com", "name": "David Blackburn", "orcid": "0000-0002-1810-9886" }, "deprecated": true, "description": "Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource", "download_obo": "http://aber-owl.net/media/ontologies/ATO/2/ato.obo", "example": "0000000", "homepage": "http://www.amphibanat.org", "keywords": [ "obo", "ontology", "taxonomic classification", "taxonomy" ], "mappings": { "aberowl": "ATO", "biocontext": "ATO", "bioportal": "ATO", "fairsharing": "FAIRsharing.ayjdsm", "obofoundry": "ato" }, "name": "Amphibian taxonomy", "pattern": "^\\d{7}$", "preferred_prefix": "ATO", "rdf_uri_format": "http://purl.obolibrary.org/obo/ATO_$1", "uri_format": "http://purl.obolibrary.org/obo/ATO_$1" }, "atol": { "contact": { "email": "pylebail@rennes.inra.fr", "name": "Pierre-Yves LeBail", "orcid": "0000-0002-8310-5195" }, "description": "ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientificand educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production.", "download_owl": "http://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=atol.owl", "example": "0002233", "homepage": "http://www.atol-ontology.com", "keywords": [ "agriculture", "animal husbandry", "life science", "livestock", "ontology", "phenotype" ], "mappings": { "aberowl": "ATOL", "agroportal": "ATOL", "bioportal": "ATOL", "fairsharing": "FAIRsharing.wsfk5z", "ols": "atol" }, "name": "Animal Trait Ontology for Livestock", "pattern": "^\\d{7}$", "preferred_prefix": "atol", "uri_format": "http://opendata.inra.fr/ATOL/ATOL_$1", "version": "2018-09-13" }, "autdb": { "description": "AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder.", "example": "ADA", "homepage": "http://autism.mindspec.org/autdb/", "mappings": { "biocontext": "AUTDB", "miriam": "autdb", "n2t": "autdb" }, "name": "AutDB", "pattern": "^[A-Z]+[A-Z-0-9]{2,}$", "preferred_prefix": "autdb", "uri_format": "http://autism.mindspec.org/GeneDetail/$1" }, "authenticus": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "ID of a researcher in Authenticus website", "example": "P-008-GD6", "homepage": "https://www.authenticus.pt", "keywords": [ "person", "researcher" ], "mappings": { "wikidata": "P7834" }, "name": "Authenticus ID", "pattern": "^[A-Z]-[0-9A-Z]{3}-[0-9A-Z]{3}$", "preferred_prefix": "authenticus", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1171" ], "uri_format": "https://www.authenticus.pt/$1" }, "authorea.author": { "description": "identifier for an author on the Authorea writing service", "example": "229233", "homepage": "https://www.authorea.com", "mappings": { "wikidata": "P5039" }, "name": "Authorea author ID", "pattern": "^[1-9]\\d*$", "preferred_prefix": "authorea.author", "uri_format": "https://www.authorea.com/users/$1" }, "babelon": { "contact": { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" }, "contributor": { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" }, "description": "Babelon is a simple standard for managing ontology translations and language profiles. Profiles are managed as TSV files, see for example https://github.com/obophenotype/hpo-translations/tree/main/babelon. The goal of Babelon as a data model and vocabulary is to capture the minimum data required to capture important metadata such as confidence and precision of translation.", "example": "translation_language", "github_request_issue": 903, "homepage": "https://monarch-initiative.github.io/babelon/", "license": "MIT", "name": "Babelon", "pattern": "^[a-z][a-z0-9_]+[a-z0-9]$", "preferred_prefix": "babelon", "repository": "https://github.com/monarch-initiative/babelon", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://w3id.org/babelon/$1" }, "bacdive": { "contact": { "email": "contact@bacdive.de", "name": "Lorenz Reimer", "orcid": "0000-0002-7805-0660" }, "description": "BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity.", "example": "131392", "homepage": "https://bacdive.dsmz.de/", "keywords": [ "biodiversity", "life science", "microbiology" ], "mappings": { "fairsharing": "FAIRsharing.aSszvY", "miriam": "bacdive", "n2t": "bacdive", "re3data": "r3d100013060", "wikidata": "P2946" }, "name": "BacDive", "pattern": "^[0-9]+$", "preferred_prefix": "bacdive", "publications": [ { "doi": "10.1093/nar/gky879", "pmc": "PMC6323973", "pubmed": "30256983", "title": "BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis", "year": 2019 }, { "doi": "10.1016/j.jbiotec.2017.05.004", "pubmed": "28487186", "title": "Mobilization and integration of bacterial phenotypic data-Enabling next generation biodiversity analysis through the BacDive metadatabase", "year": 2017 }, { "doi": "10.1093/nar/gkv983", "pmc": "PMC4702946", "pubmed": "26424852", "title": "BacDive--The Bacterial Diversity Metadatabase in 2016", "year": 2015 }, { "doi": "10.1093/nar/gkt1058", "pmc": "PMC3965005", "pubmed": "24214959", "title": "BacDive--the Bacterial Diversity Metadatabase", "year": 2013 } ], "uri_format": "https://bacdive.dsmz.de/strain/$1" }, "bacmap.biog": { "description": "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information.", "example": "1050", "homepage": "http://bacmap.wishartlab.com/", "mappings": { "biocontext": "BACMAP.BIOG", "miriam": "bacmap.biog", "n2t": "bacmap.biog" }, "name": "BacMap Biography", "pattern": "^\\d+$", "preferred_prefix": "bacmap.biog", "uri_format": "http://bacmap.wishartlab.com/organisms/$1" }, "bacmap.map": { "description": "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information.", "example": "AP011135", "homepage": "http://bacmap.wishartlab.com/", "mappings": { "biocontext": "BACMAP.MAP", "miriam": "bacmap.map", "n2t": "bacmap.map" }, "name": "BacMap Map", "pattern": "^\\w+(\\_)?\\d+(\\.\\d+)?$", "preferred_prefix": "bacmap.map", "uri_format": "http://bacmap.wishartlab.com/maps/$1/index.html" }, "bactibase": { "contact": { "email": "ismail.fliss@fsaa.ulaval.ca", "name": "Ismail Fliss", "orcid": "0000-0002-8467-9414" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Bactibase is a database describing the physical and chemical properties of bacteriocins from gram-negative and gram-positive bacteria.", "example": "BAC045", "homepage": "http://bactibase.hammamilab.org", "keywords": [ "life science", "protein" ], "mappings": { "fairsharing": "FAIRsharing.5f5mfm", "prefixcommons": "bactibase", "re3data": "r3d100012755" }, "name": "Bactibase", "preferred_prefix": "bactibase", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/bactibase:$1" } ], "publications": [ { "doi": "10.1186/1471-2180-10-22", "pmc": "PMC2824694", "pubmed": "20105292", "title": "BACTIBASE second release: a database and tool platform for bacteriocin characterization", "year": 2010 }, { "doi": "10.1186/1471-2180-7-89", "pmc": "PMC2211298", "pubmed": "17941971", "title": "BACTIBASE: a new web-accessible database for bacteriocin characterization", "year": 2007 } ], "uri_format": "http://bactibase.hammamilab.org/$1" }, "bams": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "description": "BAMS (Brain Architectural Management System) describes vertebrate neuroinformatics data at four levels of organization: expressed molecules, neuron types and classes, brain regions, and networks of brain regions.", "homepage": "https://bams1.org", "name": "Brain Architecture Knowledge Management System Neuroanatomical Ontology", "preferred_prefix": "bams", "references": [ "https://www.frontiersin.org/articles/10.3389/neuro.11.002.2008/full" ] }, "bao": { "contact": { "email": "sschurer@med.miami.edu", "name": "Stephan Schurer" }, "description": "The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis.", "download_owl": "http://www.bioassayontology.org/bao/bao_complete.owl", "example": "0002989", "homepage": "http://bioassayontology.org", "keywords": [ "assay", "biochemistry", "biological process", "biomedical science", "cell", "chemical entity", "life science", "molecular entity", "ontology", "protein", "reagent", "target" ], "mappings": { "aberowl": "BAO", "biocontext": "BAO", "bioportal": "BAO", "fairsharing": "FAIRsharing.mye76w", "miriam": "bao", "n2t": "bao", "ols": "bao", "ontobee": "BAO" }, "name": "BioAssay Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "bao", "publications": [ { "doi": "10.1186/2041-1480-5-s1-s5", "pmc": "PMC4108877", "pubmed": "25093074", "title": "Evolving BioAssay Ontology (BAO): modularization, integration and applications", "year": 2014 }, { "doi": "10.1371/journal.pone.0049198", "pmc": "PMC3498356", "pubmed": "23155465", "title": "Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO)", "year": 2012 }, { "doi": "10.1186/1471-2105-12-257", "pmc": "PMC3149580", "pubmed": "21702939", "title": "BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results", "year": 2011 }, { "doi": "10:1371/journal.pone.0049198", "pubmed": "10", "title": "Digitoxin metabolism by rat liver microsomes", "year": 1975 } ], "repository": "https://github.com/BioAssayOntology/BAO", "synonyms": [ "BAO" ], "uri_format": "http://www.bioassayontology.org/bao#BAO_$1", "version": "2.8.11" }, "bartoc": { "contact": { "email": "voss@gbv.de", "github": "nichtich", "name": "Jakob Voß", "orcid": "0000-0002-7613-4123" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "email": "voss@gbv.de", "github": "nichtich", "name": "Jakob Voß", "orcid": "0000-0002-7613-4123" } ], "description": "The Basic Register of Thesauri, Ontologies & Classifications (BARTOC) is a database of Knowledge Organization Systems and KOS related registries.\nThe main goal of BARTOC is to list as many Knowledge Organization Systems as possible at one place in order to achieve greater visibility, highlight their features, make them searchable and comparable, and foster knowledge sharing. BARTOC includes any kind of KOS from any subject area, in any language, any publication format, and any form of accessibility. BARTOC’s search interface is available in 20 European languages and provides two search options: Basic Search by keywords, and Advanced Search by taxonomy terms. A circle of editors has gathered around BARTOC from all across Europe and BARTOC has been approved by the International Society for Knowledge Organization (ISKO).", "example": "241", "homepage": "https://bartoc.org", "keywords": [ "knowledge and information systems", "ontology and terminology" ], "license": "PDDL 1.0", "mappings": { "bartoc": "2054", "fairsharing": "FAIRsharing.f1777e", "wikidata": "P2689" }, "name": "Basic Register of Thesauri, Ontologies & Classifications", "owners": [ { "name": "Verbundzentrale des GBV", "partnered": false, "ror": "048vdhs48" } ], "pattern": "^[1-9][0-9]*$", "preferred_prefix": "bartoc", "rdf_uri_format": "http://bartoc.org/en/node/$1", "references": [ "https://github.com/biopragmatics/bioregistry/issues/783" ], "repository": "https://github.com/gbv/bartoc.org", "uri_format": "https://bartoc.org/en/node/$1" }, "bbkg": { "description": "Blue Brain Project's published data as knowledge graphs and Web Studios.", "example": "topological-sampling/studios/f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a", "homepage": "https://portal.bluebrain.epfl.ch", "mappings": { "miriam": "bbkg" }, "name": "Blue Brain Project Knowledge Graph", "pattern": "^[-\\w]+(?:\\/[-\\w]+)(?:\\/\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b)$", "preferred_prefix": "bbkg", "uri_format": "https://bbp.epfl.ch/nexus/web/studios/public/$1" }, "bbtp": { "description": "Input data and analysis results for the paper \"Topology of synaptic connectivity constrains neuronal stimulus representation, predicting two complementary coding strategies (https://www.biorxiv.org/content/10.1101/2020.11.02.363929v2 ).", "example": "f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a", "homepage": "https://portal.bluebrain.epfl.ch", "mappings": { "miriam": "bbtp" }, "name": "Blue Brain Project Topological sampling Knowledge Graph", "pattern": "^\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b$", "preferred_prefix": "bbtp", "uri_format": "https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1" }, "bcbc": { "description": "One of the many goals of the BCBC was to develop and maintain databases of useful research resources. A total of 813 different scientific resources were generated and submitted by BCBC investigators over the 14 years it existed. Information pertaining to 495 selected resources, judged to be the most scientifically-useful, has been converted into a static catalog, as shown below. In addition, the metadata for these 495 resources have been transferred to dkNET in the form of RDF descriptors, and all genomics data have been deposited to either ArrayExpress or GEO. [from homepage]", "example": "4623", "homepage": "http://www.betacell.org/", "keywords": [ "adenovirus", "antibody", "basic research", "basic science", "beta cell", "cell line", "cell regeneration", "cell replacement", "cell reprogramming", "data set", "data sharing", "embryonic stem cell", "embryonic stem cell line", "functional genomics", "gene", "gene expression", "genomics", "mouse", "mouse embryonic stem cell line", "mouse strain", "pancreas", "pancreatic development", "pancreatic islet", "pancreatic islet development", "pancreatic islet function", "protocol" ], "mappings": { "integbio": "nbdc00375", "rrid": "BCBC" }, "name": "Beta Cell Biology Consortium", "pattern": "^\\d+$", "preferred_prefix": "bcbc", "uri_format": "https://scicrunch.org/resolver/RRID:BCBC_$1" }, "bcgo": { "contact": { "email": "jiezheng@pennmedicine.upenn.edu", "github": "zhengj2007", "name": "Jie Zheng", "orcid": "0000-0002-2999-0103" }, "deprecated": true, "description": "An application ontology built for beta cell genomics studies.", "download_owl": "https://github.com/obi-bcgo/bcgo/raw/master/ontology/bcgo.owl", "example": "0000015", "homepage": "https://github.com/obi-bcgo/bcgo", "keywords": [ "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "BCGO", "biocontext": "BCGO", "bioportal": "BCGO", "cellosaurus": "BCGO", "obofoundry": "bcgo", "ols": "bcgo", "ontobee": "BCGO" }, "name": "Beta Cell Genomics Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "BCGO", "rdf_uri_format": "http://purl.obolibrary.org/obo/BCGO_$1", "repository": "https://github.com/obi-bcgo/bcgo", "uri_format": "http://www.ontobee.org/ontology/BCGO?iri=http://purl.obolibrary.org/obo/$1", "version": "2015-07-08" }, "bcio": { "contact": { "email": "srodriguez142857@gmail.com", "name": "Sergio José Rodríguez Méndez", "orcid": "0000-0001-7203-8399" }, "description": "The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation.", "download_owl": "http://humanbehaviourchange.org/ontology/bcio.owl", "example": "040000", "homepage": "https://www.humanbehaviourchange.org/", "keywords": [ "ontology" ], "mappings": { "aberowl": "BCI-O", "bioportal": "BCI-O", "ols": "bcio" }, "name": "The Behaviour Change Intervention Ontology", "pattern": "^\\d{6}$", "preferred_prefix": "bcio", "uri_format": "https://w3id.org/BCI-ontology#$1", "version": "2024-08-06" }, "bco": { "appears_in": [ "fovt" ], "contact": { "email": "rlwalls2008@gmail.com", "github": "ramonawalls", "name": "Ramona Walls", "orcid": "0000-0001-8815-0078" }, "description": "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.", "download_owl": "http://purl.obolibrary.org/obo/bco.owl", "example": "0000081", "homepage": "https://github.com/BiodiversityOntologies/bco", "keywords": [ "biodiversity", "biological sample", "biological sample annotation", "ecology", "environmental material", "metagenomics", "obo", "ontology", "taxonomic classification", "taxonomy" ], "license": "CC0-1.0", "mappings": { "aberowl": "BCO", "agroportal": "BCO", "biocontext": "BCO", "bioportal": "BCO", "ecoportal": "BCO", "fairsharing": "FAIRsharing.8ktkqy", "obofoundry": "bco", "ols": "bco", "ontobee": "BCO" }, "name": "Biological Collections Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "BCO", "publications": [ { "doi": "10.1371/journal.pone.0089606", "pmc": "PMC3940615", "pubmed": "24595056", "title": "Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies", "year": 2014 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/BCO_$1", "repository": "https://github.com/BiodiversityOntologies/bco", "uri_format": "http://purl.obolibrary.org/obo/BCO_$1", "version": "2021-11-14" }, "bcrc": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Cell line collections (Providers)", "example": "60316", "homepage": "https://catalog.bcrc.firdi.org.tw", "keywords": [ "cell lines" ], "mappings": { "cellosaurus": "BCRC" }, "name": "BCRC Strain Collection Catalog", "pattern": "^\\d+$", "preferred_prefix": "bcrc", "uri_format": "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1" }, "bcrj": { "description": "Cell line collections (Providers)", "example": "0278", "homepage": "https://bcrj.org.br/pesquisa/", "mappings": { "cellosaurus": "BCRJ" }, "name": "Banco de Celulas do Rio de Janeiro", "pattern": "^\\d{4}$", "preferred_prefix": "bcrj", "uri_format": "http://bcrj.org.br/celula/$1" }, "bdgp.est": { "description": "The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI).", "example": "EY223054.1", "has_canonical": "dbest", "homepage": "https://www.ncbi.nlm.nih.gov/dbEST/index.html", "keywords": [ "genome" ], "mappings": { "biocontext": "BDGP.EST", "miriam": "bdgp.est", "n2t": "bdgp.est", "ncbi": "BDGP_EST", "prefixcommons": "flybase.est" }, "name": "Berkeley Drosophila Genome Project EST database", "pattern": "^\\w+(\\.)?(\\d+)?$", "preferred_prefix": "bdgp.est", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/flybase.est:$1" } ], "uri_format": "https://www.ncbi.nlm.nih.gov/nucest/$1" }, "bdgp.insertion": { "contact": { "email": "spradling@ciwemb.edu", "name": "Allan Spradling", "orcid": "0000-0002-5251-1801" }, "description": "BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element.", "example": "KG09531", "homepage": "http://flypush.imgen.bcm.tmc.edu/pscreen/", "keywords": [ "gene", "sequence" ], "mappings": { "biocontext": "BDGP.INSERTION", "miriam": "bdgp.insertion", "n2t": "bdgp.insertion", "prefixcommons": "bdgp" }, "name": "BDGP insertion DB", "pattern": "^\\w+$", "preferred_prefix": "bdgp.insertion", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/bdgp:$1" } ], "publications": [ { "doi": "10.1534/genetics.104.026427", "pmc": "PMC1470905", "pubmed": "15238527", "title": "The BDGP gene disruption project: single transposon insertions associated with 40% of Drosophila genes", "year": 2004 } ], "uri_format": "http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1" }, "bdsc": { "description": "The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research.", "example": "33607", "homepage": "https://bdsc.indiana.edu/about/mission.html", "keywords": [ "database", "deficiency", "deletion", "disease model", "duplication", "faseb list", "fly", "gene", "genetic", "genetic analysis", "genetic construct", "germline", "human disease model", "insertion", "invertebrate", "mutation", "protein trap", "scientist", "sequenced strain", "somatic", "stock", "transposon", "transposon insertion" ], "mappings": { "miriam": "bdsc", "n2t": "bdsc", "rrid": "BDSC" }, "name": "Bloomington Drosophila Stock Center", "pattern": "^\\d+$", "preferred_prefix": "bdsc", "uri_format": "https://bdsc.indiana.edu/stocks/$1" }, "beetlebase": { "contact": { "email": "sjbrown@ksu.edu", "name": "Susan J. Brown", "orcid": "0000-0002-7984-0445" }, "description": "BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications.", "example": "TC010103", "homepage": "http://beetlebase.org/", "keywords": [ "computational biology", "genome", "life science" ], "mappings": { "biocontext": "BEETLEBASE", "fairsharing": "FAIRsharing.h5f091", "integbio": "nbdc01820", "miriam": "beetlebase", "n2t": "beetlebase", "ncbi": "BEETLEBASE", "prefixcommons": "beetlebase", "re3data": "r3d100010921" }, "name": "Tribolium Genome Database -- Insertion", "pattern": "^TC\\d+$", "preferred_prefix": "beetlebase", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/beetlebase:$1" } ], "publications": [ { "doi": "10.1093/nar/gkp807", "pmc": "PMC2808946", "pubmed": "19820115", "title": "BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum", "year": 2009 } ], "uri_format": "http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1" }, "begdb": { "contact": { "email": "pavel.hobza@uochb.cas.cz", "name": "Pavel Hobza", "orcid": "0000-0001-5292-6719" }, "description": "The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods.", "example": "4214", "homepage": "http://www.begdb.com", "keywords": [ "life science" ], "mappings": { "biocontext": "BEGDB", "fairsharing": "FAIRsharing.nbe4fq", "miriam": "begdb", "n2t": "begdb", "re3data": "r3d100011166" }, "name": "Benchmark Energy & Geometry Database", "pattern": "^[0-9]+$", "preferred_prefix": "begdb", "publications": [ { "doi": "10.1135/cccc20081261", "title": "Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples", "year": 2008 } ], "uri_format": "http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1" }, "beiresources": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Cell line collections (Providers)", "example": "MRA-253", "homepage": "https://www.beiresources.org", "keywords": [ "cell lines" ], "mappings": { "cellosaurus": "BEI_Resources" }, "name": "BEI Resources", "preferred_prefix": "beiresources", "synonyms": [ "BEI_Resources" ], "uri_format": "https://www.beiresources.org/Catalog/cellBanks/$1.aspx" }, "bel": { "comment": "INDRA uses bel as a catch-all for scomp/sfam", "contact": { "email": "support@bel.bio", "name": "William Hayes", "orcid": "0000-0003-0728-781X" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Biological Expression Language is a domain-specific language for describing causal, correlative, and associative relationships between a variety of biological agents.", "example": "9-1-1 Complex", "homepage": "https://biological-expression-language.github.io/", "keywords": [ "biology" ], "mappings": { "fairsharing": "FAIRsharing.dp0jvd" }, "name": "Biological Expression Language", "preferred_prefix": "bel" }, "bfo": { "appears_in": [ "ado", "agro", "aism", "cdno", "colao", "duo", "ecocore", "epio", "foodon", "fovt", "hso", "lepao", "mco", "ons", "pcl", "pco", "psdo", "rbo", "uberon", "xpo", "zp" ], "contact": { "email": "phismith@buffalo.edu", "github": "phismith", "name": "Barry Smith", "orcid": "0000-0003-1384-116X" }, "description": "The upper level ontology upon which OBO Foundry ontologies are built.", "download_obo": "http://purl.obolibrary.org/obo/bfo.obo", "download_owl": "http://purl.obolibrary.org/obo/bfo.owl", "example": "0000001", "homepage": "http://ifomis.org/bfo/", "keywords": [ "data retrieval", "obo", "ontology", "subject agnostic" ], "license": "CC-BY-4.0", "logo": "https://avatars2.githubusercontent.com/u/12972134?v=3&s=200", "mappings": { "aberowl": "BFO", "agroportal": "BFO", "biocontext": "BFO", "bioportal": "BFO", "fairsharing": "FAIRsharing.wcpd6f", "go": "BFO", "obofoundry": "bfo", "ols": "bfo", "ontobee": "BFO" }, "name": "Basic Formal Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "BFO", "rdf_uri_format": "http://purl.obolibrary.org/obo/BFO_$1", "repository": "https://github.com/BFO-ontology/BFO", "uri_format": "http://purl.obolibrary.org/obo/BFO_$1", "version": "2019-08-26" }, "bgee.family": { "contributor_extras": [ { "github": "smoretti", "name": "Sébastien Moretti", "orcid": "0000-0003-3947-488X" } ], "deprecated": true, "description": "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression across species.", "example": "ENSFM00500000270089", "homepage": "http://bgee.unil.ch/bgee/bgee", "mappings": { "biocontext": "BGEE.FAMILY", "miriam": "bgee.family", "n2t": "bgee.family" }, "name": "Bgee family", "pattern": "^(ENSFM|ENSGTV:)\\d+$", "preferred_prefix": "bgee.family", "references": [ "https://github.com/biopragmatics/bioregistry/issues/889" ], "uri_format": "http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1" }, "bgee.gene": { "contact": { "email": "sebastien.moretti@sib.swiss", "github": "smoretti", "name": "Sebastien Moretti", "orcid": "0000-0003-3947-488X" }, "contributor_extras": [ { "email": "sebastien.moretti@sib.swiss", "github": "smoretti", "name": "Sebastien Moretti", "orcid": "0000-0003-3947-488X" } ], "description": "Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (bulk RNA-Seq, scRNA-Seq, Affymetrix, in situ hybridization, and EST data). This collection references genes in Bgee.", "example": "FBgn0000015", "homepage": "https://www.bgee.org", "keywords": [ "gene expression" ], "mappings": { "biocontext": "BGEE.GENE", "miriam": "bgee.gene", "n2t": "bgee.gene", "prefixcommons": "bgee" }, "name": "Bgee gene", "pattern": "^[A-Za-z0-9]+$", "preferred_prefix": "bgee.gene", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/bgee:$1" } ], "references": [ "https://github.com/biopragmatics/bioregistry/issues/890" ], "uri_format": "https://www.bgee.org/gene/$1" }, "bgee.organ": { "contributor_extras": [ { "github": "smoretti", "name": "Sébastien Moretti", "orcid": "0000-0003-3947-488X" } ], "deprecated": true, "description": "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. 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This collection references individual models.", "example": "iECABU_c1320", "homepage": "http://bigg.ucsd.edu/models", "mappings": { "biocontext": "BIGG.MODEL", "miriam": "bigg.model", "n2t": "bigg.model" }, "name": "BiGG Model", "pattern": "^[a-z_A-Z0-9]+$", "preferred_prefix": "bigg.model", "uri_format": "http://bigg.ucsd.edu/models/$1" }, "bigg.reaction": { "description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions.", "example": "13GS", "homepage": "http://bigg.ucsd.edu/universal/reactions", "mappings": { "biocontext": "BIGG.REACTION", "miriam": "bigg.reaction", "n2t": "bigg.reaction" }, "name": "BiGG Reaction", "pattern": "^[a-z_A-Z0-9]+$", "preferred_prefix": "bigg.reaction", "uri_format": "http://bigg.ucsd.edu/models/universal/reactions/$1" }, "bila": { "contact": { "email": "henrich@embl.de", "github": "ThorstenHen", "name": "Thorsten Henrich", "orcid": "0000-0002-1548-3290" }, "deprecated": true, "description": "This is a record of the Bilateria anatomy terminology and ontology. 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/4dxpress:$1" } ], "publications": [ { "doi": "10.1093/nar/gkm797", "pmc": "PMC2238840", "pubmed": "17916571", "title": "4DXpress: a database for cross-species expression pattern comparisons", "year": 2007 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/BILA_$1", "uri_format": "http://4dx.embl.de/4DXpress/reg/all/cview/gene.do?geneID=$1", "version": "2019-06-12" }, "bind": { "deprecated": true, "description": "Accession number of an entry from the BIND database.", "example": "98346", "homepage": "http://bind.ca", "keywords": [ "interaction", "pathway", "small molecule" ], "mappings": { "biocontext": "BIND", "edam": "1129", "pathguide": "1", "prefixcommons": "bind" }, "name": "BIND accession number", "preferred_prefix": "bind", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/bind:$1" } ], "publications": [ { "doi": "10.1093/nar/gkg056", "pmc": "PMC165503", "pubmed": "12519993", "title": "BIND: the Biomolecular Interaction Network Database", "year": 2003 }, { "doi": "10.1093/bioinformatics/16.5.465", "pubmed": "10871269", "title": "BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways", "year": 2000 } ], "uri_format": "http://www.bind.ca/Action?identifier=bindid&idsearch=$1" }, "bindingdb": { "contact": { "email": "mgilson@health.ucsd.edu", "name": "Michael K. 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/bindingdb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkv1072", "pmc": "PMC4702793", "pubmed": "26481362", "title": "BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology", "year": 2015 }, { "doi": "10.1093/nar/gkl999", "pmc": "PMC1751547", "pubmed": "17145705", "title": "BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities", "year": 2006 } ], "uri_format": "http://www.bindingdb.org/compact/$1" }, "biocarta.pathway": { "description": "BioCarta is a supplier and distributor of characterized reagents and assays for biopharmaceutical and academic research. It catalogs community produced online maps depicting molecular relationships from areas of active research, generating classical pathways as well as suggestions for new pathways. This collections references pathway maps.", "example": "h_aktPathway", "homepage": "https://www.biocarta.com/", "mappings": { "biocontext": "BIOCARTA.PATHWAY", "miriam": "biocarta.pathway", "n2t": "biocarta.pathway" }, "name": "BioCarta Pathway", "pattern": "^([hm]\\_)?\\w+Pathway$", "preferred_prefix": "biocarta.pathway", "uri_format": "https://cgap.nci.nih.gov/Pathways/BioCarta/$1" }, "biocatalogue.service": { "contact": { "email": "carole.goble@manchester.ac.uk", "github": "CaroleGoble", "name": "Carole Goble", "orcid": "0000-0003-1219-2137" }, "description": "The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all.", "example": "614", "homepage": "https://www.biocatalogue.org/", "keywords": [ "registry" ], "mappings": { "biocontext": "BIOCATALOGUE.SERVICE", "miriam": "biocatalogue.service", "n2t": "biocatalogue.service", "prefixcommons": "biocatalogue" }, "name": "BioCatalogue Service", "pattern": "^\\d+$", "preferred_prefix": "biocatalogue.service", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/biocatalogue:$1" } ], "publications": [ { "doi": "10.1093/nar/gkq394", "pmc": "PMC2896129", "pubmed": "20484378", "title": "BioCatalogue: a universal catalogue of web services for the life sciences", "year": 2010 } ], "uri_format": "https://www.biocatalogue.org/services/$1" }, "biocompute": { "contact": { "email": "mazumder@gwu.edu", "name": "Raja Mazumder", "orcid": "0000-0001-8823-9945" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "BioCompute is shorthand for the IEEE 2791-2020 standard for Bioinformatics Analyses Generated by High-Throughput Sequencing (HTS) to facilitate communication. This pipeline documentation approach has been adopted by a few FDA centers. The goal is to ease the communication burdens between research centers, organizations, and industries. This web portal allows users to build a BioCompute Objects through the interface in a human and machine readable format.", "example": "000001", "homepage": "https://biocomputeobject.org", "name": "Biocompute Object", "pattern": "^\\d+$", "preferred_prefix": "biocompute", "publications": [ { "pubmed": "27974626", "title": "BioCompute objects - a step towards evaluation and validation of bio-medical scientific computations", "year": 2017 } ], "repository": "https://github.com/biocompute-objects/BCO_Specification", "uri_format": "https://biocomputeobject.org/BCO_$1" }, "biocyc": { "contact": { "email": "pkarp@ai.sri.com", "github": "pkarp111", "name": "Peter D. Karp", "orcid": "0000-0002-5876-6418" }, "description": "BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms.", "example": "ECOLI:CYT-D-UBIOX-CPLX", "homepage": "http://biocyc.org", "keywords": [ "genome", "pathway", "sequence" ], "mappings": { "biocontext": "BIOCYC", "edam": "2104", "go": "BioCyc", "integbio": "nbdc00252", "miriam": "biocyc", "n2t": "biocyc", "pathguide": "8", "prefixcommons": "biocyc", "uniprot": "DB-0005" }, "name": "BioCyc collection of metabolic pathway databases", "pattern": "^[A-Z-0-9]+(\\:)?[A-Za-z0-9+_.%-:]+$", "preferred_prefix": "biocyc", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/biocyc:$1" } ], "publications": [ { "doi": "10.1093/bib/bbx085", "pubmed": "29447345" }, { "doi": "10.1093/nar/gkv1164", "pmc": "PMC4702838", "pubmed": "26527732", "title": "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases", "year": 2015 }, { "doi": "10.1093/nar/gki892", "pmc": "PMC1266070", "pubmed": "16246909", "title": "Expansion of the BioCyc collection of pathway/genome databases to 160 genomes", "year": 2005 } ], "uri_format": "http://biocyc.org/getid?id=$1" }, "biofactoid": { "contact": { "email": "jeffvin.wong@utoronto.ca", "github": "jvwong", "name": "Jeffrey Wong", "orcid": "0000-0002-8912-5699" }, "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. 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"uri_format": "https://www.biorxiv.org/content/10.1101/$1" }, "biosample": { "contact": { "email": "mizrachi@ncbi.nlm.nih.gov", "name": "Ilene Karsch-Mizrachi", "orcid": "0000-0002-0289-7101" }, "description": "The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. 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Record access may be affected due to different release cycles and inter-institutional synchronisation.", "example": "SAMEA2397676", "homepage": "https://www.ebi.ac.uk/biosamples/", "keywords": [ "biology", "biomaterial", "cell", "cell line", "dna", "gold standard", "rna", "stem cell" ], "mappings": { "biocontext": "BIOSAMPLE", "cellosaurus": "BioSamples", "fairsharing": "FAIRsharing.qr6pqk", "miriam": "biosample", "n2t": "biosample", "re3data": "r3d100012828", "rrid": "SAMN", "togoid": "Biosample" }, "name": "BioSample", "pattern": "^SAM[NED](\\w)?\\d+$", "preferred_prefix": "biosample", "providers": [ { "code": "ddbj", "description": "BioSample at DNA Data Bank of Japan", "homepage": "http://trace.ddbj.nig.ac.jp/biosample/", "name": "BioSample at DNA Data Bank of Japan", "uri_format": "http://trace.ddbj.nig.ac.jp/BSSearch/biosample?acc=$1" }, { "code": "ncbi", "description": "BioSample at NCBI", "homepage": "http://www.ncbi.nlm.nih.gov/biosample", "name": "BioSample at NCBI", "uri_format": "http://www.ncbi.nlm.nih.gov/biosample?term=$1" } ], "publications": [ { "doi": "10.1093/nar/gkr1163", "pmc": "PMC3245069", "pubmed": "22139929", "title": "BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata", "year": 2011 } ], "synonyms": [ "biosamples" ], "uri_format": "https://www.ebi.ac.uk/biosamples/sample/$1" }, "bioschemas": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Bioschemas aims to improve the Findability on the Web of life sciences resources such as datasets, software, and training materials. It does this by encouraging people in the life sciences to use Schema.org markup in their websites so that they are indexable by search engines and other services. Bioschemas encourages the consistent use of markup to ease the consumption of the contained markup across many sites. This structured information then makes it easier to discover, collate, and analyse distributed resources. [from BioSchemas.org]", "example": "Dataset", "homepage": "https://bioschemas.org", "mappings": { "biolink": "bioschemas" }, "name": "BioSchemas", "preferred_prefix": "bioschemas", "repository": "https://github.com/BioSchemas/specifications", "synonyms": [ "bioschema" ], "twitter": "bioschemas", "uri_format": "https://bioschemas.org/profiles/$1" }, "biosimulations": { "description": "BioSimulations is an open repository of simulation projects, including simulation experiments, their results, and data visualizations of their results. BioSimulations supports a broad range of model languages, modeling frameworks, simulation algorithms, and simulation software tools.", "example": "Yeast-cell-cycle-Irons-J-Theor-Biol-2009", "homepage": "https://icahn.mssm.edu/", "mappings": { "miriam": "biosimulations", "re3data": "r3d100013361" }, "name": "biosimulations", "pattern": "^[a-zA-Z0-9_-]{3,}$", "preferred_prefix": "biosimulations", "uri_format": "https://biosimulations.org/projects/$1" }, "biosimulators": { "contact": { "email": "karr@mssm.edu", "name": "Jonathan Karr", "orcid": "0000-0002-2605-5080" }, "description": "BioSimulators is a registry of containerized simulation tools that support a common interface. The containers in BioSimulators support a range of modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BGNL, SBML, SED-ML).", "example": "vcell", "homepage": "https://biosimulators.org/", "keywords": [ "computational biology", "systems biology" ], "mappings": { "fairsharing": "FAIRsharing.pwEima", "miriam": "biosimulators", "re3data": "r3d100013432" }, "name": "BioSimulators", "pattern": "^[a-zA-Z0-9-_]+$", "preferred_prefix": "biosimulators", "repository": "https://github.com/biosimulators/Biosimulators/issues/new/choose", "uri_format": "https://biosimulators.org/simulators/$1" }, "biostudies": { "contact": { "email": "ugis@ebi.ac.uk", "name": "Ugis Sarkans", "orcid": "0000-0001-9227-8488" }, "description": "The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication.", "example": "S-EPMC6266652", "homepage": "https://www.ebi.ac.uk/biostudies/", "keywords": [ "biomedical science", "life science" ], "mappings": { "fairsharing": "FAIRsharing.mtjvme", "integbio": "nbdc02279", "miriam": "biostudies", "n2t": "biostudies", "re3data": "r3d100012627" }, "name": "BioStudies database", "pattern": "^S-[A-Z]{4}[\\-\\_A-Z\\d]+$", "preferred_prefix": "biostudies", "publications": [ { "doi": "10.1093/nar/gkx965", "pmc": "PMC5753238", "pubmed": "29069414", "title": "The BioStudies database-one stop shop for all data supporting a life sciences study", "year": 2018 }, { "doi": "10.15252/msb.20156658", "pmc": "PMC4704487", "pubmed": "26700850", "title": "The BioStudies database", "year": 2015 } ], "uri_format": "https://www.ebi.ac.uk/biostudies/studies/$1" }, "biosystems": { "contact": { "email": "lewis.geer@nih.gov", "name": "Aron Marchler-Bauer", "orcid": "0000-0003-1516-0712" }, "contributor_extras": [ { "email": "egon.willighagen@gmail.com", "github": "egonw", "name": "Egon Willighagen", "orcid": "0000-0001-7542-0286" } ], "description": "The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources.", "example": "001", "homepage": "https://www.ncbi.nlm.nih.gov/Structure/biosystems/docs/biosystems_about.html", "keywords": [ "biology", "molecules", "pathways", "systems biology" ], "mappings": { "biocontext": "BIOSYSTEMS", "fairsharing": "FAIRsharing.w2eeqr", "integbio": "nbdc00379", "miriam": "biosystems", "n2t": "biosystems", "prefixcommons": "biosystems", "re3data": "r3d100011033" }, "name": "BioSystems", "pattern": "^\\d+$", "preferred_prefix": "biosystems", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/biosystems:$1" } ], "publications": [ { "doi": "10.1093/nar/gkp858", "pmc": "PMC2808896", "pubmed": "19854944", "title": "The NCBI BioSystems database", "year": 2009 } ], "uri_format": "https://www.ncbi.nlm.nih.gov/biosystems/$1" }, "biotools": { "contact": { "email": "haiiu@dtu.dk", "github": "hansioan", "name": "Hans Ienasescu", "orcid": "0000-0001-9727-2544" }, "description": "BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research.", "example": "bioregistry", "homepage": "https://bio.tools/", "keywords": [ "bioinformatics", "biology", "biomedical science" ], "mappings": { "biocontext": "BIOTOOLS", "fairsharing": "FAIRsharing.63520c", "miriam": "biotools", "n2t": "biotools", "re3data": "r3d100013668" }, "name": "BioTools", "pattern": "^[-A-Za-z0-9\\_]*$", "preferred_prefix": "biotools", "publications": [ { "doi": "10.1093/nar/gkv1116", "pmc": "PMC4702812", "pubmed": "26538599", "title": "Tools and data services registry: a community effort to document bioinformatics resources", "year": 2015 } ], "repository": "http://github.com/bio-tools/biotoolsregistry/", "uri_format": "https://bio.tools/$1" }, "biozil": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Redistributor of bilogics and biomedical supplies", "example": "ls-c35719-120", "homepage": "https://www.biozol.de/en", "keywords": [ "biologics", "life sciences", "vendor" ], "name": "BIOZIL", "preferred_prefix": "biozil", "uri_format": "https://www.biozol.de/en/product/$1" }, "birnlex": { "comment": "Part of the NeuroLex namespace now", "contact": { "email": "wbug@ncmir.ucsd.edu", "name": "William Bug" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design.", "download_owl": "http://aber-owl.net/media/ontologies/BIRNLEX/1/birnlex.owl", "example": "2023", "homepage": "https://bioportal.bioontology.org/ontologies/BIRNLEX", "keywords": [ "anatomy", "biomedical science", "disease", "ontology", "study design" ], "mappings": { "aberowl": "BIRNLEX", "bioportal": "BIRNLEX", "fairsharing": "FAIRsharing.jedbbt" }, "name": "Biomedical Informatics Research Network Lexicon", "pattern": "^\\d+$", "preferred_prefix": "birnlex", "uri_format": "http://uri.neuinfo.org/nif/nifstd/birnlex_$1" }, "biro": { "contact": { "email": "silvio.peroni@unibo.it", "github": "essepuntato", "name": "Silvio Peroni", "orcid": "0000-0003-0530-4305" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology meant to define bibliographic records, bibliographic references, and their compilation into bibliographic collections and bibliographic lists, respectively.", "example": "BibliographicRecord", "homepage": "http://www.sparontologies.net/ontologies/biro", "keywords": [ "bibliography", "citation", "data model", "report", "spar", "subject agnostic" ], "mappings": { "fairsharing": "FAIRsharing.99da5f", "lov": "biro" }, "name": "Bibliographic Reference Ontology", "preferred_prefix": "BiRO", "repository": "https://github.com/sparontologies/biro", "twitter": "sparontologies", "uri_format": "http://purl.org/spar/biro/$1" }, "bitbucket": { "description": "Bitbucket is a Git-based source code repository hosting service owned by Atlassian.", "example": "andreadega/systems-biology-compiler", "homepage": "https://www.atlassian.com/", "keywords": [ "knowledge and information systems", "software engineering", "subject agnostic" ], "mappings": { "fairsharing": "FAIRsharing.fc3431", "miriam": "bitbucket", "re3data": "r3d100013478" }, "name": "Bitbucket", "pattern": "^[0-9A-Za-z-_\\.]+/[0-9A-Za-z-_\\.]+$", "preferred_prefix": "bitbucket", "uri_format": "https://bitbucket.org/$1" }, "bitterdb.cpd": { "description": "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds.", "example": "46", "homepage": "http://bitterdb.agri.huji.ac.il/dbbitter.php", "mappings": { "biocontext": "BITTERDB.CPD", "miriam": "bitterdb.cpd", "n2t": "bitterdb.cpd" }, "name": "BitterDB Compound", "pattern": "^\\d+$", "preferred_prefix": "bitterdb.cpd", "uri_format": "http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$1" }, "bitterdb.rec": { "description": "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors.", "example": "1", "homepage": "http://bitterdb.agri.huji.ac.il/dbbitter.php", "mappings": { "biocontext": "BITTERDB.REC", "miriam": "bitterdb.rec", "n2t": "bitterdb.rec" }, "name": "BitterDB Receptor", "pattern": "^\\d+$", "preferred_prefix": "bitterdb.rec", "uri_format": "http://bitterdb.agri.huji.ac.il/Receptor.php?id=$1" }, "bko": { "comment": "This resource also uses SBO terms and resolves them, e.g., http://www.sbgnbricks.org/BKO/full/entry/all/SBO:0000177/.", "contact": { "email": "adrienrougny@gmail.com", "github": "adrienrougny", "name": "Adrien Rougny", "orcid": "0000-0002-2118-035X" }, "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "SBGN bricks represent biomolecular or biological concepts. BKO formally associates bricks with the concepts they represent. BKO includes terms that describe concepts, the template bricks representing these concepts, and categories that gather bricks in a broader way.", "download_owl": "http://aber-owl.net/media/ontologies/BKO/1/bko.owl", "example": "0000204", "github_request_issue": 283, "homepage": "http://www.sbgnbricks.org/", "keywords": [ "ontology" ], "mappings": { "aberowl": "BKO", "bioportal": "BKO" }, "name": "SBGN Bricks data and ontology", "pattern": "^\\d+$", "preferred_prefix": "bko", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.sbgnbricks.org/BKO/full/entry/all/BKO:$1" }, "bmrb": { "contact": { "email": "markley@nmrfam.wisc.edu", "name": "John L. 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The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy.", "example": "15000", "homepage": "http://www.bmrb.wisc.edu/", "keywords": [ "structural biology" ], "mappings": { "fairsharing": "FAIRsharing.p06nme", "integbio": "nbdc00380", "miriam": "bmrb", "re3data": "r3d100010191", "uniprot": "DB-0256" }, "name": "Biological Magnetic Resonance Data Bank", "pattern": "^(bmr|bmse|bmst)?[0-9]{1,6}$", "preferred_prefix": "bmrb", "publications": [ { "doi": "10.1007/s10858-008-9221-y", "pmc": "PMC2268728", "pubmed": "18288446", "title": "BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions", "year": 2008 }, { "doi": "10.1093/nar/gkm957", "pmc": "PMC2238925", "pubmed": "17984079", "title": "BioMagResBank", "year": 2007 } ], "uri_format": "http://rest.bmrb.wisc.edu/bmrb/$1/html" }, "bmrb.restraint": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The NMR Restraints Grid contains the original NMR data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. In addition to the original restraints, most of the distance, dihedral angle and RDC restraint data (>85%) were parsed, and those in over 500 entries were converted and filtered. The converted and filtered data sets constitute the DOCR and FRED databases respectively.", "example": "28789", "homepage": "https://restraintsgrid.bmrb.io/NRG/MRGridServlet", "keywords": [ "chemistry", "nmr", "spectrometry" ], "name": "NMR Restraints Grid", "pattern": "^\\d+$", "preferred_prefix": "bmrb.restraint", "uri_format": "https://restraintsgrid.bmrb.io/NRG/MRGridServlet?block_text_type=2-parsed&db_username=wattos1&file_detail=2-parsed&format=n%2Fa&program=STAR&request_type=block&subtype=full&type=entry&mrblock_id=$1" }, "bold.taxonomy": { "contact": { "email": "phebert@uoguelph.ca", "name": "Paul David Neil Hebert", "orcid": "0000-0002-3081-6700" }, "description": "The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information.", "example": "27267", "homepage": "http://www.boldsystems.org/", "keywords": [ "dna" ], "mappings": { "biocontext": "BOLD.TAXONOMY", "miriam": "bold.taxonomy", "n2t": "bold.taxonomy", "ncbi": "BOLD", "prefixcommons": "bold", "wikidata": "P3606" }, "name": "BOLD Systems taxon", "pattern": "^\\d+$", "preferred_prefix": "bold.taxonomy", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data.", "example": "1.1.1.1", "homepage": "https://www.brenda-enzymes.org/", "keywords": [ "enzyme", "life science" ], "mappings": { "biocontext": "BRENDA", "fairsharing": "FAIRsharing.etp533", "go": "BRENDA", "miriam": "brenda", "n2t": "brenda", "pathguide": "51", "prefixcommons": "brenda", "re3data": "r3d100010616" }, "name": "BRENDA Enzyme", "pattern": "^((\\d+\\.-\\.-\\.-)|(\\d+\\.\\d+\\.-\\.-)|(\\d+\\.\\d+\\.\\d+\\.-)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$", "preferred_prefix": "brenda", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/brenda:$1" } ], "provides": "eccode", "publications": [ { "doi": "10.1016/j.jbiotec.2017.04.020", "pubmed": "28438579", "title": "The BRENDA enzyme information system-From a database to an expert system", "year": 2017 }, { "doi": "10.1093/nar/gku1068", "pmc": "PMC4383907", "pubmed": "25378310", "title": "BRENDA in 2015: exciting developments in its 25th year of existence", "year": 2014 }, { "doi": "10.1093/nar/gks1049", "pmc": "PMC3531171", "pubmed": "23203881", "title": "BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA", "year": 2012 }, { "doi": "10.1093/nar/gkq1089", "pmc": "PMC3013686", "pubmed": "21062828", "title": "BRENDA, the enzyme information system in 2011", "year": 2010 }, { "doi": "10.1093/nar/gkn820", "pmc": "PMC2686525", "pubmed": "18984617", "title": "BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009", "year": 2008 }, { "doi": "10.1093/nar/gkl972", "pmc": "PMC1899097", "pubmed": "17202167", "title": "BRENDA, AMENDA and FRENDA: the enzyme information system in 2007", "year": 2007 }, { "doi": "10.1093/nar/gkh081", "pmc": "PMC308815", "pubmed": "14681450", "title": "BRENDA, the enzyme database: updates and major new developments", "year": 2004 }, { "doi": "10.1016/s1096-7176(03)00008-9", "pubmed": "12850129", "title": "Review of the BRENDA Database", "year": 2003 }, { "doi": "10.1016/s0968-0004(01)02027-8", "pubmed": "11796225", "title": "BRENDA: a resource for enzyme data and metabolic information", "year": 2002 }, { "doi": "10.1093/nar/30.1.47", "pmc": "PMC99121", "pubmed": "11752250", "title": "BRENDA, enzyme data and metabolic information", "year": 2002 }, { "doi": "S0168-1656(17)30183-9", "title": "The BRENDA enzyme information system-From a database to an expert system." }, { "doi": "10.1016/S1096-7176(03)00008-9", "title": "Review of the BRENDA Database." }, { "doi": "10.1016/S0968-0004(01)02027-8", "title": "BRENDA: a resource for enzyme data and metabolic information." } ], "uri_format": "https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1" }, "brenda.ligand": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Information for ligands in the BRENDA database.", "example": "278", "homepage": "https://www.brenda-enzymes.de/ligand.php", "keywords": [ "chemistry", "structrual bioinformatics" ], "name": "BRENDA Ligand", "pattern": "^\\d+$", "preferred_prefix": "brenda.ligand", "uri_format": "https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$1" }, "brenda.ligandgroup": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Information for ligand groups (chemical classes).", "example": "18030", "homepage": "https://www.brenda-enzymes.de/ligand.php", "keywords": [ "chemistry", "grouping", "structrual bioinformatics" ], "name": "BRENDA Ligand Group", "pattern": "^\\d+$", "preferred_prefix": "brenda.ligandgroup", "uri_format": "https://www.brenda-enzymes.de/ligand.php?brenda_group_id=$1" }, "bridgedb": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A vocabulary about resources, similar to bioregistry.schema, venn, idot, etc.", "example": "hasPrimaryUriPattern", "homepage": "https://bridgedb.org", "name": "BridgeDb Vocabulary", "preferred_prefix": "bridgedb", "references": [ "https://github.com/bridgedb/BridgeDb/blob/master/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl" ], "uri_format": "http://vocabularies.bridgedb.org/ops#$1" }, "broad": { "description": "Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. 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As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae.", "example": "S7000002168151102", "homepage": "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/", "mappings": { "biocontext": "BROAD", "miriam": "broad", "n2t": "broad" }, "name": "Broad Fungal Genome Initiative", "pattern": "^S\\d+$", "preferred_prefix": "broad", "uri_format": "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1" }, "bs": { "comment": "An alernative vocabulary that has been aligned and integrated in Sequence Ontology (SO).", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. 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The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies.", "download_json": "http://purl.obolibrary.org/obo/bspo.json", "download_obo": "https://raw.githubusercontent.com/obophenotype/biological-spatial-ontology/master/bspo.obo", "download_owl": "http://purl.obolibrary.org/obo/bspo.owl", "example": "0000029", "homepage": "https://github.com/obophenotype/biological-spatial-ontology", "keywords": [ "anatomy", "life science", "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "BSPO", "biocontext": "BSPO", "bioportal": "BSPO", "fairsharing": "FAIRsharing.newa3z", "obofoundry": "bspo", "ols": "bspo", "ontobee": "BSPO" }, "name": "Biological Spatial Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "BSPO", "publications": [ { "doi": "10.1186/2041-1480-5-34", "pmc": "PMC4137724", "pubmed": "25140222", "title": "Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology", "year": 2014 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/BSPO_$1", "repository": "https://github.com/obophenotype/biological-spatial-ontology", "uri_format": "http://purl.obolibrary.org/obo/BSPO_$1", "version": "2023-05-27" }, "bto": { "banana": "BTO", "contact": { "email": "c.dudek@tu-braunschweig.de", "github": "chdudek", "name": "Christian-Alexander Dudek", "orcid": "0000-0001-9117-7909" }, "description": "The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.", "download_json": "http://purl.obolibrary.org/obo/bto.json", "download_obo": "http://purl.obolibrary.org/obo/bto.obo", "download_owl": "http://purl.obolibrary.org/obo/bto.owl", "example": "0000590", "homepage": "http://www.brenda-enzymes.org", "keywords": [ "cell", "enzyme", "enzymology", "life science", "obo", "ontology", "organ", "reaction data", "tissue" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "BTO", "biocontext": "BTO", "bioportal": "BTO", "cellosaurus": "BTO", "fairsharing": "FAIRsharing.1414v8", "go": "BTO", "miriam": "bto", "n2t": "bto", "obofoundry": "bto", "ols": "bto", "ontobee": "BTO", "prefixcommons": "bto", "wikidata": "P5501" }, "name": "BRENDA Tissue Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "BTO", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/bto:$1" }, { "code": "miriam_obo_legacy", "description": "An old URI style for MIRIAM", "homepage": "https://identifiers.org/", "name": "MIRIAM OBO Legacy", "uri_format": "http://identifiers.org/obo.bto/BTO:$1" } ], "publications": [ { "doi": "10.1093/nar/gky1048", "pmc": "PMC6323942", "pubmed": "30395242", "title": "BRENDA in 2019: a European ELIXIR core data resource", "year": 2019 }, { "doi": "10.1093/nar/gku1068", "pmc": "PMC4383907", "pubmed": "25378310", "title": "BRENDA in 2015: exciting developments in its 25th year of existence", "year": 2014 }, { "doi": "10.1093/nar/gks1049", "pmc": "PMC3531171", "pubmed": "23203881", "title": "BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA", "year": 2012 }, { "doi": "10.1093/nar/gkq968", "pmc": "PMC3013802", "pubmed": "21030441", "title": "The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources", "year": 2010 }, { "doi": "10.1093/nar/gkh081", "pmc": "PMC308815", "pubmed": "14681450", "title": "BRENDA, the enzyme database: updates and major new developments", "year": 2004 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/BTO_$1", "repository": "https://github.com/BRENDA-Enzymes/BTO", "synonyms": [ "BTO" ], "uri_format": "http://purl.obolibrary.org/obo/BTO_$1", "version": "2021-10-26" }, "bugbase.expt": { "description": "BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references microarray experiments.", "example": "288", "homepage": "http://bugs.sgul.ac.uk/E-BUGS", "mappings": { "biocontext": "BUGBASE.EXPT", "miriam": "bugbase.expt", "n2t": "bugbase.expt" }, "name": "BugBase Expt", "pattern": "^\\d+$", "preferred_prefix": "bugbase.expt", "uri_format": "http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?action=view&expt_id=$1" }, "bugbase.protocol": { "description": "BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. 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It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it.", "example": "dsmz_mutz-id:ACC 291", "homepage": "http://www.cabri.org/", "keywords": [ "applied microbiology", "medical microbiology", "microbiology", "molecular biology", "molecular microbiology", "virology" ], "mappings": { "biocontext": "CABRI", "edam": "2380", "fairsharing": "FAIRsharing.qx2rvz", "miriam": "cabri", "n2t": "cabri", "ncbi": "CABRI" }, "name": "Common Access to Biological Resources and Information Project", "pattern": "^([A-Za-z]+)?(\\_)?([A-Za-z-]+)\\:([A-Za-z0-9 ]+)$", "preferred_prefix": "cabri", "providers": [ { "code": "CURATOR_REVIEW", "description": "CABRI Cell Lines catalogue in Brussels (SRS)", "homepage": "http://www.be.cabri.org/", "name": "CABRI Cell Lines catalogue in Brussels (SRS)", "uri_format": "http://www.be.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1]" } ], "publications": [ { "doi": "10.1002/cfg.376", "pmc": "PMC2447341", "pubmed": "18629057", "title": "Interoperability of CABRI Services and Biochemical Pathways Databases", "year": 2004 }, { "doi": "10.2165/00822942-200594030-00002", "pubmed": "16231959", "title": "The role of informatics in the coordinated management of biological resources collections", "year": 2005 } ], "uri_format": "http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1]" }, "cadsr": { "description": "The US National Cancer Institute (NCI) maintains and administers data elements, forms, models, and components of these items in a metadata registry referred to as the Cancer Data Standards Registry and Repository, or caDSR.", "example": "3771992", "homepage": "https://wiki.nci.nih.gov/display/caDSR/caDSR+Wiki", "mappings": { "miriam": "cadsr", "n2t": "cadsr" }, "name": "Cancer Data Standards Registry and Repository", "pattern": "^[0-9]*$", "preferred_prefix": "cadsr", "uri_format": "https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML?query=DataElement[@publicId=$1]" }, "caloha": { "contact": { "email": "Paula.Duek@sib.swiss", "github": "paulacalipho", "name": "Paula Duek Roggli", "orcid": "0000-0002-0819-0473" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This is a code repository for the SIB - Swiss Institute of Bioinformatics CALIPHO group neXtProt project, which is a comprehensive human-centric discovery platform, that offers a integration of and navigation through protein-related data. 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These predictions are regularly compared against reference structures from PDB.", "example": "2019-08-03_00000089_1", "homepage": "https://cameo3d.org", "keywords": [ "life science" ], "mappings": { "biocontext": "CAMEO", "fairsharing": "FAIRsharing.dq34p2", "miriam": "cameo", "n2t": "cameo" }, "name": "Continuous Automated Model Evaluation", "pattern": "^[0-9\\-_]+$", "preferred_prefix": "cameo", "publications": [ { "doi": "10.1093/database/bat031", "pmc": "PMC3889916", "pubmed": "23624946", "title": "The Protein Model Portal--a comprehensive resource for protein structure and model information", "year": 2013 } ], "uri_format": "https://www.cameo3d.org/sp/targets/target/$1" }, "cao": { "contact": { "email": "williams.antony@epa.gov", "name": "Antony Williams", "orcid": "0000-0002-2668-4821" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology developed as part of the Chemical Analysis Metadata Project (ChAMP) as a resource to semantically annotate standards developed using the ChAMP platform. (source: CAO ontology)", "download_owl": "https://champ.stuchalk.domains.unf.edu/images/ontology/cao.owl", "example": "000064", "homepage": "https://champ.stuchalk.domains.unf.edu", "keywords": [ "amino acid sequence", "annotation", "characterisation data heat", "gene", "genetics", "life science", "ontology", "orthologous", "phylogenetics", "protein", "transcript", "transport and kinetic data" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "CAO", "bioportal": "CAO", "fairsharing": "FAIRsharing.wp0134", "ols": "cao" }, "name": "Chemical Analysis Ontology", "pattern": "^\\d+$", "preferred_prefix": "cao", "publications": [ { "doi": "10.1126/science.278.5338.631", "pubmed": "9381173", "title": "A genomic perspective on protein families", "year": 1997 } ], "uri_format": "http://champ-project.org/images/ontology/cao.owl#CAO_$1", "version": "0.2" }, "caps": { "description": "CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps.", "example": "434", "homepage": "http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home", "mappings": { "biocontext": "CAPS", "miriam": "caps", "n2t": "caps" }, "name": "CAPS-DB", "pattern": "^\\d+$", "preferred_prefix": "caps", "uri_format": "http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=$1" }, "caro": { "appears_in": [ "aism", "colao", "ehdaa2", "gallont", "lepao", "pco" ], "contact": { "email": "haendel@ohsu.edu", "github": "mellybelly", "name": "Melissa Haendel", "orcid": "0000-0001-9114-8737" }, "description": "The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies.", "download_json": "http://purl.obolibrary.org/obo/caro.json", "download_obo": "http://purl.obolibrary.org/obo/caro.obo", "download_owl": "http://purl.obolibrary.org/obo/caro.owl", "example": "0000000", "homepage": "https://github.com/obophenotype/caro/", "keywords": [ "anatomy", "annotation", "interoperability", "life science", "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "CARO", "biocontext": "CARO", "bioportal": "CARO", "fairsharing": "FAIRsharing.3kcgmr", "go": "CARO", "obofoundry": "caro", "ols": "caro", "ontobee": "CARO" }, "name": "Common Anatomy Reference Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CARO", "providers": [ { "code": "obo.1", "description": "This incorrect encoding was found inside IDO-COVID-19", "homepage": "http://purl.obolibrary.org", "name": "Nonstandard OBO PURL", "uri_format": "http://purl.obolibrary.org/obo/ido.owl/CARO_$1" } ], "publications": [ { "doi": "10.1007/978-1-84628-885-2_16", "title": "CARO – The Common Anatomy Reference Ontology", "year": 2008 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/CARO_$1", "repository": "https://github.com/obophenotype/caro", "uri_format": "http://purl.obolibrary.org/obo/CARO_$1", "version": "2023-03-15" }, "cas": { "contact": { "email": "ajacobs@cas.org", "name": "Andrea Jacobs", "orcid": "0000-0001-9316-9400" }, "description": "CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information.", "example": "50-00-0", "homepage": "https://commonchemistry.cas.org/", "keywords": [ "chemical", "chemical entity", "cheminformatics", "structure" ], "mappings": { "biocontext": "CAS", "cheminf": "000446", "edam": "1002", "fairsharing": "FAIRsharing.r7Kwy7", "go": "CAS", "hl7": "2.16.840.1.113883.6.61", "miriam": "cas", "n2t": "cas", "prefixcommons": "cas", "wikidata": "P231" }, "name": "CAS Registry Number", "pattern": "^\\d{1,7}\\-\\d{2}\\-\\d$", "preferred_prefix": "cas", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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These ontologies are effectively retired and CASSPC terms are only also used in Phenoscape.", "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "contributor_extras": [ { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } ], "deprecated": true, "example": "5359", "homepage": "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp", "mappings": { "go": "CASSPC" }, "name": "Eschmeyer's Catalog of Fishes", "pattern": "^\\d+$", "preferred_prefix": "casspc", "uri_format": "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=$1" }, "cath": { "contact": { "email": "c.orengo@ucl.ac.uk", "name": "Christine Orengo", "orcid": "0000-0002-7141-8936" }, "description": "CATH is a classification of protein structural domains. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence.", "example": "1.10.8.10", "homepage": "http://www.cathdb.info", "keywords": [ "biology", "classification", "evolutionary biology", "protein", "structure" ], "mappings": { "biocontext": "CATH", "edam": "2700", "fairsharing": "FAIRsharing.xgcyyn", "integbio": "nbdc01888", "miriam": "cath", "n2t": "cath", "prefixcommons": "cath", "re3data": "r3d100012629" }, "name": "CATH Protein Structural Domain Superfamily", "pattern": "^[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+$", "preferred_prefix": "cath", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with superfamily classification.", "example": "1.10.10.200", "homepage": "http://www.cathdb.info/", "mappings": { "biocontext": "CATH.SUPERFAMILY", "miriam": "cath.superfamily", "n2t": "cath.superfamily" }, "name": "CATH superfamily", "part_of": "cath", "pattern": "^\\d+(\\.\\d+(\\.\\d+(\\.\\d+)?)?)?$", "preferred_prefix": "cath.superfamily", "uri_format": "http://www.cathdb.info/cathnode/$1" }, "cattleqtldb": { "description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. 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The long term goal is to support convergence towards a standard set of gene annotations.", "example": "CCDS13573.1", "homepage": "http://www.ncbi.nlm.nih.gov/CCDS/", "keywords": [ "gene", "life science", "protein" ], "mappings": { "biocontext": "CCDS", "fairsharing": "FAIRsharing.46s4nt", "integbio": "nbdc00023", "miriam": "ccds", "n2t": "ccds", "prefixcommons": "ccds", "togoid": "Ccds", "uniprot": "DB-0187" }, "name": "Consensus CDS", "pattern": "^CCDS\\d+\\.\\d+$", "preferred_prefix": "ccds", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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All relationships between anatomical structures and from cell types to anatomical structures are valid Uberon and CL relationships. The Spatial Ontology defines the shape, size, location, and rotation of experimental tissue and data major anatomical structures in the 3D Reference Object Library. The Specimen Ontology captures the sex, age, and other information on donors that provided tissue data used in the construction of the HRA.", "download_owl": "http://purl.org/ccf/releases/2.3.0/ccf.owl", "example": "extraction_set", "github_request_issue": 879, "homepage": "https://bioportal.bioontology.org/ontologies/CCF", "keywords": [ "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "CCF", "bioportal": "CCF", "ols": "ccf", "re3data": "r3d100012657" }, "name": "Human Reference Atlas Common Coordinate Framework Ontology", "pattern": "^\\S+$", "preferred_prefix": "ccf", "rdf_uri_format": "http://purl.org/ccf/$1", "repository": "https://github.com/hubmapconsortium/ccf-ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://bioportal.bioontology.org/ontologies/CCF/?p=classes&conceptid=http%3A%2F%2Fpurl.org%2Fccf%2F$1", "version": "2.3.0" }, "ccle": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Datasets around different cancer cell lines generated by the Broad Institute and Novartis", "example": "BT20_BREAST", "homepage": "https://www.cbioportal.org/study/summary?id=ccle_broad_2019", "license": "ODbL-1.0", "mappings": { "cellosaurus": "CCLE" }, "name": "Cancer Cell Line Encyclopedia Cells", "preferred_prefix": "ccle", "synonyms": [ "ccle.cell" ], "uri_format": "https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId=$1" }, "cco": { "banana": "CCO", "contact": { "email": "kuiper@bio.ntnu.no", "github": "makuintnu", "name": "Martin Kuiper", "orcid": "0000-0002-1171-9876" }, "description": "The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process.", "download_obo": "https://www.bio.ntnu.no/ontology/CCO/cco.obo", "download_owl": "https://www.bio.ntnu.no/ontology/CCO/cco.owl", "example": "0000003", "homepage": "http://www.semantic-systems-biology.org/apo", "keywords": [ "cell", "cell cycle", "functional genomics", "genomics", "life science", "molecular function", "obo", "ontology", "proteomics" ], "mappings": { "aberowl": "CCO", "bartoc": "20461", "biocontext": "CCO", "bioportal": "CCO", "fairsharing": "FAIRsharing.xhwrnr", "miriam": "cco", "n2t": "cco", "ols": "cco", "prefixcommons": "cco" }, "name": "Cell Cycle Ontology", "namespace_in_lui": true, "pattern": "^\\w+$", "preferred_prefix": "cco", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/cco:$1" } ], "publications": [ { "doi": "10.1186/gb-2009-10-5-r58", "pmc": "PMC2718524", "pubmed": "19480664", "title": "The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process", "year": 2009 } ], "uri_format": "https://www.ebi.ac.uk/ols4/ontologies/cco/terms?obo_id=CCO:$1" }, "ccrid": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Cell line databases/resources", "example": "4201PAT-CCTCC00348", "homepage": "http://www.cellresource.cn", "mappings": { "cellosaurus": "CCRID" }, "name": "National Experimental Cell Resource Sharing Platform", "preferred_prefix": "ccrid", "uri_format": "http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1" }, "cdao": { "contact": { "email": "balhoff@renci.org", "github": "balhoff", "name": "Jim Balhoff", "orcid": "0000-0002-8688-6599" }, "description": "a formalization of concepts and relations relevant to evolutionary comparative analysis", "download_owl": "http://purl.obolibrary.org/obo/cdao.owl", "example": "0000072", "homepage": "https://github.com/evoinfo/cdao", "keywords": [ "bioinformatics", "biomedical science", "evolution", "evolutionary biology", "life science", "molecular biology", "obo", "ontology", "phylogenetics", "taxonomy" ], "license": "CC0-1.0", "mappings": { "aberowl": "CDAO", "agroportal": "CDAO", "biocontext": "CDAO", "bioportal": "CDAO", "fairsharing": "FAIRsharing.kay31r", "obofoundry": "cdao", "ols": "cdao", "ontobee": "CDAO" }, "name": "Comparative Data Analysis Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CDAO", "publications": [ { "doi": "10.4137/ebo.s2320", "pmc": "PMC2747124", "pubmed": "19812726", "title": "Initial implementation of a comparative data analysis ontology", "year": 2009 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/CDAO_$1", "repository": "https://github.com/evoinfo/cdao", "uri_format": "http://purl.obolibrary.org/obo/CDAO_$1", "version": "2024-01-25" }, "cdd": { "description": "The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution.", "example": "cd00400", "homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd", "keywords": [ "earth science", "geology", "protein", "structure" ], "mappings": { "biocontext": "CDD", "edam": "2666", "fairsharing": "FAIRsharing.ea287c", "go": "CDD", "integbio": "nbdc00401", "miriam": "cdd", "n2t": "cdd", "ncbi": "CDD", "prefixcommons": "cdd", "re3data": "r3d100012041", "uniprot": "DB-0214" }, "name": "Conserved Domain Database at NCBI", "pattern": "^(cd)?\\d{5}$", "preferred_prefix": "cdd", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/cdd:$1" } ], "publications": [ { "doi": "10.1093/nar/gkac1096", "pubmed": "36477806" }, { "doi": "10.1093/nar/gku1221", "pmc": "PMC4383992", "pubmed": "25414356", "title": "CDD: NCBI's conserved domain database", "year": 2014 }, { "doi": "10.1093/nar/gkn845", "pmc": "PMC2686570", "pubmed": "18984618", "title": "CDD: specific functional annotation with the Conserved Domain Database", "year": 2008 } ], "uri_format": "https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1" }, "cdno": { "contact": { "email": "landreshdz@gmail.com", "github": "LilyAndres", "name": "Liliana Andres Hernandez", "orcid": "0000-0002-7696-731X" }, "depends_on": [ "bfo", "chebi", "envo", "pato", "ro" ], "description": "The CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet. These terms are intended primarily to be associated with datasets that quantify concentration of chemical nutritional components derived from samples taken from any stage in the production of food raw materials (including from crops, livestock, fisheries) and through processing and supply chains. Additional knowledge associated with these dietary sources may be represented by terms that describe functional, physical and other attributes. Whilst recognising that dietary nutrients within food substrates may be present as complex and dynamic physical and chemical structures or mixtures, CDNO focuses on components typically quantified in an analytical chemistry laboratory. The primary CDNO class ‘dietary nutritional component’ contains hierarchical sets of terms organised to reflect commonly used classifications of chemical food composition. This class does not represent an exhaustive classification of chemical components, but focuses on structuring terms according to widely accepted categories. This class is independent of, but may be used in conjunction with, classes that describe ‘analytical methods’ for quantification, ‘physical properties’ or ‘dietary function’. Quantification data may be used and reported in research literature, to inform food composition tables and labelling, or for supply chain quality assurance and control. More specifically, terms within the ‘nutritional component concentration’ class may be used to represent quantification of components described in the ‘dietary nutritional component’ class. Concentration data are intended to be described in conjunction with post-composed metadata concepts, such as represented by the Food Ontology (FoodOn) ‘Food product by organism’, which derives from some food or anatomical entity and a NCBI organismal classification ontology (NCBITaxon) entity. The common vocabulary and relationships defined within CDNO should facilitate description, communication and exchange of material entity-derived nutritional composition datasets typically generated by analytical laboratories. The organisation of the vocabulary is structured to reflect common categories variously used by those involved in crop, livestock or other organismal production, associated R&D and breeding, as well as the food processing and supply sector, and nutritionists, inlcuding compilers and users of food composition databases. The CDNO therefore supports characterisation of genetic diversity and management of biodiversity collections, as well as sharing of knowledge relating to dietary composition between a wider set of researchers, breeders, farmers, processors and other stakeholders. Further development of the functional class should also assist in understanding how interactions between organismal genetic and environmental variation contribute to human diet and health in the farm to fork continuum.", "download_obo": "http://purl.obolibrary.org/obo/cdno.obo", "download_owl": "http://purl.obolibrary.org/obo/cdno.owl", "example": "0000013", "homepage": "https://cdno.info/", "keywords": [ "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "CDNO", "agroportal": "CDNO", "bioportal": "CDNO", "obofoundry": "cdno", "ols": "cdno", "ontobee": "CDNO" }, "name": "Compositional Dietary Nutrition Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CDNO", "publications": [ { "doi": "10.3389/fnut.2022.928837", "title": "Establishing a Common Nutritional Vocabulary - From Food Production to Diet" }, { "doi": "10.1002/csc2.20092", "title": "Knowledge representation and data sharing to unlock crop variation for nutritional food security", "year": 2020 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/CDNO_$1", "repository": "https://github.com/CompositionalDietaryNutritionOntology/cdno", "uri_format": "http://purl.obolibrary.org/obo/CDNO_$1", "version": "2024-08-13" }, "cdpd": { "description": "The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN).", "example": "63250", "homepage": "http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp", "mappings": { "biocontext": "CDPD", "miriam": "cdpd", "n2t": "cdpd" }, "name": "Canadian Drug Product Database", "pattern": "^\\d+$", "preferred_prefix": "cdpd", "uri_format": "http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$1" }, "cdt": { "appears_in": [ "ohd" ], "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Code on Dental Procedures and Nomenclature (the CDT Code) assures consistency in documenting dental treatment.\n\nNote that CDT codes should look like D2150 but for some reason the ontology conversion that is reused across OBO rewrites them as CPT_000 + the four numbers without the leading D.", "download_owl": "https://raw.githubusercontent.com/oral-health-and-disease-ontologies/ohd-ontology/f19378ff192b6f9ea16133e85671e8359fc371cd/src/ontology/archive/CDTCodes%20as%20Classes_pruned.owl", "example": "1000001", "homepage": "https://www.ada.org/publications/CDT", "keywords": [ "ontology" ], "mappings": { "bartoc": "20299", "hl7": "2.16.840.1.113883.6.116" }, "name": "Current Dental Terminology", "pattern": "^\\d{7}$", "preferred_prefix": "cdt" }, "cell_biolabs": { "description": "Cell line collections (Providers)", "example": "AKR-270", "homepage": "https://www.cellbiolabs.com", "mappings": { "cellosaurus": "Cell_Biolabs" }, "name": "Cell Biolabs cell line products", "preferred_prefix": "cell_biolabs", "uri_format": "https://www.cellbiolabs.com/search?keywords=$1" }, "cell_model_passport": { "description": "Cell line databases/resources", "example": "SIDM01262", "homepage": "https://cellmodelpassports.sanger.ac.uk/", "mappings": { "cellosaurus": "Cell_Model_Passport" }, "name": "Sanger Cell Model Passports", "preferred_prefix": "cell_model_passport", "uri_format": "https://cellmodelpassports.sanger.ac.uk/passports/$1" }, "cellbank.australia": { "description": "CellBank Australia collects novel cell lines, developed by Australian researchers, submits these cell lines to rigorous testing to confirm their integrity, and then distributes the cell lines to researchers throughout the world.", "example": "ab-1-ha", "homepage": "https://www.cellbankaustralia.com/cellbank-australia-exclusive-lines/", "mappings": { "cellosaurus": "CBA" }, "name": "CellBank Australia", "preferred_prefix": "cellbank.australia", "uri_format": "https://www.cellbankaustralia.com/$1.html" }, "cellimage": { "contact": { "email": "dorloff@ncmir.ucsd.edu", "name": "David N. Orloff", "orcid": "0000-0001-7594-0820" }, "description": "The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes.", "example": "24801", "homepage": "http://cellimagelibrary.org/", "keywords": [ "cell biology", "image", "life science" ], "mappings": { "biocontext": "CELLIMAGE", "fairsharing": "FAIRsharing.8t18te", "miriam": "cellimage", "n2t": "cellimage", "prefixcommons": "cellimage", "re3data": "r3d100000023" }, "name": "Cell Image Library", "pattern": "^\\d+$", "preferred_prefix": "cellimage", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/cellimage:$1" } ], "publications": [ { "doi": "10.1093/nar/gks1257", "pmc": "PMC3531121", "pubmed": "23203874", "title": "The cell: an image library-CCDB: a curated repository of microscopy data", "year": 2012 } ], "twitter": "CellImageLibrar", "uri_format": "http://cellimagelibrary.org/images/$1" }, "cellopub": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Cellosaurus identifeirs for publications, like Pubmed", "example": "CLPUB00496", "homepage": "https://web.expasy.org/cellosaurus/", "mappings": { "cellosaurus": "CelloPub" }, "name": "Cellosaurus Publication", "pattern": "^CLPUB\\d+$", "preferred_prefix": "cellopub", "uri_format": "https://web.expasy.org/cellosaurus/cellopub/$1" }, "cellosaurus": { "banana": "CVCL", "banana_peel": "_", "contact": { "email": "Amos.Bairoch@sib.swiss", "github": "AmosBairoch", "name": "Amos Bairoch", "orcid": "0000-0003-2826-6444" }, "description": "The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.", "download_obo": "https://ftp.expasy.org/databases/cellosaurus/cellosaurus.obo", "example": "0440", "homepage": "https://cellosaurus.org", "keywords": [ "cell lines", "controlled vocabularies", "life science", "ontologies", "ontology", "thesaurus" ], "license": "CC-BY-4.0", "mappings": { "biocontext": "CELLOSAURUS", "cellosaurus": "Cellosaurus", "fairsharing": "FAIRsharing.hkk309", "integbio": "nbdc02180", "miriam": "cellosaurus", "n2t": "cellosaurus", "re3data": "r3d100013293", "rrid": "CVCL", "togoid": "Cellosaurus", "wikidata": "P3289" }, "mastodon": "cellosaurus@fediscience.org", "name": "Cellosaurus", "pattern": "^[A-Z0-9]{4}$", "preferred_prefix": "cellosaurus", "providers": [ { "code": "legacy", "description": "The legacy URI for the Cellosaurus website, updated on August 30, 2022 [ref](https://twitter.com/Cellosaurus/status/1564658792691810305).", "homepage": "https://web.expasy.org/cellosaurus", "name": "Legacy Endpoint", "uri_format": "https://web.expasy.org/cellosaurus/CVCL_$1" }, { "code": "nextprot", "description": "The neXtProt endpoint for exploring Cellosaurus", "homepage": "https://www.nextprot.org/", "name": "neXtProt Cellosaurus Browser", "uri_format": "https://www.nextprot.org/term/CVCL_$1" } ], "publications": [ { "doi": "10.1002/ijc.32639", "pubmed": "31444973", "title": "CLASTR: The Cellosaurus STR similarity search tool - A precious help for cell line authentication", "year": 2019 }, { "doi": "10.7171/jbt.18-2902-002", "pmc": "PMC5945021", "pubmed": "29805321", "title": "The Cellosaurus, a Cell-Line Knowledge Resource", "year": 2018 } ], "repository": "https://github.com/calipho-sib/cellosaurus", "synonyms": [ "CVCL" ], "twitter": "cellosaurus", "uri_format": "https://www.cellosaurus.org/CVCL_$1" }, "cellosaurus.resource": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The set of prefixes used in the Cellosaurus resource", "example": "4DN", "homepage": "https://web.expasy.org/cellosaurus/", "keywords": [ "cell lines", "cells", "registry" ], "name": "Cellosaurus Registry", "preferred_prefix": "cellosaurus.resource", "uri_format": "https://bioregistry.io/metaregistry/cellosaurus/$1" }, "cellrepo": { "description": "The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines", "example": "82", "homepage": "https://www.cellrepo.com/", "mappings": { "miriam": "cellrepo" }, "name": "Cell Version Control Repository", "pattern": "^[0-9]+$", "preferred_prefix": "cellrepo", "uri_format": "https://www.cellrepo.com/repositories/$1" }, "cemo": { "contact": { "email": "n.queralt_rosinach@lumc.nl", "github": "NuriaQueralt", "name": "Núria Queralt Rosinach", "orcid": "0000-0003-0169-8159" }, "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "The covid-19 epidemiology and monitoring ontology (cemo) provides a common ontological model to make epidemiological quantitative data for monitoring the covid-19 outbreak machine-readable and interoperable to facilitate its exchange, integration and analysis, to eventually support evidence-based rapid response.", "download_json": "https://raw.githubusercontent.com/cthoyt/covid19-epidemiology-ontology/add-artifacts/owl/cemo.json", "download_owl": "https://raw.githubusercontent.com/NuriaQueralt/covid19-epidemiology-ontology/main/owl/cemo.owl", "example": "secondary_attack_rate", "github_request_issue": 593, "homepage": "https://github.com/NuriaQueralt/covid19-epidemiology-ontology", "keywords": [ "ontology" ], "license": "CC0-1.0", "name": "The COVID-19 epidemiology and monitoring ontology", "pattern": "^[0-9a-z_-]+$", "preferred_prefix": "cemo", "providers": [ { "code": "obo", "description": "This represents misconfigured base IRIs, even though this ontology isn't an OBO Foundry ontology", "homepage": "http://purl.obolibrary.org/obo/", "name": "Legacy OBO PURL", "uri_format": "http://purl.obolibrary.org/obo/cemo.owl#$1" } ], "repository": "https://github.com/NuriaQueralt/covid19-epidemiology-ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://biopragmatics.github.io/providers/cemo/$1" }, "ceph": { "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "deprecated": true, "description": "An anatomical and developmental ontology for cephalopods", "download_obo": "https://raw.githubusercontent.com/obophenotype/cephalopod-ontology/master/ceph.obo", "download_owl": "http://purl.obolibrary.org/obo/ceph.owl", "example": "0000109", "homepage": "https://github.com/obophenotype/cephalopod-ontology", "keywords": [ "anatomy", "fisheries science", "life cycle", "obo", "ontology", "zoology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "CEPH", "biocontext": "CEPH", "bioportal": "CEPH", "fairsharing": "FAIRsharing.p58bm4", "obofoundry": "ceph", "ols": "ceph", "ontobee": "CEPH" }, "name": "Cephalopod Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CEPH", "rdf_uri_format": "http://purl.obolibrary.org/obo/CEPH_$1", "repository": "https://github.com/obophenotype/cephalopod-ontology", "uri_format": "http://purl.obolibrary.org/obo/CEPH_$1", "version": "2016-01-12" }, "cgd": { "contact": { "email": "gsherloc@stanford.edu", "name": "Gavin Sherlock", "orcid": "0000-0002-1692-4983" }, "description": "The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products.", "example": "CAL0003079", "homepage": "http://www.candidagenome.org/", "keywords": [ "eukaryotic", "genome", "life science", "nucleotide" ], "mappings": { "biocontext": "CGD", "fairsharing": "FAIRsharing.j7j53", "go": "CGD", "integbio": "nbdc00391", "miriam": "cgd", "n2t": "cgd", "ncbi": "CGD", "prefixcommons": "cgd", "re3data": "r3d100010617", "uniprot": "DB-0126" }, "name": "Candida Genome Database", "pattern": "^CAL\\d{7}$", "preferred_prefix": "cgd", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/cgd:$1" } ], "publications": [ { "doi": "10.1093/nar/gkw924", "pmc": "PMC5210628", "pubmed": "27738138", "title": "The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data", "year": 2016 }, { "doi": "10.1093/nar/gkr945", "pmc": "PMC3245171", "pubmed": "22064862", "title": "The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata", "year": 2011 }, { "doi": "10.1093/nar/gki003", "pmc": "PMC539957", "pubmed": "15608216", "title": "The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information", "year": 2005 } ], "uri_format": "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1" }, "cghdb": { "description": "Cell line databases/resources", "example": "300165/p13898_2106T", "homepage": "http://www.cghtmd.jp/CGHDatabase/index_e.jsp", "mappings": { "cellosaurus": "CGH-DB" }, "name": "CGH Data Base", "preferred_prefix": "cghdb", "uri_format": "http://www.cghtmd.jp/CGHDatabase/mapViewer?hid=$1&aid=%t&lang=en" }, "cgnc": { "contact": { "email": "fionamcc@arizona.edu", "name": "Fiona M McCarthy", "orcid": "0000-0003-2175-5464" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Nomenclature Consortium around Chicken genes (analogous to the HGNC for humans)", "example": "10087", "homepage": "http://birdgenenames.org/cgnc/", "keywords": [ "gene" ], "mappings": { "prefixcommons": "cgnc", "re3data": "r3d100012429" }, "name": "Chicken Gene Nomenclature Consortium", "pattern": "^\\d+$", "preferred_prefix": "cgnc", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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These entries are supplemented with additional properties, related information and links back to original data sources.", "example": "56586", "homepage": "http://www.chemspider.com/", "keywords": [ "chemistry", "life science", "molecules", "structure" ], "mappings": { "biocontext": "CHEMSPIDER", "cheminf": "000405", "edam": "1173", "fairsharing": "FAIRsharing.96f3gm", "integbio": "nbdc01863", "miriam": "chemspider", "n2t": "chemspider", "prefixcommons": "chemspider", "re3data": "r3d100010205", "wikidata": "P661" }, "name": "ChemSpider", "pattern": "^\\d+$", "preferred_prefix": "chemspider", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/chemspider:$1" } ], "publications": [ { "doi": "10.1021/ed100697w", "title": "ChemSpider: An Online Chemical Information Resource", "year": 2010 } ], "rdf_uri_format": "http://rdf.chemspider.com/$1", "synonyms": [ "ChemSpiderID", "Chemspider" ], "twitter": "ChemSpider", "uri_format": "http://www.chemspider.com/Chemical-Structure.$1.html" }, "chickenqtldb": { "description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references chicken QTLs.", "example": "14362", "homepage": "https://www.animalgenome.org/QTLdb", "keywords": [ "dna", "genome" ], "mappings": { "biocontext": "CHICKENQTLDB", "miriam": "chickenqtldb", "n2t": "chickenqtldb", "prefixcommons": "chickenqtldb" }, "name": "Animal Genome Chicken QTL", "part_of": "qtldb", "pattern": "^\\d+$", "preferred_prefix": "chickenqtldb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/chickenqtldb:$1" } ], "uri_format": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1" }, "chictr": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Established in 2005 by professor Wu Taixiang and Li Youping team, West China Hospital, Sichuan University, and the Ministry of Health of China assigned it to be the representative of China to join WHO ICTRP in 2007. The Chinese Clinical Trial Registry provides the services include register for trials, consultation for trial design, central randomization for an allocation sequence, peer review for draft articles and training for peer reviewers. (from website)", "example": "ChiCTR2300070727", "homepage": "https://www.chictr.org.cn", "logo": "https://www.chictr.org.cn/images/top.jpg", "name": "Chinese Clinical Trial Registry", "pattern": "^ChiCTR(-[A-Z]+-)?\\d+$", "preferred_prefix": "chictr", "references": [ "https://www.chictr.org.cn/showproj.html?proj=187605" ] }, "chiro": { "contact": { "email": "vasilevs@ohsu.edu", "github": "nicolevasilevsky", "name": "Nicole Vasilevsky", "orcid": "0000-0001-5208-3432" }, "depends_on": [ "chebi", "go", "hp", "mp", "ncbitaxon", "pr", "uberon" ], "description": "CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes.", "download_obo": "http://purl.obolibrary.org/obo/chiro.obo", "download_owl": "http://purl.obolibrary.org/obo/chiro.owl", "homepage": "https://github.com/obophenotype/chiro", "keywords": [ "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "CHIRO", "bioportal": "CHIRO", "obofoundry": "chiro", "ols": "chiro", "ontobee": "CHIRO" }, "name": "ChEBI Integrated Role Ontology", "no_own_terms": true, "preferred_prefix": "CHIRO", "publications": [ { "doi": "10.26434/chemrxiv.12591221", "title": "Extension of Roles in the ChEBI Ontology", "year": 2020 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/CHIRO_$1", "repository": "https://github.com/obophenotype/chiro", "uri_format": "http://purl.obolibrary.org/obo/CHIRO_$1", "version": "2015-11-23" }, "chmo": { "appears_in": [ "rbo", "scdo" ], "contact": { "email": "batchelorc@rsc.org", "github": "batchelorc", "name": "Colin Batchelor", "orcid": "0000-0001-5985-7429" }, "description": "CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI).", "download_obo": "http://purl.obolibrary.org/obo/chmo.obo", "download_owl": "http://purl.obolibrary.org/obo/chmo.owl", "example": "0002902", "homepage": "https://github.com/rsc-ontologies/rsc-cmo", "keywords": [ "assay", "chemistry", "chromatography", "electron microscopy", "mass spectrometry assay", "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "CHMO", "bartoc": "20509", "biocontext": "CHMO", "bioportal": "CHMO", "fairsharing": "FAIRsharing.9j4wh2", "obofoundry": "chmo", "ols": "chmo", "ontobee": "CHMO" }, "name": "Chemical Methods Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CHMO", "rdf_uri_format": "http://purl.obolibrary.org/obo/CHMO_$1", "repository": "https://github.com/rsc-ontologies/rsc-cmo", "uri_format": "http://purl.obolibrary.org/obo/CHMO_$1", "version": "2022-04-19" }, "cido": { "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", "name": "Yongqun Oliver He", "orcid": "0000-0001-9189-9661" }, "description": "The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment.", "download_owl": "https://github.com/CIDO-ontology/cido/raw/master/cido.owl", "example": "0000005", "homepage": "https://github.com/cido-ontology/cido", "keywords": [ "bioinformatics", "covid-19", "disease", "drug", "drug discovery", "drug interaction", "drug repositioning", "epidemiology", "infection", "obo", "ontology", "virology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "CIDO", "bioportal": "CIDO", "fairsharing": "FAIRsharing.aVmpKl", "obofoundry": "cido", "ols": "cido", "ontobee": "CIDO" }, "name": "Coronavirus Infectious Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CIDO", "publications": [ { "doi": "10.1186/s13326-022-00279-z", "pmc": "PMC9585694", "pubmed": "36271389", "title": "A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology", "year": 2022 }, { "doi": "10.1038/s41597-020-0523-6", "pmc": "PMC7293349", "pubmed": "32533075", "title": "CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis", "year": 2020 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/CIDO_$1", "repository": "https://github.com/cido-ontology/cido", "uri_format": "http://purl.obolibrary.org/obo/CIDO_$1", "version": "2024-02-16" }, "cienciavitae": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "identifier of scientific author in www.cienciavitae.pt", "example": "0C1F-DA6C-4B02", "homepage": "https://www.ciencia-id.pt", "keywords": [ "person", "researcher" ], "mappings": { "wikidata": "P7893" }, "name": "CIÊNCIAVITAE ID", "pattern": "^([0-9A-F]{4}-){2}[0-9A-F]{4}$", "preferred_prefix": "cienciavitae", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1171" ], "uri_format": "https://www.cienciavitae.pt/$1" }, "cio": { "contact": { "email": "frederic.bastian@unil.ch", "github": "fbastian", "name": "Frédéric Bastian", "orcid": "0000-0002-9415-5104" }, "description": "An ontology to capture confidence information about annotations.", "download_obo": "http://purl.obolibrary.org/obo/cio.obo", "download_owl": "http://purl.obolibrary.org/obo/cio.owl", "example": "0000040", "homepage": "https://github.com/BgeeDB/confidence-information-ontology", "keywords": [ "annotation", "biology", "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "CIO", "biocontext": "CIO", "bioportal": "CIO", "fairsharing": "FAIRsharing.e3t0yw", "obofoundry": "cio", "ols": "cio", "ontobee": "CIO" }, "name": "Confidence Information Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CIO", "publications": [ { "doi": "10.1093/database/bav043", "pmc": "PMC4425939", "pubmed": "25957950", "title": "The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations", "year": 2015 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/CIO_$1", "repository": "https://github.com/BgeeDB/confidence-information-ontology", "uri_format": "http://purl.obolibrary.org/obo/CIO_$1", "version": "2015-03-10" }, "citexplore": { "contact": { "email": "maria.taboada@usc.es", "name": "Maria Taboada", "orcid": "0000-0002-2353-596X" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "One of the precursors to the EuropePMC project. Now EuropePMC is able to resolve CiteXplore codes.", "example": "C6155", "homepage": "https://www.ebi.ac.uk/citexplore/", "keywords": [ "biomedical science", "brain", "disease", "genetics", "lipid", "phenotype", "preclinical studies" ], "mappings": { "fairsharing": "FAIRsharing.619eqr", "prefixcommons": "citexplore" }, "name": "CiteXplore", "preferred_prefix": "citexplore", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/citexplore:$1" } ], "publications": [ { "doi": "10.1097/mol.0b013e328362df13", "pubmed": "23759795", "title": "Cerebrotendinous xanthomatosis", "year": 2013 } ], "references": [ "https://www.embl.de/aboutus/communication_outreach/media_relations/2006/061127_hinxton/" ], "synonyms": [ "CTX" ], "uri_format": "https://europepmc.org/article/CTX/$1" }, "cito": { "contact": { "email": "silvio.peroni@unibo.it", "github": "essepuntato", "name": "Silvio Peroni", "orcid": "0000-0003-0530-4305" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology that enables characterization of the nature or type of citations, both factually and rhetorically.", "example": "sharesAuthorInstitutionWith", "homepage": "http://www.sparontologies.net/ontologies/cito", "keywords": [ "citation", "data model", "knowledge and information systems", "spar" ], "mappings": { "fairsharing": "FAIRsharing.b220d4", "lov": "cito" }, "name": "Citation Typing Ontology", "preferred_prefix": "CiTO", "publications": [ { "doi": "10.1016/j.websem.2012.08.001", "title": "FaBiO and CiTO: Ontologies for describing bibliographic resources and citations", "year": 2012 } ], "repository": "https://github.com/sparontologies/cito", "twitter": "sparontologies", "uri_format": "http://purl.org/spar/cito/$1" }, "civic.aid": { "contact": { "email": "mgriffit@wustl.edu", "github": "malachig", "name": "Malachi Griffith", "orcid": "0000-0002-6388-446X" }, "description": "A CIViC assertion classifies the clinical significance of a variant-disease relationship under recognized guidelines. The CIViC Assertion (AID) summarizes a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic, prognostic or predisposing clinical information for a variant in a specific cancer context. CIViC currently has two main types of Assertions: those based on variants of primarily somatic origin (predictive/therapeutic, prognostic, and diagnostic) and those based on variants of primarily germline origin (predisposing). When the number and quality of Predictive, Prognostic, Diagnostic or Predisposing Evidence Items (EIDs) in CIViC sufficiently cover what is known for a particular variant and cancer type, then a corresponding assertion be created in CIViC.", "example": "3", "homepage": "https://civicdb.org/", "license": "CC0-1.0", "mappings": { "miriam": "civic.aid" }, "name": "CIViC Assertion", "part_of": "civic", "pattern": "^[0-9]+$", "preferred_prefix": "civic.aid", "synonyms": [ "civic.assertion" ], "uri_format": "https://civicdb.org/links/assertions/$1" }, "civic.did": { "contact": { "email": "mgriffit@wustl.edu", "github": "malachig", "name": "Malachi Griffith", "orcid": "0000-0002-6388-446X" }, "description": "Within the CIViC database, the disease should be the cancer or cancer subtype that is a result of the described variant. The disease selected should be as specific as possible should reflect the disease type used in the source that supports the evidence statement.", "example": "46", "homepage": "https://civicdb.org/", "license": "CC0-1.0", "mappings": { "miriam": "civic.did" }, "name": "CIViC Disease", "part_of": "civic", "pattern": "^[0-9]+$", "preferred_prefix": "civic.did", "synonyms": [ "civic.disease" ], "uri_format": "https://civicdb.org/links/diseases/$1" }, "civic.eid": { "contact": { "email": "mgriffit@wustl.edu", "github": "malachig", "name": "Malachi Griffith", "orcid": "0000-0002-6388-446X" }, "description": "Evidence Items are the central building block of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece of information that has been manually curated from trustable medical literature about a Variant or genomic ‘event’ that has implications in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy, Oncogenicity or protein Function. For example, an Evidence Item might describe a line of evidence supporting the notion that tumors with a somatic BRAF V600 mutation generally respond well to the drug dabrafenib. A Variant may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds to a single citable Source (a publication or conference abstract).", "example": "1199", "homepage": "https://civicdb.org/", "license": "CC0-1.0", "mappings": { "miriam": "civic.eid" }, "name": "CIViC Evidence", "part_of": "civic", "pattern": "^[0-9]+$", "preferred_prefix": "civic.eid", "synonyms": [ "civic.evidence" ], "uri_format": "https://civicdb.org/links/evidence/$1" }, "civic.gid": { "contact": { "email": "mgriffit@wustl.edu", "github": "malachig", "name": "Malachi Griffith", "orcid": "0000-0002-6388-446X" }, "description": "A CIViC Gene Summary is created to provide a high-level overview of clinical relevance of cancer variants for the gene. Gene Summaries in CIViC focus on emphasizing the clinical relevance from a molecular perspective rather than describing the biological function of the gene unless necessary to contextualize its clinical relevance in cancer. Gene Summaries include relevant cancer subtypes, specific treatments for the gene’s associated variants, pathway interactions, functional alterations caused by the variants in the gene, and normal/abnormal functions of the gene with associated roles in oncogenesis", "example": "272", "homepage": "https://civicdb.org/", "license": "CC0-1.0", "mappings": { "miriam": "civic.gid", "wikidata": "P11277" }, "name": "CIViC gene", "part_of": "civic", "pattern": "^[0-9]+$", "preferred_prefix": "civic.gid", "synonyms": [ "civic.gene" ], "uri_format": "https://civicdb.org/links/gene/$1" }, "civic.mpid": { "contact": { "email": "mgriffit@wustl.edu", "github": "malachig", "name": "Malachi Griffith", "orcid": "0000-0002-6388-446X" }, "description": "CIViC Molecular Profiles are combinations of one or more CIViC variants. Most Molecular Profiles are “Simple” Molecular Profiles comprised of a single variant. In most cases, these can be considered equivalent to the CIViC concept of a Variant. However, increasingly clinical significance must be considered in the context of multiple variants simultaneously. Complex Molecular Profiles in CIViC allow for curation of such variant combinations. Regardless of the nature of the Molecular Profile (Simple or Complex), it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional clinical relevance to be entered in CIViC.", "example": "559", "homepage": "https://civicdb.org/", "license": "CC0-1.0", "mappings": { "miriam": "civic.mpid" }, "name": "CIViC Molecular Profile", "pattern": "^[0-9]+$", "preferred_prefix": "civic.mpid", "synonyms": [ "civic.molecularprofile" ], "uri_format": "https://civicdb.org/links/molecular_profile/$1" }, "civic.sid": { "contact": { "email": "mgriffit@wustl.edu", "github": "malachig", "name": "Malachi Griffith", "orcid": "0000-0002-6388-446X" }, "description": "In CIViC, each Evidence Item must be associated with a Source Type and Source ID, which link the Evidence Item to the original source of information supporting clinical claims. Currently, CIViC accepts publications indexed on PubMed OR abstracts published through the American Society of Clinical Oncology (ASCO). Each such source entered into CIViC is assigned a unique identifier and expert curators can curate guidance that assists future curators in the interpretation of information from this source.", "example": "62", "homepage": "https://civicdb.org/", "license": "CC0-1.0", "mappings": { "miriam": "civic.sid" }, "name": "CIViC Source", "part_of": "civic", "pattern": "^[0-9]+$", "preferred_prefix": "civic.sid", "synonyms": [ "civic.source" ], "uri_format": "https://civicdb.org/links/sources/$1" }, "civic.tid": { "contact": { "email": "mgriffit@wustl.edu", "github": "malachig", "name": "Malachi Griffith", "orcid": "0000-0002-6388-446X" }, "description": "Therapies (often drugs) in CIViC are associated with Predictive Evidence Types, which describe sensitivity, resistance or adverse response to therapies when a given variant is present. The Therapy field may also be used to describe more general treatment types and regimes, such as FOLFOX or Radiation, as long as the literature derived Evidence Item makes a scientific association between the Therapy (treatment type) and the presence of the variant.", "example": "14", "homepage": "https://civicdb.org/", "license": "CC0-1.0", "mappings": { "miriam": "civic.tid" }, "name": "CIViC Therapy", "part_of": "civic", "pattern": "^[0-9]+$", "preferred_prefix": "civic.tid", "synonyms": [ "civic.therapy" ], "uri_format": "https://civicdb.org/links/drugs/$1" }, "civic.vgid": { "contact": { "email": "mgriffit@wustl.edu", "github": "malachig", "name": "Malachi Griffith", "orcid": "0000-0002-6388-446X" }, "description": "Variant Groups in CIViC provide user-defined grouping of Variants within and between genes based on unifying characteristics. CIViC curators are required to define a cohesive rationale for grouping these variants together, summarize their relevance to cancer diagnosis, prognosis or treatment and highlight any treatments or cancers of particular relevance", "example": "16", "homepage": "https://civicdb.org/", "license": "CC0-1.0", "mappings": { "miriam": "civic.vgid" }, "name": "CIViC Variant Group", "pattern": "^[0-9]+$", "preferred_prefix": "civic.vgid", "synonyms": [ "civic.variantgroup" ], "uri_format": "https://civicdb.org/links/variant_group/$1" }, "civic.vid": { "contact": { "email": "mgriffit@wustl.edu", "github": "malachig", "name": "Malachi Griffith", "orcid": "0000-0002-6388-446X" }, "description": "CIViC variants are usually genomic alterations, including single nucleotide variants (SNVs), insertion/deletion events (indels), copy number alterations (CNV’s such as amplification or deletion), structural variants (SVs such as translocations and inversions), and other events that differ from the “normal” genome. In some cases a CIViC variant may represent events of the transcriptome or proteome. For example, ‘expression’ or ‘over-expression’ is a valid variant. Regardless of the variant, it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional relevance that is clinical in nature to be entered in CIViC. i.e. There must be some rationale for why curation of this variant could ultimately aid clinical decision making.", "example": "12", "homepage": "https://civicdb.org/", "license": "CC0-1.0", "mappings": { "miriam": "civic.vid", "wikidata": "P3329" }, "name": "CIViC variant", "part_of": "civic", "pattern": "^[0-9]+$", "preferred_prefix": "civic.vid", "synonyms": [ "civic.variant" ], "uri_format": "https://civicdb.org/links/variant/$1" }, "cl": { "appears_in": [ "clo", "ecao", "ehdaa2", "go", "mco", "pcl", "uberon", "xpo" ], "banana": "CL", "contact": { "email": "addiehl@buffalo.edu", "github": "addiehl", "name": "Alexander Diehl", "orcid": "0000-0001-9990-8331" }, "contributor_extras": [ { "github": "anitacaron", "name": "Anita Caron", "orcid": "0000-0002-6523-4866" } ], "depends_on": [ "chebi", "go", "ncbitaxon", "pato", "pr", "ro", "uberon" ], "description": "The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi.", "download_obo": "https://github.com/obophenotype/cell-ontology/raw/master/cl.obo", "download_owl": "http://purl.obolibrary.org/obo/cl.owl", "example": "0000062", "homepage": "https://obophenotype.github.io/cell-ontology/", "keywords": [ "anatomy", "annotation", "cell", "cell biology", "life science", "morphology", "obo", "ontology" ], "license": "CC-BY-4.0", "logo": "https://obofoundry.org/images/CL-logo.jpg", "mappings": { "aberowl": "CL", "agroportal": "CL", "biocontext": "CL", "bioportal": "CL", "cellosaurus": "CL", "fairsharing": "FAIRsharing.j9y503", "go": "CL", "miriam": "cl", "n2t": "cl", "obofoundry": "cl", "ols": "cl", "ontobee": "CL", "prefixcommons": "cl", "wikidata": "P7963" }, "name": "Cell Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "CL", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/cl:$1" }, { "code": "cellguide", "description": "CellGuide is a comprehensive resource for knowledge about cell types.", "homepage": "https://cellxgene.cziscience.com/cellguide", "name": "Cell Guide", "uri_format": "https://cellxgene.cziscience.com/cellguide/CL_$1" }, { "code": "cellxgene", "description": "Explore single cell data through the CZ CELLxGENE portal", "homepage": "https://onto.cellxgene-labs.prod.si.czi.technology", "name": "CELLxGENE", "uri_format": "https://onto.cellxgene-labs.prod.si.czi.technology/a/ontology/CL/CL:$1" } ], "publications": [ { "doi": "10.1186/s13326-016-0088-7", "pmc": "PMC4932724", "pubmed": "27377652", "title": "The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability", "year": 2016 }, { "doi": "10.1186/1471-2105-12-6", "pmc": "PMC3024222", "pubmed": "21208450", "title": "Logical development of the cell ontology", "year": 2011 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/CL_$1", "repository": "https://github.com/obophenotype/cell-ontology", "twitter": "CellOntology", "uri_format": "http://purl.obolibrary.org/obo/CL_$1", "version": "2024-08-16" }, "clao": { "contact": { "email": "lagonzalezmo@unal.edu.co", "github": "luis-gonzalez-m", "name": "Luis González-Montaña", "orcid": "0000-0002-9136-9932" }, "depends_on": [ "ro" ], "description": "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).", "download_obo": "http://purl.obolibrary.org/obo/clao.obo", "download_owl": "http://purl.obolibrary.org/obo/clao.owl", "example": "0000088", "homepage": "https://github.com/luis-gonzalez-m/Collembola", "keywords": [ "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "CLAO", "bioportal": "CLAO", "obofoundry": "clao", "ols": "clao", "ontobee": "CLAO" }, "name": "Collembola Anatomy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CLAO", "rdf_uri_format": "http://purl.obolibrary.org/obo/CLAO_$1", "repository": "https://github.com/luis-gonzalez-m/Collembola", "uri_format": "http://purl.obolibrary.org/obo/CLAO_$1", "version": "2021-09-27" }, "classyfire": { "banana": "C", "comment": "There's a mismatch between the MIRIAM URI format string, which has a C prefix in front of class identifiers and the ontology which does not use them.", "description": "ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textual description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds. Moreover, ClassyFire allows for text-based search via its web interface. It can be accessed via the web interface or via the ClassyFire API.", "download_obo": "http://classyfire.wishartlab.com/system/downloads/1_0/chemont/ChemOnt_2_1.obo.zip", "example": "0004828", "homepage": "http://classyfire.wishartlab.com/", "keywords": [ "ontology" ], "mappings": { "miriam": "classyfire" }, "name": "ClassyFire", "pattern": "^\\d{7}$", "preferred_prefix": "classyfire", "synonyms": [ "CHEMONTID" ], "uri_format": "http://classyfire.wishartlab.com/tax_nodes/C$1" }, "clb": { "description": "ChecklistBank is an index and repository for taxonomic and nomenclatural datasets", "example": "1010", "homepage": "https://www.checklistbank.org", "mappings": { "miriam": "clb" }, "name": "ChecklistBank", "pattern": "^[0-9]+(LR)?$", "preferred_prefix": "clb", "uri_format": "https://www.checklistbank.org/dataset/$1" }, "cldb": { "description": "The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. 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Studies listed in the database are conducted in 175 countries", "example": "NCT00222573", "homepage": "https://clinicaltrials.gov/", "keywords": [ "disease", "drug", "human" ], "mappings": { "biocontext": "CLINICALTRIALS", "miriam": "clinicaltrials", "n2t": "clinicaltrials", "prefixcommons": "clinicaltrials", "wikidata": "P3098" }, "name": "ClinicalTrials.gov", "pattern": "^NCT\\d{8}$", "preferred_prefix": "clinicaltrials", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/clinicaltrials:$1" }, { "code": "smartpatients", "description": "Smart Patients is an online community for patients and their families. Join us to talk with other patients about the latest research for your condition.", "homepage": "https://www.smartpatients.com", "name": "Smart Patients", "uri_format": "https://www.smartpatients.com/trials/$1" } ], "synonyms": [ "NCT", "clinicaltrial", "ctgov" ], "uri_format": "https://www.clinicaltrials.gov/study/$1" }, "clinvar": { "contact": { "email": "maglott@ncbi.nlm.nih.gov", "name": "Donna R. Maglott", "orcid": "0000-0001-7451-4467" }, "description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier.", "example": "12345", "homepage": "http://www.ncbi.nlm.nih.gov/clinvar/", "keywords": [ "biomedical science", "clinical studies", "genomics", "preclinical studies" ], "mappings": { "biocontext": "ClinVarVariant", "biolink": "CLINVAR", "cellosaurus": "ClinVar", "fairsharing": "FAIRsharing.wx5r6f", "hl7": "2.16.840.1.113883.6.319", "integbio": "nbdc01514", "miriam": "clinvar", "n2t": "clinvar", "re3data": "r3d100013331", "togoid": "Clinvar", "wikidata": "P1929" }, "name": "ClinVar Variation", "pattern": "^\\d+$", "preferred_prefix": "clinvar", "publications": [ { "doi": "10.1093/nar/gkt1113", "pmc": "PMC3965032", "pubmed": "24234437", "title": "ClinVar: public archive of relationships among sequence variation and human phenotype", "year": 2013 } ], "synonyms": [ "clinvar.variant", "clinvar.variation" ], "uri_format": "https://www.ncbi.nlm.nih.gov/clinvar/variation/$1" }, "clinvar.record": { "description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession.", "example": "RCV000033555.3", "homepage": "http://www.ncbi.nlm.nih.gov/clinvar/", "mappings": { "biocontext": "CLINVAR.RECORD", "miriam": "clinvar.record", "n2t": "clinvar.record" }, "name": "ClinVar Record", "part_of": "clinvar", "pattern": "^RCV\\d+(\\.\\d+)?$", "preferred_prefix": "clinvar.record", "uri_format": "http://www.ncbi.nlm.nih.gov/clinvar/$1" }, "clinvar.submission": { "description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession.", "example": "SCV000151292", "homepage": "http://www.ncbi.nlm.nih.gov/clinvar/", "mappings": { "biocontext": "CLINVAR.SUBMISSION", "miriam": "clinvar.submission", "n2t": "clinvar.submission" }, "name": "ClinVar Submission", "pattern": "^SCV\\d+(\\.\\d+)?$", "preferred_prefix": "clinvar.submission", "uri_format": "http://www.ncbi.nlm.nih.gov/clinvar?term=$1" }, "clinvar.submitter": { "description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters (Submitter IDs). Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submitters (submitter ids) that submit the submissions (SCVs).", "example": "26957", "homepage": "https://www.ncbi.nlm.nih.gov/clinvar/", "mappings": { "miriam": "clinvar.submitter" }, "name": "ClinVar Submitter", "pattern": "^\\d+$", "preferred_prefix": "clinvar.submitter", "uri_format": "https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1" }, "clo": { "appears_in": [ "mco" ], "contact": { "email": "zhengj2007@gmail.com", "github": "zhengj2007", "name": "Jie Zheng", "orcid": "0000-0002-2999-0103" }, "depends_on": [ "cl", "doid", "ncbitaxon", "uberon" ], "description": "The Cell Line Ontology is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns.", "download_owl": "http://purl.obolibrary.org/obo/clo.owl", "example": "0000091", "homepage": "https://github.com/CLO-Ontology/CLO", "keywords": [ "cell", "cell biology", "cell line", "life science", "morphology", "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "CLO", "biocontext": "CLO", "bioportal": "CLO", "cellosaurus": "CLO", "fairsharing": "FAIRsharing.4dvtcz", "miriam": "clo", "obofoundry": "clo", "ols": "clo", "ontobee": "CLO", "prefixcommons": "clo", "wikidata": "P2158" }, "name": "Cell Line Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CLO", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/clo:$1" }, { "code": "bioportal", "description": "Our vision is that all biomedical knowledge and data are disseminated on the Internet using principled ontologies in such a way that the knowledge and data are semantically interoperable and useful for furthering biomedical science and clinical care. Our mission is to create software and support services for the application of principled ontologies in biomedical science and clinical care, ranging from tools for application developers to software for end-users.", "homepage": "https://bioportal.bioontology.org", "name": "Center for Biomedical Informatics Research, Stanford", "uri_format": "https://bioportal.bioontology.org/ontologies/CLO/?p=classes&conceptid=http://purl.obolibrary.org/obo/CLO_$1" } ], "publications": [ { "doi": "10.1186/2041-1480-5-37", "pmc": "PMC4387853", "pubmed": "25852852", "title": "CLO: The cell line ontology", "year": 2014 }, { "doi": "10.1186/gb-2005-6-2-r21", "pmc": "PMC551541", "pubmed": "15693950", "title": "An ontology for cell types", "year": 2005 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/CLO_$1", "repository": "https://github.com/CLO-Ontology/CLO", "synonyms": [ "CLO" ], "uri_format": "http://purl.obolibrary.org/obo/CLO_$1", "version": "2.1.188" }, "cls": { "description": "Cell line collections (Providers)", "example": "300108/p3934_A-172", "homepage": "https://www.cytion.com/", "mappings": { "cellosaurus": "CLS" }, "name": "Cell Lines Service", "preferred_prefix": "cls", "uri_format": "https://www.cytion.com/$1" }, "clyh": { "contact": { "email": "lucas.leclere@obs-vlfr.fr", "github": "L-Leclere", "name": "Lucas Leclere", "orcid": "0000-0002-7440-0467" }, "depends_on": [ "iao", "ro", "uberon" ], "description": "Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica.", "download_obo": "http://purl.obolibrary.org/obo/clyh.obo", "download_owl": "http://purl.obolibrary.org/obo/clyh.owl", "example": "1000100", "homepage": "https://github.com/EBISPOT/clyh_ontology", "keywords": [ "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "CLYH", "bioportal": "CLYH", "obofoundry": "clyh", "ols": "clyh", "ontobee": "CLYH" }, "name": "Clytia hemisphaerica Development and Anatomy Ontology", "pattern": "^\\d+$", "preferred_prefix": "CLYH", "rdf_uri_format": "http://purl.obolibrary.org/obo/CLYH_$1", "repository": "https://github.com/EBISPOT/clyh_ontology", "uri_format": "http://purl.obolibrary.org/obo/CLYH_$1", "version": "2020-05-29" }, "cmecs": { "contact": { "email": "kate.rose@noaa.gov", "name": "Kate Rose" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard.", "download_owl": "http://aber-owl.net/media/ontologies/CMECS/2/cmecs.owl", "example": "595", "homepage": "https://cmecscatalog.org/cmecs", "keywords": [ "ecology", "marine ecology", "ontology" ], "mappings": { "aberowl": "CMECS", "bioportal": "CMECS" }, "name": "Costal and Marine Ecological Classification Standard", "pattern": "^\\d+$", "preferred_prefix": "cmecs", "references": [ "http://www.natureserve.org/sites/default/files/publications/files/cmecs_version_06-2012_final.pdf" ], "uri_format": "https://cmecscatalog.org/cmecs/classification/unit/$1.html" }, "cmf": { "contact": { "email": "engelsta@ohsu.edu", "name": "Mark Engelstad", "orcid": "0000-0001-5889-4463" }, "deprecated": true, "description": "This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain", "homepage": "https://code.google.com/p/craniomaxillofacial-ontology/", "keywords": [ "obo", "ontology" ], "mappings": { "aberowl": "CMF", "biocontext": "CMF", "obofoundry": "cmf", "ontobee": "CMF" }, "name": "CranioMaxilloFacial ontology", "preferred_prefix": "CMF", "rdf_uri_format": "http://purl.obolibrary.org/obo/CMF_$1", "uri_format": "http://purl.obolibrary.org/obo/CMF_$1" }, "cmo": { "appears_in": [ "scdo" ], "contact": { "email": "jrsmith@mcw.edu", "github": "jrsjrs", "name": "Jennifer Smith", "orcid": "0000-0002-6443-9376" }, "description": "Morphological and physiological measurement records generated from clinical and model organism research and health programs.", "download_obo": "http://purl.obolibrary.org/obo/cmo.obo", "download_owl": "http://purl.obolibrary.org/obo/cmo.owl", "example": "0001350", "homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html", "keywords": [ "biomedical science", "disease", "electronic health record", "life science", "model organism", "obo", "ontology", "phenotype", "preclinical studies" ], "license": "CC0-1.0", "logo": "http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif", "mappings": { "aberowl": "CMO", "biocontext": "CMO", "bioportal": "CMO", "fairsharing": "FAIRsharing.dq78pn", "obofoundry": "cmo", "ols": "cmo", "ontobee": "CMO" }, "name": "Clinical measurement ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CMO", "publications": [ { "doi": "10.1186/2041-1480-4-26", "pmc": "PMC3882879", "pubmed": "24103152", "title": "The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications", "year": 2013 }, { "doi": "10.3389/fgene.2012.00087", "pmc": "PMC3361058", "pubmed": "22654893", "title": "Three ontologies to define phenotype measurement data", "year": 2012 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/CMO_$1", "repository": "https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology", "twitter": "ratgenome", "uri_format": "http://purl.obolibrary.org/obo/CMO_$1", "version": "2.224" }, "cmpo": { "contact": { "email": "jupp@ebi.ac.uk", "name": "Simon Jupp", "orcid": "0000-0002-0643-3144" }, "description": "CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations.", "download_owl": "http://www.ebi.ac.uk/cmpo/releases/2017-12-19/cmpo.owl", "example": "0000435", "homepage": "http://www.ebi.ac.uk/cmpo", "keywords": [ "cell", "cell biology", "cellular component", "microscopy", "ontology", "phenotype" ], "mappings": { "aberowl": "CMPO", "bioportal": "CMPO", "fairsharing": "FAIRsharing.knp11s", "ols": "cmpo" }, "name": "Cellular Microscopy Phenotype Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "cmpo", "publications": [ { "doi": "10.1186/s13326-016-0074-0", "pmc": "PMC4870745", "pubmed": "27195102", "title": "The cellular microscopy phenotype ontology", "year": 2016 } ], "repository": "https://github.com/EBISPOT/CMPO", "twitter": "EBIOLS", "uri_format": "http://www.ebi.ac.uk/cmpo/CMPO_$1", "version": "2017-12-19" }, "cnrs": { "comment": "Motivated to add because of appearance in ROR", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "identifier for an academic research group issued by the CNRS", "example": "UMR7315", "homepage": "https://annuaire.cnrs.fr", "mappings": { "wikidata": "P4550" }, "name": "French National Center for Scientific Research - Research Group Identifier", "pattern": "^(UMR|UMS|UMI|UPR|URA|USR|GDR|EA|FR|SNC|ERL|FRC|FRE|IFR|MOY)\\d+$", "preferred_prefix": "cnrs", "uri_format": "https://web-ast.dsi.cnrs.fr/l3c/owa/structure.infos_admin?&p_lab=$1&p_origine_appel=u" }, "co_320": { "contact": { "email": "j.detras@cgiar.org", "name": "Jeffrey A. 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ICRISAT - July 2015", "example": "0000140", "homepage": "https://cropontology.org/ontology/CO_341/Pigeonpea", "keywords": [ "agriculture", "botany", "food", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_341", "cropoct": "CO_341", "fairsharing": "FAIRsharing.ehe3yp", "ols": "co_341" }, "name": "Pigeonpea ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_341", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_341:$1", "version": "2019-11-18" }, "co_343": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk" }, "description": "version 2019 - pvs", "example": "0100010", "homepage": "https://cropontology.org/ontology/CO_343/Yam", "keywords": [ "agriculture", "botany", "food", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_343", "cropoct": "CO_343", "fairsharing": "FAIRsharing.7e9cff", "ols": "co_343" }, "name": "Yam ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_343", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_343:$1", "version": "2019-10-09" }, "co_345": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk" }, "description": "Brachiaria (forages) ontology TD v5 - Version Oct 2016", "example": "0000127", "homepage": "https://cropontology.org/ontology/CO_345/Brachiaria", "keywords": [ "agriculture", "botany", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_345", "cropoct": "CO_345", "fairsharing": "FAIRsharing.9e9683", "ols": "co_345" }, "name": "Brachiaria ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_345", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_345:$1", "version": "2019-10-09" }, "co_346": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk" }, "description": "oct 2016", "example": "0000199", "homepage": "https://cropontology.org/ontology/CO_346/Mungbean", "keywords": [ "agriculture", "food", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_346", "cropoct": "CO_346", "fairsharing": "FAIRsharing.fgd5gq", "ols": "co_346" }, "name": "Mungbean ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_346", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_346:$1", "version": "2019-10-09" }, "co_347": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk" }, "description": "March 2017 version ", "example": "0000108", "homepage": "http://www.cropontology.org/ontology/CO_347/Castor%20bean", "keywords": [ "agriculture", "botany", "food", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_347", "cropoct": "CO_347", "fairsharing": "FAIRsharing.qrrvyk", "ols": "co_347" }, "name": "Castor bean ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_347", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_347:$1" }, "co_348": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "helpdesk cropontology" }, "description": "Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France).", "example": "1100107", "homepage": "https://cropontology.org/ontology/CO_348/Brassica", "keywords": [ "agriculture", "botany", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_348", "cropoct": "CO_348", "fairsharing": "FAIRsharing.af7a2d", "ols": "co_348" }, "name": "Brassica ontology", "pattern": "^\\d+$", "preferred_prefix": "CO_348", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_348:$1", "version": "2019-11-29" }, "co_350": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Jean-Luc Jannink", "orcid": "0000-0003-4849-628X" }, "description": "Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo", "example": "0000215", "homepage": "https://cropontology.org/ontology/CO_350/Oat", "keywords": [ "agriculture", "botany", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_350", "cropoct": "CO_350", "fairsharing": "FAIRsharing.35e1c3", "ols": "co_350" }, "name": "Oat ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_350", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_350:$1", "version": "2019-10-09" }, "co_356": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Cyril Pommier" }, "description": "Grape Ontology including OIV and bioversity descriptors. INRA July 2017", "example": "4000027", "homepage": "https://cropontology.org/ontology/CO_356/Vitis", "keywords": [ "agriculture", "botany", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_356", "cropoct": "CO_356", "fairsharing": "FAIRsharing.c7f4d7", "ols": "co_356" }, "name": "Vitis ontology", "pattern": "^\\d+$", "preferred_prefix": "CO_356", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_356:$1", "version": "2019-11-29" }, "co_357": { "contact": { "email": "celia.michotey@inrae.fr", "name": "Célia Michotey", "orcid": "0000-0003-1877-1703" }, "description": "This ontology lists all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). Curators: Celia Michotey (INRAE) & Ines Chaves (IBET) - Version 2 submitted on Jun 2020 by INRAE.", "example": "1000290", "homepage": "http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology", "keywords": [ "botany", "life science", "phenotype" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_357", "cropoct": "CO_357", "fairsharing": "FAIRsharing.2b04ae", "ols": "co_357" }, "name": "Woody Plant Ontology ontology", "pattern": "^\\d+$", "preferred_prefix": "CO_357", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_357:$1" }, "co_358": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk" }, "description": "Cotton ontology from CottonGen database - June 2019", "example": "0000139", "homepage": "https://cropontology.org/ontology/CO_358/Cotton", "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_358", "cropoct": "CO_358", "ols": "co_358" }, "name": "Cotton ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_358", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_358:$1", "version": "2020-01-03" }, "co_359": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk" }, "description": "December 2019", "example": "0000947", "homepage": "https://cropontology.org/ontology/CO_359/Sunflower", "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_359", "cropoct": "CO_359", "ols": "co_359" }, "name": "Sunflower ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_359", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_359:$1" }, "co_360": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk" }, "description": "Sugar Kelp trait ontology", "example": "0000071", "homepage": "http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait", "keywords": [ "botany", "life science", "marine environment", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_360", "cropoct": "CO_360", "fairsharing": "FAIRsharing.1c1738", "ols": "co_360" }, "name": "Sugar Kelp trait ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_360", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_360:$1" }, "co_365": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "ICARDA Ethiopia" }, "description": "developed by ICARDA - Dec 2018", "example": "0000205", "homepage": "https://cropontology.org/ontology/CO_365/Fababean", "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_365", "cropoct": "CO_365", "ols": "co_365" }, "name": "Fababean ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_365", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_365:$1", "version": "2019-10-15" }, "co_366": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk" }, "description": "version Dec 2019", "example": "0000072", "homepage": "http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut", "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_366", "cropoct": "CO_366", "ols": "co_366" }, "name": "Bambara groundnut ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_366", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_366:$1" }, "co_367": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk" }, "description": "Quinoa Ontology database of the Crop Ontology (CO_367) of the Generation Challenge Program (GCP) describe traits variables of Quinoa Germinate Database http://germinate.quinoadb.org. Quinoa Phenotyping Consortium Creation Date 23.05.2021", "example": "0000004", "homepage": "http://cropontology.org/term/CO_367:ROOT", "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_367", "cropoct": "CO_367" }, "name": "Quinoa Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_367", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_367:$1" }, "co_370": { "contact": { "email": "ekaterina.chuprikova@eurac.edu", "name": "Ekaterina Chuprikova", "orcid": "0000-0002-8981-0442" }, "description": "Apple (Malus domestica) defines crop traits and variables to support the standardisation of apple breeding databases providing description of agronomic, morphological, physiological, quality traits, its methods and scales.", "example": "0000890", "homepage": "http://cropontology.org/term/CO_370:ROOT", "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_370", "cropoct": "CO_370" }, "name": "Apple Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_370", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_370:$1" }, "cob": { "contact": { "email": "bpeters@lji.org", "github": "bpeters42", "name": "Bjoern Peters", "orcid": "0000-0002-8457-6693" }, "description": "COB brings together key terms from a wide range of OBO projects to improve interoperability.", "download_owl": "http://purl.obolibrary.org/obo/cob.owl", "example": "0000080", "homepage": "https://obofoundry.org/COB/", "keywords": [ "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "COB", "bioportal": "COB", "obofoundry": "cob", "ols": "cob", "ontobee": "COB" }, "name": "Core Ontology for Biology and Biomedicine", "pattern": "^\\d{7}$", "preferred_prefix": "COB", "rdf_uri_format": "http://purl.obolibrary.org/obo/COB_$1", "repository": "https://github.com/OBOFoundry/COB", "uri_format": "http://purl.obolibrary.org/obo/COB_$1", "version": "2023-11-16" }, "coconut": { "comment": "@mSorok is the dev of the resource, hope I got it right!", "contributor": { "email": "adriano.rutz@ik.me", "github": "adafede", "name": "Adriano Rutz", "orcid": "0000-0003-0443-9902" }, "description": "COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source project for Natural Products (NPs) storage, search and analysis. It gathers data from over 50 open NP resources and is available free of charge and without any restriction. Each entry corresponds to a \"flat\" NP structure, and is associated, when available, to their known stereochemical forms, literature, organisms that produce them, natural geographical presence and diverse pre-computed molecular properties.", "example": "CNP0171505", "example_extras": [ "CNP0018459.2" ], "github_request_issue": 221, "homepage": "https://coconut.naturalproducts.net", "keywords": [ "chemistry", "natural producs", "organic chemistry" ], "name": "COlleCtion of Open Natural ProdUcTs", "pattern": "^CNP\\d{7}(\\.\\d+)?$", "preferred_prefix": "coconut", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://coconut.naturalproducts.net/compound/coconut_id/$1" }, "codelink": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray targets most of the known and predictive genes of the human genome as it is described today in the public domain. It is comprised of approximately 55,000 30-mer probes designed to conserved exons across the transcripts of targeted genes. These 55,000 probes represent well annotated, full length, and partial human gene sequences from major public databases. GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8, 2004 release).", "example": "GE86325", "homepage": "https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt", "keywords": [ "microarray", "transcriptomics" ], "name": "GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray", "pattern": "^GE\\d+$", "preferred_prefix": "codelink", "references": [ "https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-8060/A-GEOD-8060.adf.txt", "https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt" ] }, "cog": { "contact": { "email": "cogs@ncbi.nlm.nih.gov", "name": "Michael Y Galperin", "orcid": "0000-0002-2265-5572" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "COGs stands for Clusters of Orthologous Genes. The database was initially created in 1997 (Tatusov et al., PMID: 9381173) followed by several updates, most recently in 2014 (Galperin et al., PMID: 25428365). The current update includes complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. The new features include ~250 updated COG annotations with corresponding references and PDB links, where available; new COGs for proteins involved in CRISPR-Cas immunity, sporulation, and photosynthesis, and the lists of COGs grouped by pathways and functional systems.", "example": "COG0001", "homepage": "https://www.ncbi.nlm.nih.gov/research/cog/", "keywords": [ "genome", "life science", "protein" ], "mappings": { "biolink": "COG", "fairsharing": "FAIRsharing.djsbw2", "go": "COG_Cluster", "miriam": "cog", "prefixcommons": "cog", "togoid": "Cog" }, "name": "Cluster of orthologous genes", "pattern": "^COG\\d+$", "preferred_prefix": "cog", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/cog:$1" } ], "publications": [ { "doi": "10.1126/science.278.5338.631", "pubmed": "9381173", "title": "A genomic perspective on protein families", "year": 1997 }, { "doi": "10.1093/nar/gku1223", "pmc": "PMC4383993", "pubmed": "25428365", "title": "Expanded microbial genome coverage and improved protein family annotation in the COG database", "year": 2014 } ], "synonyms": [ "COG_Cluster" ], "uri_format": "https://www.ncbi.nlm.nih.gov/research/cog/cog/$1" }, "cog.category": { "contact": { "email": "cogs@ncbi.nlm.nih.gov", "name": "Michael Y Galperin", "orcid": "0000-0002-2265-5572" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Higher-level classifications of COG Pathways", "example": "K", "homepage": "https://www.ncbi.nlm.nih.gov/research/cog/", "keywords": [ "pathways" ], "name": "COG Categories", "part_of": "cog", "preferred_prefix": "cog.category", "uri_format": "https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/$1" }, "cog.pathway": { "contact": { "email": "cogs@ncbi.nlm.nih.gov", "name": "Michael Y Galperin", "orcid": "0000-0002-2265-5572" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Database of Clusters of Orthologous Genes grouped by pathways and functional systems. It includes the complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera.", "example": "NAD%20biosynthesis", "homepage": "https://www.ncbi.nlm.nih.gov/research/cog/pathways", "mappings": { "go": "COG_Pathway" }, "name": "COG Pathways", "part_of": "cog", "preferred_prefix": "cog.pathway", "uri_format": "https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1" }, "cohd": { "comment": "not really sure where the source is. this also links to a system called athena. I was not able to figure out what COHD stands for.", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "MIMIC-III is a dataset comprising health-related data associated with over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess Medical Center between 2001 and 2012", "homepage": "https://github.com/MIT-LCP/mimic-omop", "keywords": [ "clinical data", "clinical trials", "health", "health sciences" ], "name": "MIMIC III Database", "no_own_terms": true, "preferred_prefix": "cohd", "repository": "https://github.com/MIT-LCP/mimic-omop" }, "coi": { "contact": { "email": "coi@bot.uc.pt", "name": "COI Catalogue" }, "contributor": { "email": "shah.tanay2@northeastern.edu", "github": "tanayshah2", "name": "Tanay Shah", "orcid": "0009-0001-1912-5132" }, "description": "COI Catalogue is a herbarium with c. 800.000 specimens, organised in separate collections due to the research priorities over the years.", "example": "63812", "homepage": "https://coicatalogue.uc.pt/index.php", "name": "COI Catalogue", "preferred_prefix": "coi", "publications": [ { "doi": "10.1038/s41597-024-03520-9", "pmc": "PMC11193818", "pubmed": "38909064", "title": "O armário: Fruiting phenology data for 4,462 plant taxa in Portugal (1926-2013)", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://coicatalogue.uc.pt/index.php?t=specimen&COINumber=$1" }, "col": { "description": "Identifier of a taxon or synonym in the Catalogue of Life", "example": "4QHKG", "homepage": "https://www.checklistbank.org", "mappings": { "bartoc": "1915", "miriam": "col" }, "name": "Catalogue of Life", "pattern": "^[23456789BCDFGHJKLMNPQRSTVWXYZ]{1,6}$", "preferred_prefix": "col", "providers": [ { "code": "col", "description": "The Catalogue of Life website providing a view onto the latest release of the COL Checklist.", "homepage": "https://www.catalogueoflife.org", "name": "Catalogue of Life (COL)", "uri_format": "https://www.catalogueoflife.org/data/taxon/$1" } ], "uri_format": "https://www.checklistbank.org/dataset/3LR/taxon/$1" }, "col.taiwan": { "contributor": { "email": "meghan.balk@gmail.com", "github": "megbalk", "name": "Meghan Balk", "orcid": "0000-0003-2699-3066" }, "description": "Identifier (name code) for a taxon in the catalogue of life in taiwan", "example": "431472", "github_request_issue": 466, "homepage": "http://taibnet.sinica.edu.tw/home.php", "mappings": { "wikidata": "P3088" }, "name": "Catalogue of Life in Taiwan", "pattern": "^[1-9]\\d{5}$", "preferred_prefix": "col.taiwan", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code=$1" }, "colao": { "contact": { "email": "entiminae@gmail.com", "github": "JCGiron", "name": "Jennifer C. Giron", "orcid": "0000-0002-0851-6883" }, "depends_on": [ "aism", "bfo", "bspo", "caro", "pato", "ro", "uberon" ], "description": "The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research.", "download_obo": "http://purl.obolibrary.org/obo/colao.obo", "download_owl": "http://purl.obolibrary.org/obo/colao.owl", "example": "0000000", "homepage": "https://github.com/insect-morphology/colao", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "COLAO", "bioportal": "COLAO", "obofoundry": "colao", "ols": "colao", "ontobee": "COLAO" }, "name": "Coleoptera Anatomy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "COLAO", "rdf_uri_format": "http://purl.obolibrary.org/obo/COLAO_$1", "repository": "https://github.com/insect-morphology/colao", "uri_format": "http://purl.obolibrary.org/obo/COLAO_$1", "version": "2024-06-21" }, "collagenmutdb": { "description": "This database aims to record all published accounts of variants resulting in osteogenesis imperfecta. Such variants occur in the COL1A1, COL1A2, CRTAP, FKBP10, LEPRE1 and PPIB genes.", "example": "COL3A1", "homepage": "http://www.le.ac.uk/genetics/collagen/", "keywords": [ "gene" ], "mappings": { "prefixcommons": "cmd" }, "name": "Collagen Mutation Database", "preferred_prefix": "collagenmutdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/come:$1" } ], "uri_format": "https://www.flymine.org/come/entry?gn=$1" }, "commoncoreontology": { "contact": { "email": "mpjensen@buffalo.edu", "github": "mark-jensen", "name": "Mark Jensen", "orcid": "0000-0001-9228-8838" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Common Core Ontologies (CCO) comprise twelve ontologies that are designed to represent and integrate taxonomies of generic classes and relations across all domains of interest.\n\nCCO is a mid-level extension of Basic Formal Ontology (BFO), an upper-level ontology framework widely used to structure and integrate ontologies in the biomedical domain (Arp, et al., 2015). BFO aims to represent the most generic categories of entity and the most generic types of relations that hold between them, by defining a small number of classes and relations. CCO then extends from BFO in the sense that every class in CCO is asserted to be a subclass of some class in BFO, and that CCO adopts the generic relations defined in BFO (e.g., has_part) (Smith and Grenon, 2004). Accordingly, CCO classes and relations are heavily constrained by the BFO framework, from which it inherits much of its basic semantic relationships.", "example": "DirectiveInformationContentEntity", "homepage": "http://www.ontologyrepository.com", "keywords": [ "ontology", "upper-level ontology" ], "license": "CC-BY-4.0", "name": "Common Core Ontologies", "preferred_prefix": "commoncoreontology", "repository": "https://github.com/CommonCoreOntology/CommonCoreOntologies", "uri_format": "http://www.ontologyrepository.com/CommonCoreOntologies/$1" }, "complexportal": { "contact": { "email": "bmeldal@ebi.ac.uk", "github": "bmeldal-eg", "name": "Birgit Meldal", "orcid": "0000-0003-4062-6158" }, "description": "A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases.", "example": "CPX-263", "homepage": "https://www.ebi.ac.uk/complexportal", "license": "CC0-1.0", "mappings": { "biocontext": "COMPLEXPORTAL", "biolink": "ComplexPortal", "go": "ComplexPortal", "miriam": "complexportal", "n2t": "complexportal", "re3data": "r3d100013295", "uniprot": "DB-0228", "wikidata": "P7718" }, "name": "Complex Portal", "pattern": "^CPX-[0-9]+$", "preferred_prefix": "complexportal", "publications": [ { "doi": "10.1093/nar/gky1001", "pubmed": "30357405" }, { "doi": "10.1093/nar/gku975", "pmc": "PMC4384031", "pubmed": "25313161", "title": "The complex portal--an encyclopaedia of macromolecular complexes", "year": 2014 } ], "synonyms": [ "ComplexPortal" ], "uri_format": "https://www.ebi.ac.uk/complexportal/complex/$1" }, "comptox": { "description": "The Chemistry Dashboard is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks.", "example": "DTXSID2021028", "homepage": "https://comptox.epa.gov/dashboard", "mappings": { "biocontext": "COMPTOX", "miriam": "comptox", "n2t": "comptox", "wikidata": "P3117" }, "name": "DSSTox substance", "pattern": "^DTXSID\\d+$", "preferred_prefix": "comptox", "uri_format": "https://comptox.epa.gov/dashboard/$1" }, "compulyeast": { "description": "Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. 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"https://www.confident-conference.org/index.php/Category:Event", "keywords": [ "conferences", "meetings", "metascience" ], "name": "ConfIDent Event", "pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$", "preferred_prefix": "confident.event", "uri_format": "https://www.confident-conference.org/index.php/Event:$1" }, "confident.series": { "contact": { "email": "Philip.Stroemert@tib.eu", "github": "StroemPhi", "name": "Philip Strömert", "orcid": "0000-0002-1595-3213" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating.", "example": "AAC", "github_request_issue": 519, "homepage": "https://www.confident-conference.org/index.php/Category:Event_Series", "keywords": [ "conferences", "grouping", "meetings", "metascience" ], "name": "ConfIDent Event Series", "preferred_prefix": "confident.series", "uri_format": "https://www.confident-conference.org/index.php/Event_Series:$1" }, "conoserver": { "contact": { "email": "d.craik@imb.uq.edu.au", "name": "David Craik", "orcid": "0000-0003-0007-6796" }, "description": "ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails.", "example": "2639", "homepage": "http://www.conoserver.org/", "keywords": [ "life science", "neurophysiology", "statistics", "synthetic biology" ], "mappings": { "biocontext": "CONOSERVER", "fairsharing": "FAIRsharing.y00hz4", "miriam": "conoserver", "n2t": "conoserver", "uniprot": "DB-0156" }, "name": "ConoServer", "pattern": "^\\d+$", "preferred_prefix": "conoserver", "publications": [ { "doi": "10.1093/nar/gkr886", "pmc": "PMC3245185", "pubmed": "22058133", "title": "ConoServer: updated content, knowledge, 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"pattern": "^\\d+$", "preferred_prefix": "cordis.article", "uri_format": "https://cordis.europa.eu/article/id/$1" }, "cordis.project": { "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. 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This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies.", "example": "37232", "homepage": "https://www.animalgenome.org", "keywords": [ "animal genetics", "genetics", "life science", "systems biology" ], "mappings": { "fairsharing": "FAIRsharing.IziuCK", "miriam": "corrdb", "re3data": "r3d100011496" }, "name": "CorrDB", "pattern": "^[0-9]+$", "preferred_prefix": "corrdb", "uri_format": "https://www.animalgenome.org/CorrDB/q/?id=CorrID:$1" }, "corum": { "contact": { "email": "andreas.ruepp@helmholtz-muenchen.de", "name": "Andreas Ruepp", "orcid": "0000-0003-1705-3515" }, "description": "The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. 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The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.", "example": "101", "homepage": "http://ctdbase.org/", "mappings": { "biocontext": "CTD.GENE", "biolink": "CTD.GENE", "miriam": "ctd.gene", "n2t": "ctd.gene", "uniprot": "DB-0140" }, "name": "CTD Gene", "part_of": "ctd", "pattern": "^\\d+$", "preferred_prefix": "ctd.gene", "provides": "ncbigene", "publications": [ { "doi": "10.1093/nar/gkaa891", "pmc": "PMC7779006", "pubmed": "33068428", "title": "Comparative Toxicogenomics Database (CTD): update 2021", "year": 2021 } ], "uri_format": "http://ctdbase.org/detail.go?type=gene&acc=$1" }, "cteno": { "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "depends_on": [ "ro", "uberon" ], "description": "An anatomical and developmental ontology for ctenophores (Comb Jellies)", "download_obo": "https://raw.githubusercontent.com/obophenotype/ctenophore-ontology/master/cteno.obo", "download_owl": "http://purl.obolibrary.org/obo/cteno.owl", "example": "0000047", "homepage": "https://github.com/obophenotype/ctenophore-ontology", "keywords": [ "anatomy", "developmental biology", "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "CTENO", "biocontext": "CTENO", "bioportal": "CTENO", "fairsharing": "FAIRsharing.mgxgza", "obofoundry": "cteno", "ols": "cteno", "ontobee": "CTENO" }, "name": "Ctenophore Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CTENO", "rdf_uri_format": "http://purl.obolibrary.org/obo/CTENO_$1", "repository": "https://github.com/obophenotype/ctenophore-ontology", "uri_format": "http://purl.obolibrary.org/obo/CTENO_$1", "version": "2016-10-19" }, "ctis": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This website supports the undertaking and oversight of clinical trials in the European Union (EU) and European Economic Area (EEA). It is part of a broad initiative to transform the EU/EEA clinical trials environment in support of large clinical trials in multiple European countries, to the benefit of medical innovation and patients. (from homepage)", "example": "2023-503698-40-00", "homepage": "https://euclinicaltrials.eu/", "name": "Clinical Trials Information System", "pattern": "^\\d{4}-\\d+-\\d+-\\d+$", "preferred_prefix": "ctis", "uri_format": "https://euclinicaltrials.eu/app/#/view/$1" }, "cto": { "contact": { "email": "alpha.tom.kodamullil@scai.fraunhofer.de", "github": "akodamullil", "name": "Dr. Alpha Tom Kodamullil", "orcid": "0000-0001-9896-3531" }, "description": "The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials.", "download_owl": "http://purl.obolibrary.org/obo/cto.owl", "example": "0000022", "homepage": "https://github.com/ClinicalTrialOntology/CTO/", "keywords": [ "biomedical science", "disease", "neurobiology", "obo", "ontology", "preclinical studies" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "CTO", "bioportal": "CTO", "fairsharing": "FAIRsharing.qp211a", "obofoundry": "cto", "ols": "cto", "ontobee": "CTO" }, "name": "Clinical Trials Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CTO", "rdf_uri_format": "http://purl.obolibrary.org/obo/CTO_$1", "repository": "https://github.com/ClinicalTrialOntology/CTO", "uri_format": "http://purl.obolibrary.org/obo/CTO_$1", "version": "1.0.0" }, "ctri": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The mission of the Clinical Trials Registry-India (CTRI) is to ensure that all clinical trials conducted in India are prospectively registered, i.e. before the enrolment of the first participant. Additionally, post-marketing surveillance studies, BA/BE studies as well as clinical studies as part of PG thesis are also expected to be registered in the CTRI. (from homepage)\n\nNote that the identifier in this semantic space is not the one used in the webpages", "example": "CTRI/2023/04/052053", "homepage": "https://ctri.nic.in", "name": "India Clinical Trials Registry", "pattern": "^CTRI/\\d{4}/\\d{2,3}/\\d+$", "preferred_prefix": "ctri", "references": [ "https://www.ctri.nic.in/Clinicaltrials/pmaindet2.php?trialid=82487" ], "uri_format": "https://trialsearch.who.int/Trial2.aspx?TrialID=$1" }, "cubedb": { "comment": "website down as of 2021-10-04", "deprecated": true, "description": "Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available.", "example": "AKR", "homepage": "http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html", "mappings": { "biocontext": "CUBEDB", "integbio": "nbdc02094", "miriam": "cubedb", "n2t": "cubedb" }, "name": "Cube db", "pattern": "^[A-Za-z_0-9]+$", "preferred_prefix": "cubedb", "uri_format": "http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/" }, "cutg": { "description": "Codon usage in individual genes has been calculated using the nucleotide sequence data obtained from the GenBank Genetic Sequence Database. The compilation of codon usage is synchronized with each major release of GenBank.", "example": "9606", "homepage": "http://www.kazusa.or.jp/codon/", "keywords": [ "dna", "gene" ], "mappings": { "prefixcommons": "cutg" }, "name": "Codon Usage Tabulated from GenBank", "preferred_prefix": "cutg", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/cutg:$1" } ], "provides": "ncbitaxon", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=$1" }, "cvdo": { "contact": { "email": "paul.fabry@usherbrooke.ca", "github": "pfabry", "name": "Paul Fabry", "orcid": "0000-0002-3336-2476" }, "description": "An ontology to describe entities related to cardiovascular diseases", "download_owl": "http://purl.obolibrary.org/obo/cvdo.owl", "example": "0000546", "homepage": "https://github.com/OpenLHS/CVDO", "keywords": [ "cardiology", "cardiovascular disease", "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "CVDO", "biocontext": "CVDO", "bioportal": "CVDO", "fairsharing": "FAIRsharing.2basyz", "obofoundry": "cvdo", "ols": "cvdo", "ontobee": "CVDO" }, "name": "Cardiovascular Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CVDO", "rdf_uri_format": "http://purl.obolibrary.org/obo/CVDO_$1", "repository": "https://github.com/OpenLHS/CVDO", "uri_format": "http://purl.obolibrary.org/obo/CVDO_$1", "version": "2024-05-17" }, "cvx": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The CDC's National Center of Immunization and Respiratory Diseases (NCIRD) developed and maintains the CVX (vaccine administered) code set. The table below has the most up to date values. It includes both active and inactive vaccines available in the US. CVX codes for inactive vaccines allow transmission of historical immunization records.", "example": "54", "homepage": "https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=cvx", "mappings": { "hl7": "2.16.840.1.113883.6.59" }, "name": "Vaccine administered code set", "pattern": "^\\d+$", "preferred_prefix": "cvx", "uri_format": "https://biopragmatics.github.io/providers/cvx/$1" }, "d1id": { "description": "DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences.", "example": "00030692-0FE1-4A1B-955E-A2E55D659267", "homepage": "https://www.dataone.org", "mappings": { "biocontext": "D1ID", "miriam": "d1id", "n2t": "d1id" }, "name": "DataONE", "pattern": "^\\S+$", "preferred_prefix": "d1id", "uri_format": "https://cn.dataone.org/cn/v2/resolve/{$1}" }, "dailymed": { "description": "DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read.", "example": "973a9333-fec7-46dd-8eb5-25738f06ee54", "homepage": "https://dailymed.nlm.nih.gov/dailymed/", "mappings": { "biocontext": "DAILYMED", "miriam": "dailymed", "n2t": "dailymed", "prefixcommons": "dailymed" }, "name": "DailyMed", "pattern": "^[A-Za-z0-9-]+$", "preferred_prefix": "dailymed", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/dailymed:$1" } ], "uri_format": "https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1" }, "dandi": { "contact": { "email": "yoh@dartmouth.edu", "name": "Yaroslav Halchenko", "orcid": "0000-0003-3456-2493" }, "description": "DANDI works with BICCN and other BRAIN Initiative awardees to curate data using community data standards such as NWB and BIDS, and to make data and software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable, and Reusable).\nDANDI references electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data.\nThese data will help scientists uncover and understand cellular level mechanisms of brain function. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders.", "example": "000017", "homepage": "https://dandiarchive.org/", "keywords": [ "neurophysiology" ], "mappings": { "fairsharing": "FAIRsharing.f2c119", "miriam": "dandi", "re3data": "r3d100013638" }, "name": "Distributed Archives for Neurophysiology Data Integration", "pattern": "^\\d{6}(\\/\\d+\\.\\d+\\.\\d+)?$", "preferred_prefix": "dandi", "repository": "https://github.com/dandi/dandiarchive", "twitter": "dandiarchive", "uri_format": "https://dandiarchive.org/dandiset/$1" }, "darc": { "contact": { "email": "daniel.wilson@uni-hamburg.de", "name": "Daniel N. Wilson", "orcid": "0000-0003-3816-3828" }, "description": "DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors.", "example": "1250", "homepage": "http://darcsite.genzentrum.lmu.de/darc/index.php", "keywords": [ "life science" ], "mappings": { "biocontext": "DARC", "fairsharing": "FAIRsharing.evfe2s", "miriam": "darc", "n2t": "darc" }, "name": "Database of Aligned Ribosomal Complexes", "pattern": "^\\d+$", "preferred_prefix": "darc", "publications": [ { "doi": "10.1093/nar/gkr824", "pmc": "PMC3245104", "pubmed": "22009674", "title": "The DARC site: a database of aligned ribosomal complexes", "year": 2011 } ], "uri_format": "http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1" }, "dashr": { "contact": { "email": "dashr@lisanwanglab.org", "name": "Li-San Wang", "orcid": "0000-0002-3684-0031" }, "description": "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records.", "example": "hsa-mir-200a", "homepage": "http://lisanwanglab.org/DASHR/", "keywords": [ "life science" ], "mappings": { "biocontext": "DASHR", "fairsharing": "FAIRsharing.ztvs34", "miriam": "dashr", "n2t": "dashr" }, "name": "Database of small human noncoding RNAs", "pattern": "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$", "preferred_prefix": "dashr", "publications": [ { "doi": "10.1093/nar/gkv1188", "pmc": "PMC4702848", "pubmed": "26553799", "title": "DASHR: database of small human noncoding RNAs", "year": 2015 } ], "uri_format": "http://lisanwanglab.org/DASHR/entry/$1" }, "dashr.expression": { "description": "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression.", "example": "hsa-mir-200a", "homepage": "https://dashr1.lisanwanglab.org/show-expression-table.php?start=0", "mappings": { "biocontext": "DASHR.EXPRESSION", "miriam": "dashr.expression", "n2t": "dashr.expression" }, "name": "DASHR expression", "pattern": "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$", "preferred_prefix": "dashr.expression", "uri_format": "https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable" }, "datacite": { "contact": { "email": "silvio.peroni@unibo.it", "github": "essepuntato", "name": "Silvio Peroni", "orcid": "0000-0003-0530-4305" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology that enables the metadata properties of the DataCite Metadata Schema Specification (i.e., a list of metadata properties for the accurate and consistent identification of a resource for citation and retrieval purposes) to be described in RDF.", "download_owl": "http://aber-owl.net/media/ontologies/DATACITE/2/datacite.owl", "example": "AgentIdentifierScheme", "homepage": "http://www.sparontologies.net/ontologies/datacite", "keywords": [ "bibliography", "citation", "data model", "ontology", "report", "subject agnostic" ], "mappings": { "aberowl": "DATACITE", "bioportal": "DATACITE", "fairsharing": "FAIRsharing.c06f1e" }, "name": "DataCite Ontology", "preferred_prefix": "DataCite", "repository": "https://github.com/sparontologies/datacite", "twitter": "datacite", "uri_format": "http://purl.org/spar/datacite/$1" }, "datacommons": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A large RDF store built from American governmental data. This semantic space has a mixture of direct terms and subspaces.", "example": "Gene", "homepage": "https://datacommons.org", "mappings": { "biolink": "dcid" }, "name": "Data Commons", "preferred_prefix": "datacommons", "repository": "https://github.com/datacommonsorg/website", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://datacommons.org/browser/$1" }, "datanator.gene": { "description": "Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms.", "example": "K00973", "homepage": "https://datanator.info/", "mappings": { "miriam": "datanator.gene" }, "name": "Datanator Gene", "part_of": "datanator", "pattern": "^K[0-9]+$", "preferred_prefix": "datanator.gene", "uri_format": "https://www.datanator.info/gene/$1" }, "datanator.metabolite": { "description": "Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms.", "example": "OUYCCCASQSFEME-MRVPVSSYSA-N", "homepage": "https://datanator.info/", "mappings": { "miriam": "datanator.metabolite" }, "name": "Datanator Metabolite", "part_of": "datanator", "pattern": "^[A-Z\\-]+$", "preferred_prefix": "datanator.metabolite", "uri_format": "https://www.datanator.info/metabolite/$1" }, "datanator.reaction": { "description": "\tDatanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms.", "example": "XLYOFNOQVPJJNP-UHFFFAOYSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N--%3ENBIIXXVUZAFLBC-UHFFFAOYSA-N,WQZGKKKJIJFFOK-GASJEMHNSA-N", "homepage": "https://icahn.mssm.edu/", "mappings": { "miriam": "datanator.reaction" }, "name": "Datanator Reaction", "pattern": "^.*?--%3E.*?$", "preferred_prefix": "datanator.reaction", "uri_format": "https://datanator.info/reaction/$1" }, "datf": { "deprecated": true, "description": "DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals.", "example": "AT1G01030.1", "homepage": "http://datf.cbi.pku.edu.cn/", "keywords": [ "regulation" ], "mappings": { "biocontext": "DATF", "miriam": "datf", "n2t": "datf", "pathguide": "518", "prefixcommons": "datf" }, "name": "Database of Arabidopsis Transcription Factors", "pattern": "^AT[1-5]G\\d{5}(\\.\\d+)?$", "preferred_prefix": "datf", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/datf:$1" } ], "uri_format": "http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1" }, "dbd": { "description": "The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins.", "example": "0045310", "homepage": "http://www.transcriptionfactor.org/", "keywords": [ "genome", "regulation" ], "mappings": { "biocontext": "DBD", "edam": "2716", "miriam": "dbd", "n2t": "dbd", "pathguide": "496", "prefixcommons": "dbd" }, "name": "Transcription Factor Database", "pattern": "^\\d+$", "preferred_prefix": "dbd", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/dbd:$1" } ], "uri_format": "http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD" }, "dbest": { "contact": { "email": "tmjlowe@ucsc.edu", "name": "Todd M Lowe", "orcid": "0000-0003-3253-6021" }, "description": "The dbEST contains sequence data and other information on \"single-pass\" cDNA sequences, or \"Expressed Sequence Tags\", from a number of organisms.", "example": "BP100000", "homepage": "https://www.ncbi.nlm.nih.gov/nucest", "keywords": [ "bioinformatics", "dna", "life science" ], "mappings": { "biocontext": "DBEST", "edam": "1105", "fairsharing": "FAIRsharing.v9fya8", "integbio": "nbdc00413", "miriam": "dbest", "n2t": "dbest", "ncbi": "dbEST", "prefixcommons": "dbest", "re3data": "r3d100010648" }, "name": "EST database maintained at the NCBI.", "pattern": "^([A-Z]+)?\\d+(\\.\\d+)?$", "preferred_prefix": "dbest", "providers": [ { "code": "CURATOR_REVIEW", "description": "dbEST through DNA Data Bank of Japan (DDBJ)", "homepage": "http://www.ddbj.nig.ac.jp/", "name": "dbEST through DNA Data Bank of Japan (DDBJ)", "uri_format": "http://getentry.ddbj.nig.ac.jp/getentry/na/$1" }, { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/dbest:$1" }, { "code": "ebi", "description": "dbEST through European Nucleotide Archive (ENA)", "homepage": "https://www.ebi.ac.uk/ena", "name": "dbEST through European Nucleotide Archive (ENA)", "uri_format": "https://www.ebi.ac.uk/ena/data/view/$1" } ], "publications": [ { "doi": "10.1038/ng0893-332", "pubmed": "8401577", "title": "dbEST--database for \"expressed sequence tags\"", "year": 1993 } ], "uri_format": "https://www.ncbi.nlm.nih.gov/nucest/$1" }, "dbg2introns": { "contact": { "email": "zimmerly@ucalgary.ca", "name": "Steven John Zimmerly" }, "description": "The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank.", "example": "Cu.me.I1", "homepage": "http://webapps2.ucalgary.ca/~groupii/", "keywords": [ "dna" ], "mappings": { "biocontext": "DBG2INTRONS", "miriam": "dbg2introns", "n2t": "dbg2introns", "prefixcommons": "mgiid" }, "name": "DBG2 Introns", "pattern": "^\\w{1,2}\\.(\\w{1,2}\\.)?[A-Za-z0-9]+$", "preferred_prefix": "dbg2introns", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/mgiid:$1" } ], "publications": [ { "doi": "10.1093/nar/gkr1043", "pmc": "PMC3245105", "pubmed": "22080509", "title": "Database for bacterial group II introns", "year": 2011 } ], "uri_format": "http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1" }, "dbgap": { "contact": { "email": "feolo@ncbi.nlm.nih.gov", "github": "mfeolo", "name": "Michael Feolo", "orcid": "0000-0002-1650-5156" }, "description": "The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype.", "example": "phs000768.v2.p1", "homepage": "https://www.ncbi.nlm.nih.gov/gap/", "keywords": [ "biomedical science", "epigenetics", "genetics" ], "mappings": { "biocontext": "DBGAP", "cellosaurus": "dbGAP", "fairsharing": "FAIRsharing.88v2k0", "integbio": "nbdc00414", "miriam": "dbgap", "n2t": "dbgap" }, "name": "Database of Genotypes and Phenotypes", "pattern": "^phs[0-9]{6}(.v\\d+.p\\d+)?$", "preferred_prefix": "dbgap", "publications": [ { "doi": "10.1093/nar/gkt1211", "pmc": "PMC3965052", "pubmed": "24297256", "title": "NCBI's Database of Genotypes and Phenotypes: dbGaP", "year": 2013 }, { "doi": "10.1038/ng1007-1181", "pmc": "PMC2031016", "pubmed": "17898773", "title": "The NCBI dbGaP database of genotypes and phenotypes", "year": 2007 } ], "uri_format": "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1" }, "dblp.author": { "description": "identifier for author entries in the DBLP computer science bibliography (use portion of DBLP person key after pid/)", "example": "199/2168", "homepage": "https://dblp.org/", "mappings": { "wikidata": "P2456" }, "name": "DBLP author ID", "preferred_prefix": "dblp.author", "rdf_uri_format": "https://dblp.org/pid/$1.rdf", "uri_format": "https://dblp.org/pid/$1" }, "dbmhc": { "appears_in": [ "cellosaurus" ], "deprecated": true, "description": "Cell line databases/resources", "example": "48439", "homepage": "https://www.ncbi.nlm.nih.gov/gv/mhc/", "mappings": { "cellosaurus": "dbMHC", "integbio": "nbdc01831" }, "name": "Database of human Major Histocompatibility Complex", "pattern": "^\\d+$", "preferred_prefix": "dbmhc" }, "dbo": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This ontology is generated from the manually created specifications in the dbpedia mappings wiki. each release of this ontology corresponds to a new release of the dbpedia data set which contains instance data extracted from the different language versions of wikipedia. for information regarding changes in this ontology, please refer to the dbpedia mappings wiki.", "example": "careerPrizeMoney", "github_request_issue": 515, "homepage": "https://dbpedia.org/ontology", "keywords": [ "dbpedia", "ontology" ], "mappings": { "zazuko": "dbo" }, "name": "DBPedia Ontology", "preferred_prefix": "dbo", "uri_format": "https://dbpedia.org/ontology/$1" }, "dbprobe": { "description": "The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.", "example": "1000000", "homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe", "keywords": [ "nucleotide" ], "mappings": { "biocontext": "DBPROBE", "edam": "2719", "miriam": "dbprobe", "n2t": "dbprobe", "ncbi": "dbProbe", "prefixcommons": "dbprobe" }, "name": "NCBI Probe database Public registry of nucleic acid reagents", "pattern": "^\\d+$", "preferred_prefix": "dbprobe", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/dbsnp:$1" }, { "code": "sib", "description": "SNP2TFBS", "homepage": "https://ccg.epfl.ch/snp2tfbs/", "name": "SNP2TFBS", "uri_format": "https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1" } ], "publications": [ { "doi": "10.1093/nar/gkaa892", "pubmed": "33095870" }, { "doi": "10.1093/nar/gkl1031", "pmc": "PMC1781113", "pubmed": "17170002", "title": "Database resources of the National Center for Biotechnology Information", "year": 2006 }, { "doi": "10.1093/nar/29.1.308", "pmc": "PMC29783", "pubmed": "11125122", "title": "dbSNP: the NCBI database of genetic variation", "year": 2001 } ], "repository": "https://github.com/ncbi/dbsnp/tree/master/tutorials", "uri_format": "https://www.ncbi.nlm.nih.gov/snp/$1" }, "dbvar.study": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Studies in dbVar.", "example": "nstd102", "homepage": "https://www.ncbi.nlm.nih.gov/dbvar", "name": "Database of Genomic Structural Variation - Study", "preferred_prefix": "dbvar.study", "synonyms": [ "dbvar.studies" ], "uri_format": "https://www.ncbi.nlm.nih.gov/dbvar/studies/$1" }, "dbvar.variant": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Variants in dbVar.", "example": "nsv3875336", "homepage": "https://www.ncbi.nlm.nih.gov/dbvar", "name": "Database of Genomic Structural Variation - Variant", "preferred_prefix": "dbvar.variant", "synonyms": [ "dbvar.variants" ], "uri_format": "https://www.ncbi.nlm.nih.gov/dbvar/variants/$1" }, "dc": { "contact": { "email": "kdurante@stanford.edu", "name": "Kim Durante", "orcid": "0000-0001-9052-2854" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "description": "Metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes.\n\n**Deprecation Notice**: While the `/elements/1.1/` namespace will be supported indefinitely, DCMI gently encourages use of the `/terms/` namespace (i.e., `dcterms`) ([source](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-3)).", "download_owl": "http://aber-owl.net/media/ontologies/dcelements/1/dcelements.owl", "download_rdf": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/dublin_core_elements.rdf", "example": "contributor", "homepage": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/", "keywords": [ "annotation", "biomedical science", "life science", "metadata", "metadata standardization", "ontology", "resource metadata", "subject agnostic" ], "mappings": { "aberowl": "dcelements", "biocontext": "dc", "bioportal": "DC", "fairsharing": "FAIRsharing.3nx7t", "lov": "dce", "ols": "dc", "zazuko": "dc11" }, "name": "Dublin Core Elements (1.1)", "preferred_prefix": "dc", "synonyms": [ "dc.elements", "dc11", "dce" ], "uri_format": "http://purl.org/dc/elements/1.1/$1" }, "dc_cl": { "contact": { "email": "Lindsay.Cowell@utsouthwestern.edu", "name": "Lindsay Cowell", "orcid": "0000-0003-1617-8244" }, "deprecated": true, "example": "0000003", "homepage": "http://www.dukeontologygroup.org/Projects.html", "keywords": [ "obo", "ontology" ], "mappings": { "biocontext": "DC_CL", "obofoundry": "dc_cl" }, "name": "Dendritic cell", "pattern": "^\\d{7}$", "preferred_prefix": "DC_CL", "rdf_uri_format": "http://purl.obolibrary.org/obo/DC_CL_$1", "uri_format": "http://purl.obolibrary.org/obo/DC_CL_$1" }, "dcat": { "contact": { "email": "kdurante@stanford.edu", "name": "Kim Durante", "orcid": "0000-0001-9052-2854" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web", "download_owl": "http://aber-owl.net/media/ontologies/DCAT/2/dcat.owl", "example": "Dataset", "homepage": "https://www.w3.org/ns/dcat", "keywords": [ "data management", "ontology", "subject agnostic", "w3c rec" ], "mappings": { "aberowl": "DCAT", "biocontext": "dcat", "biolink": "dcat", "bioportal": "DCAT", "fairsharing": "FAIRsharing.h4j3qm", "lov": "dcat", "zazuko": "dcat" }, "name": "Data Catalog", "preferred_prefix": "dcat", "repository": "https://github.com/w3c/dxwg/", "uri_format": "http://www.w3.org/ns/dcat#$1" }, "dcterms": { "contact": { "email": "futo@stanford.edu", "name": "Michelle Futornick" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes.", "download_owl": "http://aber-owl.net/media/ontologies/dcterms/1/dcterms.owl", "download_rdf": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/dublin_core_terms.rdf", "example": "title", "homepage": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/", "keywords": [ "metadata", "metadata standardization", "ontology", "resource metadata", "subject agnostic" ], "mappings": { "aberowl": "dcterms", "biocontext": "dcterms", "biolink": "dct", "bioportal": "DCTERMS", "fairsharing": "FAIRsharing.9vtwjs", "lov": "dcterms", "ols": "dcterms", "zazuko": "dcterms" }, "name": "Dublin Core Metadata Initiative Terms", "preferred_prefix": 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"http://purl.obolibrary.org/obo/ddanat.obo", "download_owl": "http://purl.obolibrary.org/obo/ddanat.owl", "example": "0000006", "homepage": "http://dictybase.org/", "keywords": [ "anatomy", "cell", "life science", "obo", "ontology", "slime-mould" ], "license": "CC0-1.0", "mappings": { "aberowl": "DDANAT", "biocontext": "DDANAT", "bioportal": "DDANAT", "fairsharing": "FAIRsharing.z656ab", "go": "DDANAT", "obofoundry": "ddanat", "ols": "ddanat", "ontobee": "DDANAT", "prefixcommons": "ddanat" }, "name": "Dictyostelium discoideum anatomy", "pattern": "^\\d{7}$", "preferred_prefix": "DDANAT", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/ddanat:$1" } ], "publications": [ { "doi": "10.1186/1471-2164-9-130", "pmc": "PMC2323390", "pubmed": "18366659", "title": "An anatomy ontology to represent biological knowledge in Dictyostelium discoideum", "year": 2008 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/DDANAT_$1", "repository": "https://github.com/dictyBase/migration-data", "twitter": "dictybase", "uri_format": "http://purl.obolibrary.org/obo/DDANAT_$1" }, "ddc": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Dewey Decimal Classification (DDC) system, devised by library pioneer Melvil Dewey in the 1870s and owned by OCLC since 1988, provides a dynamic structure for the organization of library collections. Now in its 23rd edition, and available in print and Web versions, the DDC is the world's most widely used library classification system.", "example": "325.4", "example_extras": [ "325.4-325.9", "325", "32", "3" ], "homepage": "http://www.oclc.org/dewey/", "mappings": { "bartoc": "241" }, "name": "Dewey Decimal Classification", "pattern": "^(([0-9][0-9]?|[0-9]{3}(-[0-9]{3})?|[0-9]{3}(-[0-9]{3}(:[0-9]+)?)?|[0-9]{3}\\.[0-9]+(-[0-9]{3}\\.[0-9]+(:[0-9]+)?)?|T[1-9][A-Z]?--[0-9]+(-T[1-9][A-Z]?--[0-9]+(:[0-9]+)?)?|[1-9][A-Z]?--[0-9]+(-[1-9][A-Z]?--[0-9]+(:[0-9]+)?)?)?)$", "preferred_prefix": "ddc" }, "ddinter.drug": { "contact": { "email": "oriental-cds@163.com", "name": "Dongsheng Cao", "orcid": "0000-0003-3604-3785" }, "contributor": { "github": "sierra-moxon", "name": "Sierra Moxon", "orcid": "0000-0002-8719-7760" }, "description": "Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions. it provides abundant annotations for each ddi association including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety.", "example": "DDInter20", "github_request_issue": 492, "homepage": "http://ddinter.scbdd.com", "keywords": [ "chemistry", "drugs", "relationships" ], "license": "CC-BY-NC-SA-4.0", "name": "Curated Drug-Drug Interactions Database - 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"dialnet.journal": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "identifier of a journal in Dialnet", "example": "1119", "homepage": "http://dialnet.unirioja.es", "mappings": { "wikidata": "P1609" }, "name": "Dialnet journal ID", "pattern": "^[1-9]\\d{0,6}$", "preferred_prefix": "dialnet.journal", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1171" ], "uri_format": "https://dialnet.unirioja.es/servlet/revista?codigo=$1" }, "dicom": { "contact": { "email": "dclunie@dclunie.com", "name": "David Clunie", "orcid": "0000-0002-2406-1145" }, "description": "DICOM Controlled Terminology", "download_owl": "ftp://medical.nema.org/MEDICAL/Dicom/Resources/Ontology/DCM/dcm.owl", "example": "109082", "homepage": "http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_D.html", "keywords": [ "anatomy", "biomedical science", "medicine", "ontology" ], "mappings": { 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It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene.", "example": "DRSC05221", "homepage": "http://flyrnai.org/", "mappings": { "biocontext": "DRSC", "miriam": "drsc", "n2t": "drsc" }, "name": "Drosophila RNAi Screening Center", "pattern": "^DRSC\\d+$", "preferred_prefix": "drsc", "uri_format": "http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1" }, "drugbank": { "contact": { "email": "david.wishart@ualberta.ca", "name": "David Wishart", "orcid": "0000-0002-3207-2434" }, "description": "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/drugbank:$1" } ], "publications": [ { "doi": "10.1093/nar/gkx1037", "pubmed": "29126136" }, { "doi": "10.1093/nar/gkt1068", "pmc": "PMC3965102", "pubmed": "24203711", "title": "DrugBank 4.0: shedding new light on drug metabolism", "year": 2013 }, { "doi": "10.1093/nar/gkq1126", "pmc": "PMC3013709", "pubmed": "21059682", "title": "DrugBank 3.0: a comprehensive resource for 'omics' research on drugs", "year": 2010 }, { "doi": "10.1093/nar/gkm958", "pmc": "PMC2238889", "pubmed": "18048412", "title": "DrugBank: a knowledgebase for drugs, drug actions and drug targets", "year": 2007 }, { "doi": "10.1093/nar/gkj067", "pmc": "PMC1347430", "pubmed": "16381955", "title": "DrugBank: a comprehensive resource for in silico drug discovery and exploration", "year": 2006 } ], "synonyms": [ "DRUGBANK_ID", "DrugBank" ], "twitter": "DrugBankDB", "uri_format": "http://www.drugbank.ca/drugs/$1" }, "drugbank.bioentity": { "description": "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database.", "example": "BE0000048", "homepage": "http://www.drugbank.ca/targets", "mappings": { "biocontext": "DRUGBANKV4.TARGET", "miriam": "drugbankv4.target", "n2t": "drugbankv4.target" }, "name": "DrugBank Target v4", "part_of": "drugbank", "pattern": "^BE\\d{7}$", "preferred_prefix": "drugbank.bioentity", "synonyms": [ "drugbank.target", "drugbankv4.target" ], "uri_format": "https://go.drugbank.com/bio_entities/$1" }, "drugbank.category": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Close to 5K Categorizations for drugs, similar to ATCC.", "example": "DBCAT000600", "homepage": "https://go.drugbank.com/categories", "keywords": [ "chemistry", "drugs", "metascience", "topics" ], "name": "DrugBank Drug Category", "part_of": "drugbank", "pattern": "^DBCAT\\d+$", "preferred_prefix": "drugbank.category", "uri_format": "https://www.drugbank.ca/categories/$1" }, "drugbank.condition": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Indications and other conditions in drugbank", "example": "DBCOND0066902", "homepage": "https://go.drugbank.com", "name": "DrugBank Condition", "pattern": "^DBCOND\\d+$", "preferred_prefix": "drugbank.condition", "uri_format": "https://go.drugbank.com/indications/$1" }, "drugbank.metabolite": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Metabolites in drugbank", "example": "DBMET02292", "homepage": "https://go.drugbank.com", "name": "DrugBank Metabolite", "pattern": "^DBMET\\d+$", "preferred_prefix": "drugbank.metabolite", "uri_format": "https://go.drugbank.com/metabolites/$1" }, "drugbank.reaction": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Reactions in drugbank", "example": "1537", "homepage": "https://go.drugbank.com", "name": "DrugBank Reaction", "pattern": "^\\d+$", "preferred_prefix": "drugbank.reaction", "uri_format": "https://go.drugbank.com/reactions/$1" }, "drugbank.salt": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets.", "example": "DBSALT001211", "homepage": "http://www.drugbank.ca", "name": "DrugBank Salts", "part_of": "drugbank", "pattern": "^DBSALT\\d{6}$", "preferred_prefix": "drugbank.salt", "uri_format": "https://go.drugbank.com/salts/$1" }, "drugcentral": { "contact": { "email": "toprea@salud.unm.edu", "name": "Tudor Oprea", "orcid": "0000-0002-6195-6976" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action.", "example": "307", "homepage": "http://drugcentral.org", "keywords": [ "biomedical science", "drug development", "drug discovery", "drug repositioning", "pharmacology", "pharmacy" ], "license": "CC-BY-SA-4.0", "mappings": { "biolink": "DrugCentral", "fairsharing": "FAIRsharing.3me82d", "integbio": "nbdc02192", "miriam": "drugcentral", "uniprot": "DB-0239", "wikidata": "P11198" }, "name": "Drug Central", "pattern": "^\\d+$", "preferred_prefix": "drugcentral", "publications": [ { "doi": "10.1093/nar/gkac1085", "pubmed": "36484092" }, { "doi": "10.1093/nar/gky963", "pmc": "PMC6323925", "pubmed": "30371892", "title": "DrugCentral 2018: an update", "year": 2019 }, { "doi": "10.1093/nar/gkw993", "pmc": "PMC5210665", "pubmed": "27789690", "title": "DrugCentral: online drug compendium", "year": 2016 } ], "synonyms": [ "Drug_Central" ], "uri_format": "http://drugcentral.org/drugcard/$1" }, "dsm4": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia]", "example": "315.1", "example_extras": [ "291.89" ], "homepage": "https://en.wikipedia.org/wiki/Diagnostic_and_Statistical_Manual_of_Mental_Disorders#DSM-IV-TR_(2000)", "mappings": { "hl7": "2.16.840.1.113883.6.126", "wikidata": "P663" }, "name": "Diagnostic and Statistical Manual of Mental Disorders (4th Edition)", "pattern": "^\\d+\\.\\d+$", "preferred_prefix": "dsm4", "synonyms": [ "dsm-iv" ] }, "dsm5": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia]", "example": "312.33", "homepage": "https://en.wikipedia.org/wiki/DSM-5", "mappings": { "hl7": "2.16.840.1.113883.6.344", "wikidata": "P1930" }, "name": "Diagnostic and Statistical Manual of Mental Disorders (5th Edition)", "pattern": "^\\d{3}\\.\\d{2}$", "preferred_prefix": "dsm5", "references": [ "https://archive.org/details/diagnosticstatis0005unse" ], "synonyms": [ "dsm-v" ] }, "dsmz": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Leibniz Institute DSMZ is the most diverse biological resource center in the world and one of the largest collections of microorganisms and cell cultures worldwide (bacteria, archaea, protists, yeasts, fungi, bacteriophages, plant viruses, genomic bacterial DNA as well as human and animal cell lines). The following designations are used as part of local unique identifiers:\n\n- `PC`: positive control\n- `NC`: negative control\n- `AS`: antiserum\n- `PV`: plant viruses\n- `RT`: recommended test\n- `ACC`: human or animal cell line\n- `DSM`: microorganism cell line", "example": "ACC-1", "example_extras": [ "DSM-2", "RT-0753", "PC-0754", "AS-0753", "PV-0998" ], "homepage": "https://www.dsmz.de", "mappings": { "cellosaurus": "DSMZCellDive", "re3data": "r3d100010219" }, "name": "Deutsche Sammlung von Mikroorganismen und Zellkulturen", "pattern": "^(ACC|DSM|NC|PC|RT|AS|PV)-\\d+$", "preferred_prefix": "dsmz", "synonyms": [ "DSMZCellDive" ], "uri_format": "https://www.dsmz.de/collection/catalogue/details/culture/$1" }, "dso": { "contact": { "email": "evan@epatters.org", "github": "epatters", "name": "Evan Patterson", "orcid": "0000-0002-8600-949X" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Data Science Ontology is a research project of IBM Research AI and Stanford University Statistics. Its long-term objective is to improve the efficiency and transparency of collaborative, data-driven science.", "example": "classification-model", "homepage": "https://www.datascienceontology.org/", "keywords": [ "data science", "ontology" ], "name": "Data Science Ontology", "preferred_prefix": "dso", "repository": "https://github.com/IBM/datascienceontology", "uri_format": "https://www.datascienceontology.org/concept/$1" }, "dto": { "appears_in": [ "pr" ], "contact": { "email": "sschurer@med.miami.edu", "name": "Stephan Schurer" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "DTO integrates and harmonizes knowledge of the most important druggable protein families: kinases, GPCRs, ion channels and nuclear hormone receptors.", "download_owl": "http://aber-owl.net/media/ontologies/DTO/4/dto.owl", "example": "90000018", "homepage": "https://github.com/DrugTargetOntology/DTO", "keywords": [ "biomedical science", "disease", "drug discovery", "drug target", "ontology", "protein" ], "mappings": { "aberowl": "DTO", "bioportal": "DTO", "fairsharing": "FAIRsharing.tke3y2" }, "name": "Drug Target Ontology", "pattern": "^\\d+$", "preferred_prefix": "dto", "publications": [ { "doi": "10.1186/s13326-017-0161-x", "pmc": "PMC5679337", "pubmed": "29122012", "title": "Drug target ontology to classify and integrate drug discovery data", "year": 2017 } ], "repository": "https://github.com/DrugTargetOntology/DTO", "uri_format": "http://www.drugtargetontology.org/dto/DTO_$1" }, "duo": { "appears_in": [ "scdo" ], "contact": { "email": "mcourtot@gmail.com", "github": "mcourtot", "name": "Melanie Courtot", "orcid": "0000-0002-9551-6370" }, "depends_on": [ "bfo", "iao" ], "description": "DUO is an ontology which represent data use conditions.", "download_owl": "http://purl.obolibrary.org/obo/duo.owl", "example": "0000046", "homepage": "https://github.com/EBISPOT/DUO", "keywords": [ "biomedical science", "metadata standardization", "obo", "ontology", "subject agnostic" ], "license": "CC-BY-4.0", "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBdmdCIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--9a42083efa91d79ee5c7ed8e7868db0f7faf0b76/DUO_logo_white_background.png?disposition=inline", "mappings": { "aberowl": "DUO", "biocontext": "DUO", "bioportal": "DUO", "fairsharing": "FAIRsharing.5dnjs2", "obofoundry": "duo", "ols": "duo", "ontobee": "DUO" }, "name": "Data Use Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "DUO", "publications": [ { "doi": "10.1016/j.xgen.2021.100028", "pmc": "PMC8591903", "pubmed": "34820659", "title": "The Data Use Ontology to streamline responsible access to human biomedical datasets", "year": 2021 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/DUO_$1", "repository": "https://github.com/EBISPOT/DUO", "uri_format": "http://purl.obolibrary.org/obo/DUO_$1", "version": "2021-02-23" }, "eaglei": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Discovery tool for biomedical research resources available at institutions throughout the U.S.", "example": "0000012b-5661-2f63-2f73-b43980000000", "homepage": "https://hawaii.eagle-i.net", "mappings": { "cellosaurus": "eagle-i", "re3data": "r3d100011564" }, "name": "eagle-i", "preferred_prefix": "eaglei", "uri_format": "http://hawaii.eagle-i.net/i/$1" }, "easychair.cfp": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Conferences in EasyChair", "example": "SysBioCancer2022", "homepage": "https://easychair.org/cfp/", "keywords": [ "conferences", "metascience" ], "name": "EasyChair Call for Paper", "preferred_prefix": "easychair.cfp", "uri_format": "https://easychair.org/cfp/$1" }, "easychair.topic": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Call for paper topics in EasyChair", "example": "27106865", "homepage": "https://easychair.org/cfp/", "keywords": [ "metascience", "topics" ], "name": "EasyChair Topic", "pattern": "^\\d+$", "preferred_prefix": "easychair.topic", "uri_format": "https://easychair.org/cfp/topic.cgi?tid=$1" }, "ebisc": { "description": "Cell line collections (Providers)", "example": "ESi007-A", "example_extras": [ "EDi008-B" ], "homepage": "https://www.ebisc.org", "mappings": { "cellosaurus": "EBiSC" }, "name": "European Bank for induced pluripotent Stem Cells", "pattern": "^E(S|D)i\\d+-\\w$", "preferred_prefix": "ebisc", "uri_format": "https://cells.ebisc.org/$1" }, "ecacc": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The European Collection of Authenticated Cell Cultures (ECACC) is 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It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models.", "example": "26", "homepage": "http://e-cyanobacterium.org/models/", "mappings": { "biocontext": "ECYANO.MODEL", "miriam": "ecyano.model", "n2t": "ecyano.model" }, "name": "E-cyanobacterium model", "pattern": "^\\d+$", "preferred_prefix": "ecyano.model", "uri_format": "https://e-cyanobacterium.org/models/model/$1" }, "ecyano.rule": { "description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules.", "example": "56", "homepage": "http://www.e-cyanobacterium.org/bcs/rule/", "mappings": { "biocontext": "ECYANO.RULE", "miriam": "ecyano.rule", "n2t": "ecyano.rule" }, "name": "E-cyanobacterium rule", "part_of": "ecyano", "pattern": "^\\d+$", "preferred_prefix": "ecyano.rule", "uri_format": "https://e-cyanobacterium.org/bcs/rule/$1" }, "edam": { "contact": { "email": "matus.kalas@uib.no", "github": "matuskalas", "name": "Matúš Kalaš", "orcid": "0000-0002-1509-4981" }, "description": "EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications).", "download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo", "download_owl": "https://raw.githubusercontent.com/edamontology/edamontology/master/releases/EDAM.owl", "example": "data_1664", "homepage": "http://edamontology.org", "keywords": [ "analysis", "bioinformatics", "data acquisition", "data transformation", "life science", "obo", "ontology", "subject agnostic" ], "mappings": { "aberowl": "EDAM", "agroportal": "EDAM", "biocontext": "EDAM", "bioportal": "EDAM", "fairsharing": "FAIRsharing.a6r7zs", "miriam": "edam", "n2t": "edam", "ols": "edam", "ontobee": "EDAM", "prefixcommons": "edam" }, "name": "EDAM Ontology", "pattern": "^(data|topic|operation|format)\\_\\d{4}$", "preferred_prefix": "edam", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/edam:$1" } ], "publications": [ { "doi": "10.1093/bioinformatics/btt113", "pmc": "PMC3654706", "pubmed": "23479348", "title": "EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats", "year": 2013 }, { "doi": "10.7490/f1000research.1118900.1", "title": "EDAM: the bioscientific data analysis ontology (update 2021)", "year": 2021 }, { "doi": "10.5281/zenodo.3899895", "title": "edamontology/edamontology: EDAM 1.25", "year": 2020 } ], "rdf_uri_format": "http://edamontology.org/$1", "repository": "https://github.com/edamontology/edamontology", "twitter": "edamontology", "uri_format": "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1" }, "edam.data": { "contact": { "email": "matus.kalas@uib.no", "github": "matuskalas", "name": "Matúš Kalaš", "orcid": "0000-0002-1509-4981" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output.", "download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo", "example": "1664", "homepage": "http://edamontology.org", "keywords": [ "ontology" ], "mappings": { "biolink": "EDAM-DATA" }, "name": "EDAM Data", "part_of": "edam", "pattern": "^\\d+$", "preferred_prefix": "edam.data", "repository": "https://github.com/edamontology/edamontology", "twitter": "edamontology", "uri_format": "http://edamontology.org/data_$1" }, "edam.format": { "contact": { "email": "matus.kalas@uib.no", "github": "matuskalas", "name": "Matúš Kalaš", "orcid": "0000-0002-1509-4981" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data.", "download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo", "example": "1915", "homepage": "http://edamontology.org", "keywords": [ "ontology" ], "mappings": { "biolink": "EDAM-FORMAT" }, "name": "EDAM Format", "part_of": "edam", "pattern": "^\\d+$", "preferred_prefix": "edam.format", "repository": "https://github.com/edamontology/edamontology", "twitter": "edamontology", "uri_format": "http://edamontology.org/format_$1" }, "edam.operation": { "contact": { "email": "matus.kalas@uib.no", "github": "matuskalas", "name": "Matúš Kalaš", "orcid": "0000-0002-1509-4981" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state.", "download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo", "example": "0004", "homepage": "http://edamontology.org", "keywords": [ "ontology" ], "mappings": { "biolink": "EDAM-OPERATION" }, "name": "EDAM Operation", "part_of": "edam", "pattern": "^\\d+$", "preferred_prefix": "edam.operation", "repository": "https://github.com/edamontology/edamontology", "twitter": "edamontology", "uri_format": "http://edamontology.org/operation_$1" }, "edam.topic": { "contact": { "email": "matus.kalas@uib.no", "github": "matuskalas", "name": "Matúš Kalaš", "orcid": "0000-0002-1509-4981" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other.", "download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo", "example": "0003", "homepage": "http://edamontology.org", "keywords": [ "ontology" ], "mappings": { "biolink": "EDAM-TOPIC" }, "name": "EDAM Topic", "part_of": "edam", "pattern": "^\\d+$", "preferred_prefix": "edam.topic", "repository": "https://github.com/edamontology/edamontology", "twitter": "edamontology", "uri_format": "http://edamontology.org/topic_$1" }, "edda": { "contact": { "email": "tanja.bekhuis@tcbinfosci.com", "name": "Tanja Bekhuis", "orcid": "0000-0002-8537-9077" }, "description": "Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries.", "download_owl": "http://aber-owl.net/media/ontologies/EDDA/11/edda.owl", "example": "health_care_quality_assessment", "homepage": "https://bioportal.bioontology.org/ontologies/EDDA", "keywords": [ "medicine", "ontology" ], "mappings": { "aberowl": "EDDA", "bioportal": "EDDA", "fairsharing": "FAIRsharing.2ffmsb" }, "name": "EDDA Study Designs Taxonomy", "preferred_prefix": "edda", "uri_format": "http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#$1" }, "efo": { "contact": { "email": "plwhetzel@gmail.com", "github": "twhetzel", "name": "Trish Whetzel", "orcid": "0000-0002-3458-4839" }, "description": "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team.", "download_obo": "http://www.ebi.ac.uk/efo/efo.obo", "download_owl": "http://www.ebi.ac.uk/efo/efo.owl", "example": "0005147", "homepage": "http://www.ebi.ac.uk/efo", "keywords": [ "assay", "experimental condition", "experimental measurement", "functional genomics", "genome-wide association study", "independent variable", "ontology", "study design" ], "license": "Apache-2.0", "mappings": { "aberowl": "EFO", "agroportal": "EFO", "biocontext": "EFO", "biolink": "EFO", "bioportal": "EFO", "cellosaurus": "EFO", "fairsharing": "FAIRsharing.1gr4tz", "miriam": "efo", "n2t": "efo", "ols": "efo", "ontobee": "EFO", "wikidata": "P11956" }, "name": "Experimental Factor Ontology", "owners": [ { "name": "European Bioinformatics Institute", "partnered": false, "ror": "02catss52" } ], "pattern": "^\\d{7}$", "preferred_prefix": "EFO", "providers": [ { "code": "ebi", "description": "EFO through Functional Genomics Group (EBI)", "homepage": "https://www.ebi.ac.uk/efo/", "name": "EFO through Functional Genomics Group (EBI)", "uri_format": "https://www.ebi.ac.uk/efo/EFO_$1" } ], "publications": [ { "doi": "10.1093/bioinformatics/btq099", "pmc": "PMC2853691", "pubmed": "20200009", "title": "Modeling sample variables with an Experimental Factor Ontology", "year": 2010 } ], "repository": "https://github.com/EBISPOT/efo/", "uri_format": "http://www.ebi.ac.uk/efo/EFO_$1", "version": "3.69.0" }, "ega.dataset": { "contact": { "email": "tk2@ebi.ac.uk", "github": "tk2", "name": "Thomas Keane", "orcid": "0000-0001-7532-6898" }, "description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'.", "example": "EGAD00000000001", "homepage": "https://ega-archive.org/", "keywords": [ "biology", "biomedical science", "clinical studies", "genomics", "phenomics" ], "mappings": { "biocontext": "EGA.DATASET", "fairsharing": "FAIRsharing.mya1ff", "miriam": "ega.dataset", "n2t": "ega.dataset", "re3data": "r3d100011242" }, "name": "European Genome-phenome Archive Dataset", "owners": [ { "name": "European Bioinformatics Institute", "partnered": false, "ror": "02catss52" } ], "pattern": "^EGAD\\d{11}$", "preferred_prefix": "ega.dataset", "providers": [ { "code": "omicsdi", "description": "EGA Dataset through OmicsDI", "homepage": "https://www.omicsdi.org/", "name": "EGA Dataset through OmicsDI", "uri_format": "https://www.omicsdi.org/dataset/ega/$1" } ], "publications": [ { "doi": "10.1093/nar/gkab1059", "pmc": "PMC8728218", "pubmed": "34791407", "title": "The European Genome-phenome Archive in 2021", "year": 2022 }, { "doi": "10.1038/ng.3312", "pmc": "PMC5426533", "pubmed": "26111507", "title": "The European Genome-phenome Archive of human data consented for biomedical research", "year": 2015 } ], "twitter": "EGAarchive", "uri_format": "https://www.ebi.ac.uk/ega/datasets/$1" }, "ega.study": { "description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets.", "example": "EGAS00000000001", "homepage": "https://www.ebi.ac.uk/ega/studies", "mappings": { "biocontext": "EGA.STUDY", "miriam": "ega.study", "n2t": "ega.study" }, "name": "European Genome-phenome Archive Study", "pattern": "^EGAS\\d{11}$", "preferred_prefix": "ega.study", "uri_format": "https://www.ebi.ac.uk/ega/studies/$1" }, "eggnog": { "contact": { "email": "j.huerta@csic.es", "github": "jhcepas", "name": "Jaime Huerta-Cepas", "orcid": "0000-0003-4195-5025" }, "description": "eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).", "example": "veNOG12876", "homepage": "http://eggnog.embl.de/version_3.0/", "keywords": [ "gene", "life science" ], "mappings": { "biocontext": "EGGNOG", "fairsharing": "FAIRsharing.j1wj7d", "miriam": "eggnog", "n2t": "eggnog", "prefixcommons": "eggnog", "uniprot": "DB-0152" }, "name": "eggNOG", "pattern": "^\\w+$", "preferred_prefix": "eggnog", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/eggnog:$1" } ], "publications": [ { "doi": "10.1093/nar/gkac1022", "pubmed": "36399505" }, { "doi": "10.1093/nar/gkp951", "pmc": "PMC2808932", "pubmed": "19900971", "title": "eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations", "year": 2009 }, { "doi": "10.1093/nar/gkm796", "pmc": "PMC2238944", "pubmed": "17942413", "title": "eggNOG: automated construction and annotation of orthologous groups of genes", "year": 2007 } ], "uri_format": "http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1" }, "ehda": { "contact": { "email": "J.Bard@ed.ac.uk", "name": "Jonathan Bard" }, "deprecated": true, "description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once.", "download_obo": "http://aber-owl.net/media/ontologies/EHDA/6/ehda.obo", "example": "1", "homepage": "http://genex.hgu.mrc.ac.uk/", "keywords": [ "anatomy", "development", "human", "obo", "ontology" ], "mappings": { "aberowl": "EHDA", "biocontext": "EHDA", "bioportal": "EHDA", "obofoundry": "ehda", "prefixcommons": "ehda" }, "name": "Human developmental anatomy, timed version", "pattern": "^\\d+$", "preferred_prefix": "EHDA", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/ehda:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/EHDA_$1", "uri_format": "http://purl.obolibrary.org/obo/EHDA_$1" }, "ehdaa": { "contact": { "email": "J.Bard@ed.ac.uk", "name": "Jonathan Bard" }, "deprecated": true, "description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). Timing details will be added to the abstract version of the ontology in a future release.", "download_obo": "http://aber-owl.net/media/ontologies/EHDAA/6/ehdaa.obo", "example": "1", "homepage": "http://genex.hgu.mrc.ac.uk/", "keywords": [ "anatomy", "development", "human", "obo", "ontology" ], "mappings": { "aberowl": "EHDAA", "biocontext": "EHDAA", "bioportal": "EHDAA", "obofoundry": "ehdaa", "prefixcommons": "ehdaa" }, "name": "Human developmental anatomy, abstract version", "pattern": "^\\d+$", "preferred_prefix": "EHDAA", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations.", "download_json": "http://purl.obolibrary.org/obo/envo.json", "download_obo": "http://purl.obolibrary.org/obo/envo.obo", "download_owl": "http://purl.obolibrary.org/obo/envo.owl", "example": "09200010", "homepage": "http://environmentontology.org/", "keywords": [ "ecology", "environmental material", "environmental science", "epidemiology", "life science", "marine metagenome", "microbiome", "nutritional science", "obo", "ontology" ], "license": "CC0-1.0", "logo": "https://obofoundry.org/images/envo.png", "mappings": { "aberowl": "ENVO", "agroportal": "ENVO", "biocontext": "ENVO", "bioportal": "ENVO", "fairsharing": "FAIRsharing.azqskx", "miriam": "envo", "n2t": "envo", "obofoundry": "envo", "ols": "envo", "ontobee": "ENVO" }, "name": "Environment Ontology", "namespace_in_lui": true, "pattern": "^\\d{7,8}$", "preferred_prefix": "ENVO", "publications": [ { "doi": "10.1186/s13326-016-0097-6", "pmc": "PMC5035502", "pubmed": "27664130", "title": "The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation", "year": 2016 }, { "doi": "10.1093/database/baw005", "pmc": "PMC4761108", "pubmed": "26896844", "title": "EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation", "year": 2016 }, { "doi": "10.7717/peerj.1470", "pmc": "PMC4690371", "pubmed": "26713234", "title": "Emerging semantics to link phenotype and environment", "year": 2015 }, { "doi": "10.1186/2041-1480-4-43", "pmc": "PMC3904460", "pubmed": "24330602", "title": "The environment ontology: contextualising biological and biomedical entities", "year": 2013 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/ENVO_$1", "repository": "https://github.com/EnvironmentOntology/envo", "twitter": "envoTweets", "uri_format": "http://purl.obolibrary.org/obo/ENVO_$1", "version": "2024-07-01" }, "enzo": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Enzo Life Sciences is an antibody vendor.", "example": "ALX-210-175", "homepage": "https://www.enzolifesciences.com", "keywords": [ "antibodies", "life sciences", "vendor" ], "name": "Enzo Life Sciences", "preferred_prefix": "enzo", "synonyms": [ "Enzo Life Sciences" ], "uri_format": "https://www.enzolifesciences.com/$1" }, "eo": { "appears_in": [ "foodon" ], "banana": "EO", "contact": { "email": "jaiswalp@science.oregonstate.edu", "github": "jaiswalp", "name": "Pankaj Jaiswal", "orcid": "0000-0002-1005-8383" }, "deprecated": true, "description": "The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies.", "download_obo": "http://purl.obolibrary.org/obo/eo.obo", "download_owl": "http://purl.obolibrary.org/obo/eo.owl", "example": "0007404", "homepage": "http://planteome.org/", "keywords": [ "obo", "ontology", "plant" ], "license": "CC-BY-4.0", "logo": "http://planteome.org/sites/default/files/garland_logo.PNG", "mappings": { "aberowl": "EO", "agroportal": "EO", "biocontext": "EO", "miriam": "eo", "n2t": "eo", "obofoundry": "eo", "prefixcommons": "eo" }, "name": "Plant Environment Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "EO", "providers": [ { "code": "CURATOR_REVIEW", "description": "Plant Environment Ontology through Gramene", "homepage": "http://archive.gramene.org/db/ontology/search_term?id=EO:0007359", "name": "Plant Environment Ontology through Gramene", "uri_format": "http://archive.gramene.org/db/ontology/search?query=EO:$1" }, { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/eo:$1" } ], "publications": [ { "doi": "10.3732/ajb.1200222", "pmc": "PMC3492881", "pubmed": "22847540", "title": "Ontologies as integrative tools for plant science", "year": 2012 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/EO_$1", "repository": "https://github.com/Planteome/plant-environment-ontology", "uri_format": "http://purl.obolibrary.org/obo/EO_$1" }, "eol": { "contact": { "email": "pylebail@rennes.inra.fr", "name": "Pierre-Yves LeBail", "orcid": "0000-0002-8310-5195" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The EOL ontology describes environmental conditions of livestock farms. More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems.", "download_owl": "http://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=eol.owl", "example": "0001927", "homepage": "http://www.atol-ontology.com", "keywords": [ "agriculture", "animal husbandry", "environmental science", "livestock", "ontology", "species-environment interaction" ], "mappings": { "aberowl": "EOL", "agroportal": "EOL", "bioportal": "EOL", "fairsharing": "FAIRsharing.w7bw2y", "ols": "eol", "re3data": "r3d100011663" }, "name": "Environment Ontology for Livestock", "pattern": "^\\d{7}$", "preferred_prefix": "eol", "uri_format": "http://purl.org/obo/owlEOL_$1", "version": "2018-09-13" }, "eolife": { "contact": { "email": "secretariat@eol.org", "name": "EOL Secretariat", "orcid": "0000-0002-9943-2342" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A collaborative project intended to create an encyclopedia documenting all living species known to science", "example": "1044544", "homepage": "https://eol.org", "keywords": [ "biodiversity", "biology", "ecology", "taxonomy" ], "mappings": { "fairsharing": "FAIRsharing.3J6NYn", "re3data": "r3d100010229", "wikidata": "P830" }, "name": "Encyclopedia of Life", "pattern": "^\\d+$", "preferred_prefix": "eolife", "twitter": "eol", "uri_format": "https://eol.org/pages/$1" }, "epcc": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Collection of European paediatric cardiac coding files", "homepage": "https://www.aepc.org/european-paediatric-cardiac-coding", "name": "European Paediatric Cardiac Codes", "preferred_prefix": "epcc", "proprietary": true, "references": [ "https://www.cambridge.org/core/journals/cardiology-in-the-young/article/abs/european-paediatric-cardiac-codes-the-long-list-with-icd9-icd10-crossmapping-and-crossmap-to-epcc-short-list/FCA4DFCCB661298294A3D113FC79D5BE" ] }, "epd": { "contact": { "email": "Philipp.Bucher@sib.swiss", "name": "Philipp Bucher", "orcid": "0000-0002-0816-7775" }, "contributor_extras": [ { "email": "sebastien.moretti@sib.swiss", "github": "smoretti", "name": "Sebastien Moretti", "orcid": "0000-0003-3947-488X" } ], "description": "The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. 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", "download_owl": "http://aber-owl.net/media/ontologies/EPSO/3/epso.owl", "example": "0000400", "homepage": "http://prism.case.edu/prism/index.php/EpilepsyOntology", "keywords": [ "epilepsy", "neurology", "ontology", "patient care" ], "mappings": { "aberowl": "EPSO", "bioportal": "EPSO", "fairsharing": "FAIRsharing.ttprgy", "ontobee": "EPSO" }, "name": "Epilepsy and Seizure Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "epso", "publications": [ { "doi": "10.1136/amiajnl-2013-001696", "pmc": "PMC3912711", "pubmed": "23686934", "title": "Epilepsy and seizure ontology: towards an epilepsy informatics infrastructure for clinical research and patient care", "year": 2013 } ], "uri_format": "http://www.case.edu/EpilepsyOntology.owl#$1" }, "erm": { "contact": { "email": "egon.willighagen@gmail.com", "github": "egonw", "name": "Egon Willighagen", "orcid": "0000-0001-7542-0286" }, "description": "The European Registry of Materials is a simple registry with the sole purpose to mint material identifiers to be used by research projects throughout the life cycle of their project.", "download_rdf": "https://nanocommons.github.io/identifiers/registry", "example": "ERM00000044", "homepage": "https://nanocommons.github.io/identifiers/", "keywords": [ "chemical entity", "materials informatics", "nanotechnology" ], "mappings": { "cheminf": "000569", "fairsharing": "FAIRsharing.c26a4e", "miriam": "erm", "n2t": "erm" }, "name": "European Registry of Materials", "pattern": "^ERM[0-9]{8}$", "preferred_prefix": "erm", "providers": [ { "code": "erm.database", "description": "Database that provides links to onlnie information about materials with an European Registry of Materials (ERM) identifier", "homepage": "https://nanocommons.github.io/erm-database/", "name": "ERM Identifier Database", "uri_format": "https://nanocommons.github.io/erm-database/substance/erm/$1" } ], "publications": [ { "doi": "10.1186/s13321-022-00614-7", "pmc": "PMC9400299", "pubmed": "36002868", "title": "European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials", "year": 2022 } ], "twitter": "nanocommons", "uri_format": "https://nanocommons.github.io/identifiers/registry#$1" }, "ero": { "contact": { "email": "Marc_Ciriello@hms.harvard.edu", "name": "Marc Ciriello", "orcid": "0000-0002-3734-1859" }, "deprecated": true, "description": "An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens.", "download_owl": "http://purl.obolibrary.org/obo/ero.owl", "example": "0001655", "homepage": "https://open.med.harvard.edu/wiki/display/eaglei/Ontology", "keywords": [ "biological sample", "biomedical science", "life science", "obo", "ontology", "protocol", "reagent", "study design" ], "license": "CC BY 2.0", "mappings": { "aberowl": "ERO", "biocontext": "ERO", "bioportal": "ERO", "fairsharing": "FAIRsharing.nwgynk", "obofoundry": "ero", "ols": "ero", "ontobee": "ERO" }, "name": "eagle-i resource ontology", "pattern": "^\\d{7}$", "preferred_prefix": "ERO", "publications": [ { "doi": "10.1109/jcdl.2017.7991571", "pmc": "PMC5868434", "pubmed": "29599662", "title": "Automating data citation: the eagle-i experience", "year": 2017 }, { "doi": "10.1093/database/bar067", "pmc": "PMC3308157", "pubmed": "22434835", "title": "Research resources: curating the new eagle-i discovery system", "year": 2012 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/ERO_$1", "uri_format": "http://purl.obolibrary.org/obo/ERO_$1", "version": "2016-07-27" }, "eropmoscow": { "description": "EROP-Moscow is a curated oligopeptide (2-50 amino acid residues) sequence database which strives to provide a high level of annotations (such as descriptions of the structure of an oligopeptide, its source and function, post-translational modifications, etc.).", "example": "E00002", "homepage": "http://erop.inbi.ras.ru", "keywords": [ "protein" ], "mappings": { "integbio": "nbdc00265", "prefixcommons": "eropmoscow" }, "name": "Endogenous Regulatory OligoPeptide knowledgebase-Moscow", "preferred_prefix": "eropmoscow", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions.", "example": "HS000015122", "homepage": "http://gpcr.biocomp.unibo.it/esldb", "keywords": [ "protein" ], "mappings": { "prefixcommons": "esldb" }, "name": "eukaryotic Subcellular Localization database", "preferred_prefix": "esldb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/esldb:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://gpcr.biocomp.unibo.it/cgi-bin/predictors/esldb/dettagli.cgi?codice=$1" }, "estdab": { "comment": "Website is dead", "deprecated": true, "description": "Cell line databases/resources", "example": "046", "homepage": "https://www.ebi.ac.uk/ipd/estdab/", "mappings": { "cellosaurus": "ESTDAB" }, "name": "European Searchable Tumour Line Database", "owners": [ { "name": "European Bioinformatics Institute", "partnered": false, "ror": "02catss52" } ], "pattern": "^\\d{3}$", "preferred_prefix": "estdab", "uri_format": "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1" }, "eu89h": { "description": "The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union.", "example": "jrc-eurl-ecvam-chemagora", "homepage": "http://data.jrc.ec.europa.eu/", "mappings": { "biocontext": "EU89H", "miriam": "eu89h", "n2t": "eu89h" }, "name": "JRC Data Catalogue", "pattern": "^[a-z0-9\\-_]+$", "preferred_prefix": "eu89h", "uri_format": "http://data.europa.eu/89h/$1" }, "euclinicaltrials": { "description": "The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004.\r\nIt also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population.", "example": "2008-005144-16", "homepage": "https://www.clinicaltrialsregister.eu/", "mappings": { "biocontext": "EUCLINICALTRIALS", "miriam": "euclinicaltrials", "n2t": "euclinicaltrials" }, "name": "EU Clinical Trials", "pattern": "^\\d{4}\\-\\d{6}\\-\\d{2}$", "preferred_prefix": "euclinicaltrials", "synonyms": [ "EUCTR" ], "uri_format": "https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1" }, "eugenes": { "contact": { "email": "eugenes@iubio.bio.indiana.edu", "name": "Don Gilbert", "orcid": "0000-0002-6646-7274" }, "description": "euGenes provides a common summary of gene and genomic information from eukaryotic organism databases including gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, product information.", "example": "MGgn0008978", "homepage": "http://eugenes.org/", "keywords": [ "genome", "life science", "ontology" ], "mappings": { "fairsharing": "FAIRsharing.7fc5y6", "prefixcommons": "eugenes" }, "name": "Eukaryotic Genes", "preferred_prefix": "eugenes", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/eugenes:$1" } ], "publications": [ { "doi": "10.1093/nar/30.1.145", "pmc": "PMC99146", "pubmed": "11752277", "title": "euGenes: a eukaryote genome information system", "year": 2002 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://eugenes.org:7072/.bin/fbidq.html?$1" }, "eupath": { "appears_in": [ "scdo" ], "contact": { "email": "jiezhen@med.umich.edu", "github": "zhengj2007", "name": "Jie Zheng", "orcid": "0000-0002-2999-0103" }, "deprecated": true, "description": "The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available.", "download_owl": "http://purl.obolibrary.org/obo/eupath.owl", "example": "0010316", "homepage": "https://github.com/VEuPathDB-ontology/VEuPathDB-ontology", "keywords": [ "biomedical science", "epidemiology", "functional genomics", "microbiome", "obo", "ontology", "population genetics" ], "license": "CC-BY-4.0", "logo": "https://raw.githubusercontent.com/EuPathDB/communitysite/master/assets/images/VEuPathDB-logo-s.png", "mappings": { "aberowl": "EUPATH", "biocontext": "EUPATH", "bioportal": "EUPATH", "fairsharing": "FAIRsharing.9rhr9j", "obofoundry": "eupath", "ols": "eupath", "ontobee": "EUPATH" }, "name": "VEuPathDB ontology", "pattern": "^\\d{7}$", "preferred_prefix": "EUPATH", "publications": [ { "doi": "10.5281/zenodo.6685957", "title": "Malaria study data integration and information retrieval based on OBO Foundry ontologies", "year": 2016 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/EUPATH_$1", "repository": "https://github.com/VEuPathDB-ontology/VEuPathDB-ontology", "uri_format": "http://purl.obolibrary.org/obo/EUPATH_$1", "version": "2023-05-30" }, "eurofir": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "EuroFir (European Food Information Resource Network), the world-leading European Network of Excellence on Food Composition Databank systems, is a partnership between 48 universities, research institutes and small-to-medium sized enterprises (SMEs) from 25 European countries.", "homepage": "https://www.eurofir.org", "name": "European Food Information Resource Network", "preferred_prefix": "eurofir", "proprietary": true }, "ev": { "appears_in": [ "cl" ], "contact": { "email": "evoc@sanbi.ac.za", "name": "eVOC mailing list" }, "deprecated": true, "description": "Provides structured controlled vocabularies for the annotation of expressed sequences with respect to anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation and treatment.", "example": "0100011", "homepage": "http://www.evocontology.org/", "keywords": [ "anatomy", "cell", "development", "experiment", "obo", "ontology" ], "mappings": { "biocontext": "EV", "obofoundry": "ev", "prefixcommons": "evoc" }, "name": "eVOC (Expressed Sequence Annotation for Humans)", "pattern": "^\\d{7}$", "preferred_prefix": "EV", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/evoc:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/EV_$1", "references": [ "https://twitter.com/Bgeedb/status/1350124337815281664" ], "uri_format": "http://www.evocontology.org/site/Main/BrowseEvoc?x_termid=$1" }, "evm": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "name": "eVOC mouse development stage", "preferred_prefix": "evm", "references": [ "https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-10-r229" ] }, "exac.gene": { "description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information.", "example": "ENSG00000169174", "homepage": "http://exac.broadinstitute.org/", "mappings": { "biocontext": "EXAC.GENE", "miriam": "exac.gene", "n2t": "exac.gene" }, "name": "ExAC Gene", "pattern": "^ENSG\\d{11}$", "preferred_prefix": "exac.gene", "uri_format": "http://exac.broadinstitute.org/gene/$1" }, "exac.transcript": { "description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information.", "example": "ENST00000407236", "homepage": "http://exac.broadinstitute.org/", "mappings": { "biocontext": "EXAC.TRANSCRIPT", "miriam": "exac.transcript", "n2t": "exac.transcript" }, "name": "ExAC Transcript", "pattern": "^ENST\\d{11}$", "preferred_prefix": "exac.transcript", "uri_format": "http://exac.broadinstitute.org/transcript/$1" }, "exac.variant": { "description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information.", "example": "22-46615880-T-C", "homepage": "http://exac.broadinstitute.org/", "mappings": { "biocontext": "EXAC.VARIANT", "miriam": "exac.variant", "n2t": "exac.variant" }, "name": "ExAC Variant", "pattern": "^\\d{1,2}\\-\\d+\\-[GATC]\\-[GATC]$", "preferred_prefix": "exac.variant", "uri_format": "http://exac.broadinstitute.org/variant/$1" }, "exo": { "appears_in": [ "ecto", "scdo" ], "contact": { "email": "annethessen@gmail.com", "github": "diatomsRcool", "name": "Anne Thessen", "orcid": "0000-0002-2908-3327" }, "description": "ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics.", "download_obo": "http://purl.obolibrary.org/obo/exo.obo", "download_owl": "http://purl.obolibrary.org/obo/exo.owl", "example": "0000078", "homepage": "https://github.com/CTDbase/exposure-ontology", "keywords": [ "disease", "environmental science", "epigenetics", "exposure", "obo", "ontology", "toxicology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "EXO", "biocontext": "EXO", "biolink": "ExO", "bioportal": "EXO", "fairsharing": "FAIRsharing.6hna78", "obofoundry": "exo", "ols": "exo", "ontobee": "ExO" }, "name": "Exposure ontology", "pattern": "^\\d{7}$", "preferred_prefix": "ExO", "publications": [ { "doi": "10.1021/es2033857", "pmc": "PMC3314380", "pubmed": "22324457", "title": "Providing the missing link: the exposure science ontology ExO", "year": 2012 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/ExO_$1", "repository": "https://github.com/CTDbase/exposure-ontology", "synonyms": [ "ExO" ], "uri_format": "http://purl.obolibrary.org/obo/ExO_$1", "version": "2022-06-29" }, "fabio": { "contact": { "email": "silvio.peroni@unibo.it", "github": "essepuntato", "name": "Silvio Peroni", "orcid": "0000-0003-0530-4305" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The FRBR-aligned Bibliographic Ontology (FaBiO) is an ontology for describing entities that are published or potentially publishable (e.g., journal articles, conference papers, books), and that contain or are referred to by bibliographic references.", "download_owl": "http://aber-owl.net/media/ontologies/FaBiO/1/fabio.owl", "example": "d4e2515", "homepage": "https://github.com/sparontologies/fabio", "keywords": [ "bibliography", "citation", "data model", "ontology", "protocol", "publication", "report", "spar", "subject agnostic" ], "mappings": { "aberowl": "FaBiO", "biolink": "fabio", "fairsharing": "FAIRsharing.2f3180", "lov": "fabio" }, "name": "FaBiO, the FRBR-aligned Bibliographic Ontology", "preferred_prefix": "fabio", "publications": [ { "doi": "10.1016/j.websem.2012.08.001", "title": "FaBiO and CiTO: Ontologies for describing bibliographic resources and citations", "year": 2012 } ], "rdf_uri_format": "http://purl.org/spar/fabio/$1", "repository": "https://github.com/sparontologies/fabio", "twitter": "sparontologies", "uri_format": "https://sparontologies.github.io/fabio/current/fabio.html#$1" }, "facebase": { "contact": { "email": "ychai@usc.edu", "name": "Yang Chai", "orcid": "0000-0003-2477-7247" }, "description": "FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects.", "example": "FB00000917", "homepage": "https://www.facebase.org", "keywords": [ "anatomy", "developmental biology", "epigenetics", "genetics", "medicine" ], "mappings": { "biocontext": "FACEBASE", "fairsharing": "FAIRsharing.mqvqde", "integbio": "nbdc02022", "miriam": "facebase", "n2t": "facebase", "re3data": "r3d100013263" }, "name": "FaceBase Data Repository", "pattern": "^FB\\d{8}$", "preferred_prefix": "facebase", "publications": [ { "doi": "10.1242/dev.191213", "pmc": "PMC7522026", "pubmed": "32958507", "title": "FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research", "year": 2020 } ], "uri_format": "https://www.facebase.org/data/record/#1/isa:dataset/accession=$1" }, "fairsharing": { "contact": { "email": "allyson.lister@oerc.ox.ac.uk", "name": "Allyson Lister", "orcid": "0000-0002-7702-4495" }, "description": "The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies.", "example": "bsg-000052", "example_extras": [ "FAIRsharing.CugtbQ" ], "homepage": "https://fairsharing.org/", "keywords": [ "agriculture", "biomedical science", "data governance", "database management", "earth science", "environmental science", "humanities", "life science", "natural science", "ontology and terminology", "policy" ], "mappings": { "biocontext": "FAIRSHARING", "fairsharing": "FAIRsharing.2abjs5", "miriam": "fairsharing", "n2t": "fairsharing", "re3data": "r3d100010142" }, "mastodon": "fairsharing@fediscience.org", "name": "FAIRsharing", "pattern": "^(bsg-[dscp]?\\d{6})|(FAIRsharing\\.\\w+)$", "preferred_prefix": "fairsharing", "publications": [ { "doi": "10.1038/s41587-019-0080-8", "pmc": "PMC6785156", "pubmed": "30940948", "title": "FAIRsharing as a community approach to standards, repositories and policies", "year": 2019 }, { "doi": "10.1093/database/baw075", "pmc": "PMC4869797", "pubmed": "27189610", "title": "BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences", "year": 2016 }, { "doi": "10.5281/zenodo.5106255", "title": "FAIRsharing, a FAIR-enabling service for repositories, standards and policies", "year": 2021 } ], "repository": "https://github.com/FAIRsharing", "twitter": "fairsharing_org", "uri_format": "https://fairsharing.org/$1" }, "fairsharing.organization": { "contact": { "email": "allyson.lister@oerc.ox.ac.uk", "github": "allysonlister", "name": "Allyson Lister", "orcid": "0000-0002-7702-4495" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An organization in FAIRsharing, including universities, labs, etc.", "example": "3851", "homepage": "https://fairsharing.org", "name": "FAIRsharing Organization", "part_of": "fairsharing", "pattern": "^\\d+$", "preferred_prefix": "fairsharing.organization", "uri_format": "https://fairsharing.org/organisations/$1" }, "fairsharing.user": { "contact": { "email": "allyson.lister@oerc.ox.ac.uk", "github": "allysonlister", "name": "Allyson Lister", "orcid": "0000-0002-7702-4495" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A user of FAIRsharing", "example": "5112", "homepage": "https://fairsharing.org", "name": "FAIRsharing User", "part_of": "fairsharing", "pattern": "^\\d+$", "preferred_prefix": "fairsharing.user", "uri_format": "https://fairsharing.org/users/$1" }, "faldo": { "contact": { "email": "faldo@googlegroups.com", "name": "FALDO group" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "It is a simple ontology to describe sequence feature positions and regions as found in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics resources", "download_owl": "http://aber-owl.net/media/ontologies/FALDO/1/faldo.owl", "example": "ForwardStrandPosition", "homepage": "http://biohackathon.org/resource/faldo", "keywords": [ "binding site", "gene feature", "genetics", "geography", "nucleic acid sequence", "ontology", "sequence annotation", "sequence feature" ], "mappings": { "aberowl": "FALDO", "agroportal": "FALDO", "biocontext": "faldo", "bioportal": "FALDO", "fairsharing": "FAIRsharing.haxp7g", "lov": "faldo" }, "name": "Feature Annotation Location Description Ontology ", "preferred_prefix": "faldo", "publications": [ { "doi": "10.1186/s13326-016-0067-z", "pmc": "PMC4907002", "pubmed": "27296299", "title": "FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation", "year": 2016 } ], "repository": "https://github.com/OBF/FALDO", "uri_format": "http://biohackathon.org/resource/faldo#$1" }, "fao": { "contact": { "email": "vw253@cam.ac.uk", "github": "ValWood", "name": "Val Wood", "orcid": "0000-0001-6330-7526" }, "description": "A structured controlled vocabulary for the anatomy of fungi.", "download_obo": "http://purl.obolibrary.org/obo/fao.obo", "download_owl": "http://purl.obolibrary.org/obo/fao.owl", "example": "0000001", "homepage": "https://github.com/obophenotype/fungal-anatomy-ontology/", "keywords": [ "anatomy", "fungi", "life science", "microbiology", "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "FAO", "biocontext": "FAO", "bioportal": "FAO", "fairsharing": "FAIRsharing.xs6t67", "obofoundry": "fao", "ols": "fao", "ontobee": "FAO", "prefixcommons": "fao" }, "name": "Fungal gross anatomy", "pattern": "^\\d{7}$", "preferred_prefix": "FAO", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/fao:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/FAO_$1", "repository": "https://github.com/obophenotype/fungal-anatomy-ontology", "uri_format": "http://purl.obolibrary.org/obo/FAO_$1", "version": "2020-05-07" }, "fao.asfis": { "comment": "This resource is offered freely by FAO for download but no obvious licensing is indicated, and no caution about appropriate reuse.", "contributor": { "github": "ddooley", "name": "Damion Dooley", "orcid": "0000-0002-8844-9165" }, "description": "The FAO Statistics Team (NFISS) of Fisheries and Aquaculture Division collates world capture and aquaculture production statistics at either the species, genus, family, or higher taxonomic levels in 3,169 statistical categories (2022 data release) referred to as species items. ASFIS list of species includes 13,417 species items selected according to their interest or relation to fisheries and aquaculture. For each species item stored in a record, codes (ISSCAAP group, taxonomic and 3-alpha) and taxonomic information (scientific name, author(s), family, and higher taxonomic classification) are provided. An English name is available for most of the records, and about one third of them have also a French and Spanish name. Information is also provided about the availability of fishery production statistics on the species item in the FAO databases. (from homepage)", "example": "20560", "github_request_issue": 872, "homepage": "https://www.fao.org/fishery/en/collection/asfis/en", "name": "Aquatic Sciences and Fisheries Information System", "pattern": "^\\d+$", "preferred_prefix": "fao.asfis", "repository": "bioregistry", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "asfis" ], "uri_format": "https://www.fao.org/fishery/en/species/$1" }, "fbbi": { "contact": { "email": "wawong@gmail.com", "github": "wawong", "name": "Willy Wong", "orcid": "0000-0002-8841-5870" }, "deprecated": true, "description": "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.", "download_obo": "http://aber-owl.net/media/ontologies/FBbi/14/fbbi.obo", "download_owl": "http://purl.obolibrary.org/obo/fbbi.owl", "example": "00000268", "homepage": "http://cellimagelibrary.org/", "keywords": [ "assay", "biomedical science", "experiment", "image", "imaging", "life science", "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "FBbi", "biocontext": "FBbi", "bioportal": "FBbi", "fairsharing": "FAIRsharing.ny3z9j", "obofoundry": "fbbi", "ols": "fbbi", "ontobee": "FBbi", "prefixcommons": "fbbi" }, "name": "Biological Imaging Methods Ontology", "pattern": "^\\d+$", "preferred_prefix": "FBbi", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/fbbi:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/FBbi_$1", "repository": "https://github.com/CRBS/Biological_Imaging_Methods_Ontology", "synonyms": [ "FBbi" ], "uri_format": "http://purl.obolibrary.org/obo/FBbi_$1", "version": "2020-11-06" }, "fbbt": { "contact": { "email": "cp390@cam.ac.uk", "github": "Clare72", "name": "Clare Pilgrim", "orcid": "0000-0002-1373-1705" }, "description": "An ontology representing the gross anatomy of Drosophila melanogaster.", "download_json": "http://purl.obolibrary.org/obo/fbbt.json", "download_obo": "http://purl.obolibrary.org/obo/fbbt.obo", "download_owl": "http://purl.obolibrary.org/obo/fbbt.owl", "example": "00007294", "homepage": "http://purl.obolibrary.org/obo/fbbt", "keywords": [ "anatomy", "developmental biology", "fly", "gene expression", "image", "life cycle stage", "life science", "obo", "ontology", "phenotype" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "FBBT", "biocontext": "FBbt", "bioportal": "FB-BT", "fairsharing": "FAIRsharing.y2qkst", "go": "FBbt", "obofoundry": "fbbt", "ols": "fbbt", "ontobee": "FBbt", "prefixcommons": "fbbt" }, "name": "Drosophila gross anatomy", "pattern": "^\\d{8}$", "preferred_prefix": "FBbt", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/fbbt:$1" } ], "publications": [ { "doi": "10.1186/2041-1480-4-32", "pmc": "PMC4015547", "pubmed": "24139062", "title": "The Drosophila anatomy ontology", "year": 2013 }, { "doi": "10.1093/bioinformatics/bts113", "pubmed": "22402613", "title": "A strategy for building neuroanatomy ontologies", "year": 2012 }, { "doi": "10.1093/bioinformatics/btr677", "pubmed": "22180411", "title": "The Virtual Fly Brain browser and query interface", "year": 2011 }, { "doi": "10.1093/nar/gkj068", "pmc": "PMC1347431", "pubmed": "16381917", "title": "FlyBase: anatomical data, images and queries", "year": 2006 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/FBbt_$1", "repository": "https://github.com/FlyBase/drosophila-anatomy-developmental-ontology", "synonyms": [ "FBbt", "FBbt_root" ], "uri_format": "http://purl.obolibrary.org/obo/FBbt_$1", "version": "2024-08-08" }, "fbcv": { "appears_in": [ "ontoavida" ], "contact": { "email": "cp390@cam.ac.uk", "github": "Clare72", "name": "Clare Pilgrim", "orcid": "0000-0002-1373-1705" }, "description": "A miscellaneous ontology of terms used for curation in FlyBase, including the DPO.", "download_json": "http://purl.obolibrary.org/obo/fbcv.json", "download_obo": "https://raw.githubusercontent.com/FlyBase/flybase-controlled-vocabulary/master/fbcv.obo", "download_owl": "http://purl.obolibrary.org/obo/fbcv.owl", "example": "0000586", "homepage": "http://purl.obolibrary.org/obo/fbcv", "keywords": [ "descriptor", "expression data", "fly", "life science", "obo", "ontology", "phenotype" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "FBCV", "biocontext": "FBcv", "bioportal": "FB-CV", "fairsharing": "FAIRsharing.6tgyxf", "obofoundry": "fbcv", "ols": "fbcv", "ontobee": "FBcv", "prefixcommons": "fbcv" }, "name": "FlyBase Controlled Vocabulary", "part_of": "flybase", "pattern": "^\\d{7}$", "preferred_prefix": "FBcv", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/fbcv:$1" } ], "publications": [ { "doi": "10.1186/2041-1480-4-30", "pmc": "PMC3816596", "pubmed": "24138933", "title": "The Drosophila phenotype ontology", "year": 2013 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/FBcv_$1", "repository": "https://github.com/FlyBase/flybase-controlled-vocabulary", "synonyms": [ "FBcv" ], "uri_format": "http://purl.obolibrary.org/obo/FBcv_$1", "version": "2024-08-08" }, "fbdv": { "contact": { "email": "cp390@cam.ac.uk", "github": "Clare72", "name": "Clare Pilgrim", "orcid": "0000-0002-1373-1705" }, "description": "An ontology of Drosophila melanogaster developmental stages.", "download_json": "http://purl.obolibrary.org/obo/fbdv.json", "download_obo": "http://purl.obolibrary.org/obo/fbdv.obo", "download_owl": "http://purl.obolibrary.org/obo/fbdv.owl", "example": "00000000", "homepage": "http://purl.obolibrary.org/obo/fbdv", "keywords": [ "development", "developmental biology", "fly", "life cycle", "life cycle stage", "life science", "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "FBDV", "biocontext": "FBdv", "bioportal": "FB-DV", "fairsharing": "FAIRsharing.p52pzj", "go": "FBdv", "obofoundry": "fbdv", "ols": "fbdv", "ontobee": "FBdv", "prefixcommons": "fbdv" }, "name": "Drosophila development", "pattern": "^\\d{8}$", "preferred_prefix": "FBdv", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/fbdv:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/FBdv_$1", "repository": "https://github.com/FlyBase/drosophila-developmental-ontology", "synonyms": [ "FBdv" ], "uri_format": "http://purl.obolibrary.org/obo/FBdv_$1", "version": "2024-08-07" }, "fbol": { "comment": "Website down, checked on 2021-10-07", "deprecated": true, "description": "DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms.", "example": "2224", "homepage": "http://www.fungalbarcoding.org/", "mappings": { "biocontext": "FBOL", "miriam": "fbol", "n2t": "fbol", "ncbi": "FBOL" }, "name": "International Fungal Working Group Fungal Barcoding.", "pattern": "^\\d+$", "preferred_prefix": "fbol", "uri_format": "http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T" }, "fbql": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "example": "00005254", "name": "FlyBase Qualifiers", "pattern": "^\\d+$", "preferred_prefix": "fbql" }, "fbrf": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "FlyBase internal citation identifiers", "example": "0187632", "homepage": "https://flybase.org", "name": "FlyBase Reference Report", "part_of": "flybase", "pattern": "^\\d{7}$", "preferred_prefix": "fbrf", "uri_format": "https://flybase.org/reports/FBrf$1" }, "fbsp": { "contact": { "email": "cp390@cam.ac.uk", "github": "Clare72", "name": "Clare Pilgrim", "orcid": "0000-0002-1373-1705" }, "deprecated": true, "description": "The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.", "download_obo": "http://aber-owl.net/media/ontologies/FB-SP/7/fb-sp.obo", "download_owl": "http://purl.obolibrary.org/obo/fbsp.owl", "example": "00000000", "homepage": "http://www.flybase.org/", "keywords": [ "obo", "ontology" ], "mappings": { "aberowl": "FB-SP", "biocontext": "FBSP", "bioportal": "FB-SP", "obofoundry": "fbsp", "ols": "fbsp" }, "name": "Fly taxonomy", "part_of": "flybase", "pattern": "^\\d{8}$", "preferred_prefix": "FBSP", "rdf_uri_format": "http://purl.obolibrary.org/obo/FBSP_$1", "uri_format": "http://purl.obolibrary.org/obo/FBSP_$1", "version": "2017-11-19" }, "fbtc": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The cell line vocabulary inside FlyBase", "example": "0000190", "homepage": "https://flybase.org", "mappings": { "cellosaurus": "FlyBase_Cell_line" }, "name": "Flybase Cell Line", "part_of": "flybase", "pattern": "^\\d{7}$", "preferred_prefix": "fbtc", "synonyms": [ "FlyBase_Cell_line" ], "uri_format": "https://flybase.org/reports/FBtc$1" }, "fcb": { "description": "Created by researchers and data managers professionals, the FAIR Cookbook is an online resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable, and Reusable (FAIR).\n\n", "example": "FCB005", "homepage": "https://w3id.org", "mappings": { "miriam": "fcb" }, "name": "the FAIR Cookbook", "pattern": "^FCB\\d{3}$", "preferred_prefix": "fcb", "uri_format": "https://w3id.org/faircookbook/$1" }, "fcsfree": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Cell line databases/resources", "example": "240-17-488-3-4-12", "homepage": "https://fcs-free.org", "mappings": { "cellosaurus": "FCS-free" }, "name": "Fetal Calf Serum-Free Database", "preferred_prefix": "fcsfree", "uri_format": "https://fcs-free.org/fcs-database?$1" }, "fda.application": { "comment": "The official FDA website doesn't appear to be able to resolve application IDs but these IDs do appear in some PDF documents, e.g., https://www.fda.gov/media/159183/download.", "contributor": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "This prefix is for FDA application identifiers. There are multiple types of FDA applications (https://www.fda.gov/drugs/how-drugs-are-developed-and-approved/types-applications), including New Drug Application (NDA). 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It offers a wide range of information on all species currently known in the world: taxonomy, biology, trophic ecology, life history, and uses, as well as historical data reaching back to 250 years.", "example": "6472", "homepage": "http://fishbase.org", "mappings": { "integbio": "nbdc00270", "re3data": "r3d100010912", "wikidata": "P938" }, "name": "FishBase", "pattern": "^\\d+$", "preferred_prefix": "fishbase.species", "synonyms": [ "fishbase" ], "uri_format": "https://www.fishbase.ca/summary/$1" }, "fivestars": { "contact": { "email": "silvio.peroni@unibo.it", "github": "essepuntato", "name": "Silvio Peroni", "orcid": "0000-0003-0530-4305" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology written in OWL 2 DL to enable characterization of the five attributes of an online journal article - peer review, open access, enriched content, available datasets and machine-readable metadata.", "example": "hasOpenAccessRating", "homepage": "http://www.sparontologies.net/ontologies/fivestars", "keywords": [ "bibliography", "citation", "data model", "report", "subject agnostic" ], "mappings": { "fairsharing": "FAIRsharing.6dfe9b" }, "name": "Five Stars of Online Research Articles Ontology", "preferred_prefix": "FiveStars", "publications": [ { "doi": "10.1045/january2012-shotton", "title": "The Five Stars of Online Journal Articles - a Framework for Article Evaluation", "year": 2012 } ], "repository": "https://github.com/sparontologies/fivestars", "twitter": "sparontologies" }, "fix": { "contact": { "email": "chebi-help@ebi.ac.uk", "name": "chEBI" }, "deprecated": true, "description": "An ontology of physico-chemical methods and properties.", "download_obo": "http://purl.obolibrary.org/obo/fix.obo", "download_owl": "http://purl.obolibrary.org/obo/fix.owl", "example": "0000390", "homepage": "https://www.ebi.ac.uk/chebi/", "keywords": [ "chemistry", "experiment", "experimental measurement", "obo", "ontology", "property", "protocol" ], "mappings": { "aberowl": "FIX", "biocontext": "FIX", "bioportal": "FIX", "fairsharing": "FAIRsharing.wwy1ns", "obofoundry": "fix", "ols": "fix", "ontobee": "FIX", "prefixcommons": "fix" }, "name": "Physico-chemical methods and properties", "owners": [ { "name": "European Bioinformatics Institute", "partnered": false, "ror": "02catss52" } ], "part_of": "chebi", "pattern": "^\\d{7}$", "preferred_prefix": "FIX", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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Gyori", "orcid": "0000-0001-9439-5346" }, "description": "FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships.", "example": "GPIb_IX_V", "homepage": "https://sorgerlab.github.io/famplex/", "keywords": [ "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "FPLX", "biocontext": "FPLX", "bioportal": "FPLX", "miriam": "fplx", "n2t": "fplx" }, "name": "FamPlex", "pattern": "^[a-zA-Z0-9][A-Za-z0-9_]+$", "preferred_prefix": "fplx", "publications": [ { "doi": "10.1186/s12859-018-2211-5", "pmc": "PMC6022344", "pubmed": "29954318", "title": "FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining", "year": 2018 } ], "synonyms": [ "famplex" ], "uri_format": "https://sorgerlab.github.io/famplex/$1" }, "fr": { "contact": { "email": "silvio.peroni@unibo.it", "github": "essepuntato", "name": "Silvio Peroni", "orcid": "0000-0003-0530-4305" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology that enables the description of reviews of scientific articles and other scholarly resources.", "example": "ReviewVersion", "homepage": "http://www.sparontologies.net/ontologies/fr", "keywords": [ "bibliography", "citation", "data model", "report", "subject agnostic" ], "mappings": { "fairsharing": "FAIRsharing.e7e609" }, "name": "FAIR* Reviews Ontology", "preferred_prefix": "FR", "repository": "https://github.com/sparontologies/fr", "twitter": "sparontologies" }, "frapo": { "contact": { "email": "silvio.peroni@unibo.it", "github": "essepuntato", "name": "Silvio Peroni", "orcid": "0000-0003-0530-4305" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology for describing the administrative information of research projects, e.g., grant applications, funding bodies, project partners, etc.", "example": "Grant", "homepage": "http://www.sparontologies.net/ontologies/frapo", "keywords": [ "academy", "data model", "funding bodies", "grant application", "report", "research project", "subject agnostic" ], "mappings": { "aberowl": "FRAPO", "fairsharing": "FAIRsharing.0a2576", "lov": "frapo" }, "name": "Funding, Research Administration and Projects Ontology", "preferred_prefix": "FRAPO", "repository": "https://github.com/sparontologies/frapo", "twitter": "sparontologies", "uri_format": "http://purl.org/cerif/frapo/$1" }, "frbr": { "contact": { "email": "silvio.peroni@unibo.it", "github": "essepuntato", "name": "Silvio Peroni", "orcid": "0000-0003-0530-4305" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Essential FRBR in OWL2 DL Ontology (FRBR) is an expression in OWL 2 DL of the basic concepts and relations described in the IFLA report on the Functional Requirements for Bibliographic Records (FRBR), also described in Ian Davis's RDF vocabulary. It is imported by FaBiO and BiRO.", "example": "Expression", "homepage": "http://www.sparontologies.net/ontologies/frbr", "keywords": [ "bibliography", "citation", "data model", "frbr", "report", "subject agnostic" ], "mappings": { "fairsharing": "FAIRsharing.b34b43", "lov": "frbr", "zazuko": "frbr" }, "name": "Functional Requirements for Bibliographic Records", "preferred_prefix": "FRBR", "repository": "https://github.com/sparontologies/frbr", "twitter": "sparontologies", "uri_format": "http://purl.org/vocab/frbr/core#$1" }, "frbrer": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This is the element set of native RDF classes and properties described in the current text (Feb 2009) of the Functional Requirements for Bibliographic Records (FRBR) entity-relationship model. (from https://www.iflastandards.info/fr/frbr/frbrer.html)", "download_rdf": "http://iflastandards.info/ns/fr/frbr/frbrer.jsonld", "example": "1001", "homepage": "https://www.iflastandards.info/fr/frbr/frbrer", "keywords": [ "frbr" ], "mappings": { "lov": "frbrer" }, "name": "Functional Requirements for Bibliographic Records Entity-Relationship Model", "part_of": "frbr", "preferred_prefix": "frbrer", "uri_format": "http://iflastandards.info/ns/fr/frbr/frbrer/$1" }, "fsnp": { "description": "The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification.", "example": "rs17852708", "homepage": "http://compbio.cs.queensu.ca/F-SNP/", "keywords": [ "dna", "protein" ], "mappings": { "biocontext": "FSNP", "miriam": "fsnp", "n2t": "fsnp", "prefixcommons": "fsnp" }, "name": "F-SNP", "pattern": "^rs\\d+$", "preferred_prefix": "fsnp", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/fsnp:$1" } ], "uri_format": "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1" }, "ftt": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Types of named geographic features. Applicable also to many unnamed features but reflects the level of detail traditionally shown on maps, so some feature types specified in scientific studies may not be well represented here. Not highly specific.", "example": "273", "homepage": "https://apps.usgs.gov/thesaurus/thesaurus-full.php?thcode=3", "name": "Feature Type Thesaurus", "pattern": "^\\d+$", "preferred_prefix": "ftt", "references": [ "https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638380238036200", "https://github.com/EnvironmentOntology/envo/issues/1130" ], "uri_format": "https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code=$1" }, "funcbase.fly": { "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data.", "example": "10194", "homepage": "http://func.mshri.on.ca/fly", "mappings": { "biocontext": "FUNCBASE.FLY", "miriam": "funcbase.fly", "n2t": "funcbase.fly" }, "name": "FuncBase Fly", "pattern": "^\\d+$", "preferred_prefix": "funcbase.fly", "uri_format": "http://func.mshri.on.ca/fly/genes/list_functional_scores/$1" }, "funcbase.human": { "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data.", "example": "119514", "homepage": "http://func.mshri.on.ca/human/", "mappings": { "biocontext": "FUNCBASE.HUMAN", "miriam": "funcbase.human", "n2t": "funcbase.human" }, "name": "FuncBase Human", "pattern": "^\\d+$", "preferred_prefix": "funcbase.human", "uri_format": "http://func.mshri.on.ca/human/genes/list_functional_scores/$1" }, "funcbase.mouse": { "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse.", "example": "1351341", "homepage": "http://func.mshri.on.ca/mouse/", "mappings": { "biocontext": "FUNCBASE.MOUSE", "miriam": "funcbase.mouse", "n2t": "funcbase.mouse" }, "name": "FuncBase Mouse", "pattern": "^\\d+$", "preferred_prefix": "funcbase.mouse", "uri_format": "http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1" }, "funcbase.yeast": { "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast.", "example": "2701", "homepage": "http://func.mshri.on.ca/yeast", "mappings": { "biocontext": "FUNCBASE.YEAST", "miriam": "funcbase.yeast", "n2t": "funcbase.yeast" }, "name": "FuncBase Yeast", "pattern": "^\\d+$", "preferred_prefix": "funcbase.yeast", "uri_format": "http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1" }, "funderregistry": { "description": "The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world.", "example": "100000001", "homepage": "https://www.crossref.org/", "mappings": { "miriam": "funderregistry" }, "name": "FunderRegistry", "pattern": "^\\d{9,9}$", "preferred_prefix": "funderregistry", "providers": [ { "code": "crossref.api", "description": "Access funder data through the Crossref API", "homepage": "https://api.crossref.org", "name": "Crossref API", "uri_format": "https://api.crossref.org/funders/$1" }, { "code": "doi", "description": "Access funder data through a DOI for crossref funders.", "homepage": "https://doi.org", "name": "DOI", "uri_format": "https://dx.doi.org/10.13039/501100000995" } ], "synonyms": [ "FundRef", "crossref.funder" ], "uri_format": "http://data.crossref.org/fundingdata/funder/10.13039/$1" }, "fungidb": { "contact": { "email": "jason.stajich@ucr.edu", "name": "Jason E. Stajich", "orcid": "0000-0002-7591-0020" }, "description": "FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina.", "example": "CNBG_0001", "homepage": "https://fungidb.org/fungidb", "keywords": [ "genomics" ], "mappings": { "biocontext": "FUNGIDB", "fairsharing": "FAIRsharing.xf30yc", "miriam": "fungidb", "n2t": "fungidb", "re3data": "r3d100011906" }, "name": "FungiDB", "pattern": "^[A-Za-z_0-9]+$", "preferred_prefix": "fungidb", "publications": [ { "doi": "10.1016/j.fgb.2016.04.002", "pubmed": "27259951", "title": "Database whiplash, crowdsourcing, and FungiDB", "year": 2016 }, { "doi": "10.1128/ec.00083-14", "pmc": "PMC4135733", "pubmed": "24813190", "title": "Literature-based gene curation and proposed genetic nomenclature for cryptococcus", "year": 2014 }, { "doi": "10.1093/nar/gkr918", "pmc": "PMC3245123", "pubmed": "22064857", "title": "FungiDB: an integrated functional genomics database for fungi", "year": 2011 }, { "doi": "10.1128/EC.00083-14", "title": "Literature-based gene curation and proposed genetic nomenclature for cryptococcus." } ], "twitter": "fungidb", "uri_format": "https://fungidb.org/fungidb/app/record/gene/$1" }, "fungorum": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "identifier for a fungus taxon in Index Fungorum", "example": "154022", "homepage": "http://www.indexfungorum.org", "mappings": { "ncbi": "Fungorum", "wikidata": "P1391" }, "name": "Index Fungorum", "pattern": "^[1-9]\\d{0,5}$", "preferred_prefix": "fungorum", "uri_format": "http://www.indexfungorum.org/names/NamesRecord.asp?RecordID=$1" }, "fyeco": { "comment": "Rather than admitting FYECO to the OBO foundry, we secure the prefix here at bioregistry. The FYECO namespace shows up in a lot of ingests (basically anywhere you ingest PomBase gene-phenotype data). Future work includes mapping FYECO to other OBO ontologies, but this is way ahead in the future.", "contact": { "email": "vw253@cam.ac.uk", "github": "ValWood", "name": "Val Wood", "orcid": "0000-0001-6330-7526" }, "contributor": { "email": "vw253@cam.ac.uk", "github": "ValWood", "name": "Val Wood", "orcid": "0000-0001-6330-7526" }, "description": "PomBase manages gene and phenotype data related to Fission Yeast. FYECO contains experimental conditions relevant to fission yeast biology. The FYECO namespace shows up in data ingests from PomBase.", "example": "0000003", "github_request_issue": 268, "homepage": "https://github.com/pombase/fypo", "mappings": { "biolink": "FYECO" }, "name": "Fission Yeast Experimental Conditions Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "FYECO", "repository": "https://github.com/pombase/fypo", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } }, "fyler": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A hierarchical classification of congenital heart disease ", "example": "4447", "homepage": "https://www.elsevier.com/books/nadas-pediatric-cardiology/9781416023906", "name": "Fyler", "pattern": "^\\d+$", "preferred_prefix": "fyler", "references": [ "https://github.com/obophenotype/human-phenotype-ontology/issues/2568", "https://github.com/obophenotype/human-phenotype-ontology/issues/2511" ] }, "fypo": { "contact": { "email": "vw253@cam.ac.uk", "github": "ValWood", "name": "Val Wood", "orcid": "0000-0001-6330-7526" }, "description": "A formal ontology of phenotypes observed in fission yeast.", "download_json": "http://purl.obolibrary.org/obo/fypo.json", "download_obo": "http://purl.obolibrary.org/obo/fypo.obo", "download_owl": "http://purl.obolibrary.org/obo/fypo.owl", "example": "0001707", "homepage": "https://github.com/pombase/fypo", "keywords": [ "gene ontology enrichment", "genetics", "life science", "obo", "ontology", "phenotype", "phylogenetics" ], "license": "CC-BY-4.0", "logo": "https://github.com/pombase/website/blob/master/src/assets/FYPO_logo_tiny.png", "mappings": { "aberowl": "FYPO", "biocontext": "FYPO", "biolink": "FYPO", "bioportal": "FYPO", "fairsharing": "FAIRsharing.4vr0ys", "go": "FYPO", "obofoundry": "fypo", "ols": "fypo", "ontobee": "FYPO" }, "name": "Fission Yeast Phenotype Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "FYPO", "publications": [ { "doi": "10.1093/bioinformatics/btt266", "pmc": "PMC3694669", "pubmed": "23658422", "title": "FYPO: the fission yeast phenotype ontology", "year": 2013 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/FYPO_$1", "repository": "https://github.com/pombase/fypo", "uri_format": "http://purl.obolibrary.org/obo/FYPO_$1", "version": "2024-08-01" }, "ga4ghdos": { "description": "Assists in resolving data across cloud resources.", "example": "dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d", "homepage": "http://github.com/ga4gh/data-object-service-schemas", "mappings": { "biocontext": "GA4GHDOS", "miriam": "ga4ghdos", "n2t": "ga4ghdos" }, "name": "Data Object Service", "pattern": "^[a-zA-Z0-9\\-:#/\\.]+$", "preferred_prefix": "ga4ghdos", "uri_format": "https://dataguids.org/ga4gh/dos/v1/dataobjects/$1" }, "gabi": { "contact": { "email": "birgit.kersten@thuenen.de", "name": "Birgit Kersten", "orcid": "0000-0001-9900-9133" }, "description": "GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'.", "example": "2679240", "homepage": "http://www.gabipd.org/", "keywords": [ "gene", "genome", "plant" ], "mappings": { "biocontext": "GABI", "miriam": "gabi", "n2t": "gabi", "ncbi": "GABI", "prefixcommons": "gabi" }, "name": "Network of Different Plant Genomic Research Projects", "pattern": "^\\w+$", "preferred_prefix": "gabi", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/gabi:$1" } ], "publications": [ { "doi": "10.1093/nar/gkn611", "pmc": "PMC2686513", "pubmed": "18812395", "title": "GabiPD: the GABI primary database--a plant integrative 'omics' database", "year": 2008 } ], "uri_format": "http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject" }, "gainesville.core": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Describes typical Computational Chemistry experiments, including Molecular Publications, Molecular Systems, Molecular Calculations", "download_owl": "http://ontologies.makolab.com/gc06/gc.owl", "example": "Aromatic", "homepage": "http://ontologies.makolab.com/gc06/gc.html", "keywords": [ "ontology" ], "license": "CC-BY-3.0", "name": "Gainesville Core Ontology", "preferred_prefix": "gainesville.core", "references": [ "http://ontologies.makolab.com/gc/" ], "uri_format": "http://purl.org/gc/$1" }, "galen": { "comment": "I really tried, but could not figure out what GALEN stands for", "contact": { "email": "j@deltaflow.com", "name": "Julian Seidenberg" }, "deprecated": true, "description": "A translation of the full Galen ontology (from the OpenGALEN project) into the OWL description logic.", "download_owl": "http://aber-owl.net/media/ontologies/GALEN/1/galen.owl", "example": "MagnitudeValueType", "homepage": "https://www.opengalen.org", "keywords": [ "ontology" ], "mappings": { "aberowl": "GALEN", "bioportal": "GALEN" }, "name": "GALEN", "preferred_prefix": "galen", "uri_format": "http://www.co-ode.org/ontologies/galen#$1" }, "gallont": { "contact": { "email": "adeans@psu.edu", "github": "adeans", "name": "Andy Deans", "orcid": "0000-0002-2119-4663" }, "depends_on": [ "caro", "flopo", "ncbitaxon", "obi", "pato", "po", "poro", "ro" ], "description": "Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls.", "download_json": "http://purl.obolibrary.org/obo/gallont.json", "download_obo": "http://purl.obolibrary.org/obo/gallont.obo", "download_owl": "http://purl.obolibrary.org/obo/gallont.owl", "example": "0000001", "homepage": "https://adeans.github.io/gallont/", "keywords": [ "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "GALLONT", "agroportal": "GALLONT", "bioportal": "GALLONT", "obofoundry": "gallont", "ontobee": "GALLONT" }, "name": "Plant Gall Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "GALLONT", "rdf_uri_format": "http://purl.obolibrary.org/obo/GALLONT_$1", "repository": "https://github.com/adeans/gallont", "uri_format": "http://purl.obolibrary.org/obo/GALLONT_$1" }, "gard": { "contact": { "email": "eric.sid@nih.gov", "github": "ericsid", "name": "Eric Sid", "orcid": "0000-0001-7697-3026" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Database of rare diseases and related terms, including symptoms, healthcare resources, and organizations supporting research of the disease.", "example": "6038", "homepage": "https://rarediseases.info.nih.gov/diseases", "mappings": { "wikidata": "P4317" }, "name": "Genetic and Rare Diseases Information Center", "pattern": "^\\d+$", "preferred_prefix": "gard", "publications": [ { "doi": "10.1080/02763869.2022.2131143", "pubmed": "36394913", "title": "Genetic and Rare Diseases Information Center (GARD)", "year": 2022 }, { "doi": "10.3233/trd-170011", "pmc": "PMC5685198", "pubmed": "29152459", "title": "Marking 15 years of the Genetic and Rare Diseases Information Center", "year": 2017 } ], "synonyms": [ "GARD", "Genetic and Rare Diseases Information Center" ], "uri_format": "https://rarediseases.info.nih.gov/diseases/$1/index" }, "gateway": { "description": "The Health Data Research Innovation Gateway (the 'Gateway') provides a common entry point to discover and enquire about access to UK health datasets for research and innovation. It provides detailed information about the datasets, which are held by members of the UK Health Data Research Alliance, such as a description, size of the population, and the legal basis for access.", "example": "fd8d0743-344a-4758-bb97-f8ad84a37357", "homepage": "https://www.hdruk.ac.uk", "mappings": { "miriam": "gateway" }, "name": "Health Data Research Innovation Gateway", "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "preferred_prefix": "gateway", "uri_format": "https://web.www.healthdatagateway.org/dataset/$1" }, "gaz": { "appears_in": [ "scdo" ], "contact": { "email": "lschriml@som.umaryland.edu", "github": "lschriml", "name": "Lynn Schriml", "orcid": "0000-0001-8910-9851" }, "deprecated": true, "description": "A gazetteer constructed on ontological principles. The countries are actively maintained.", "download_obo": "http://purl.obolibrary.org/obo/gaz.obo", "download_owl": "http://purl.obolibrary.org/obo/gaz.owl", "example": "00620027", "homepage": "http://environmentontology.github.io/gaz/", "keywords": [ "environmental science", "geographical location", "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "GAZ", "biocontext": "GAZ", "bioportal": "GAZ", "fairsharing": "FAIRsharing.wkdjpb", "obofoundry": "gaz", "ols": "gaz", "ontobee": "GAZ", "wikidata": "P6778" }, "name": "Gazetteer", "pattern": "^\\d{8}$", "preferred_prefix": "GAZ", "rdf_uri_format": "http://purl.obolibrary.org/obo/GAZ_$1", "repository": "https://github.com/EnvironmentOntology/gaz", "uri_format": "http://purl.obolibrary.org/obo/GAZ_$1" }, "gbif": { "contact": { "email": "timrobertson100@gmail.com", "github": "timrobertson100", "name": "Tim Robertson", "orcid": "0000-0001-6215-3617" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Database of living organisms, taxonomic. \n The GBIF—the Global Biodiversity Information Facility—is international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth.", "example": "4238", "homepage": "https://www.gbif.org/species", "keywords": [ "biodiversity", "bioinformatics", "marine biology", "metagenomics", "natural history", "natural science", "taxonomy" ], "mappings": { "fairsharing": "FAIRsharing.zv11j3", "integbio": "nbdc00069", "re3data": "r3d100000039", "wikidata": "P846" }, "name": "Global Biodiversity Information Facility", "pattern": "^\\d+$", "preferred_prefix": "gbif", "publications": [ { "doi": "10.1371/journal.pone.0102623", "pmc": "PMC4123864", "pubmed": "25099149", "title": "The GBIF integrated publishing toolkit: facilitating the efficient publishing of biodiversity data on the internet", "year": 2014 } ], "repository": "https://github.com/gbif/", "twitter": "GBIF", "uri_format": "https://www.gbif.org/species/$1" }, "gc": { "comment": "see comment here: https://github.com/obophenotype/ncbitaxon/issues/47", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries.", "example": "11", "homepage": "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html", "name": "Genetic Code", "pattern": "^\\d+$", "preferred_prefix": "gc", "references": [ "https://github.com/obophenotype/ncbitaxon/issues/47" ], "synonyms": [ "gc_id" ], "uri_format": "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG$1" }, "gcst": { "description": "The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide.", "example": "GCST000035", "homepage": "https://www.ebi.ac.uk", "mappings": { "miriam": "gcst", "n2t": "gcst" }, "name": "GWAS Catalog", "owners": [ { "name": "European Bioinformatics Institute", "partnered": false, "ror": "02catss52" } ], "pattern": "^GCST\\d{6}\\d*$", "preferred_prefix": "gcst", "uri_format": "https://www.ebi.ac.uk/gwas/studies/$1" }, "gdc": { "description": "The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis.", "example": "ae8c77fe-e6c8-44d5-8265-4a38c637bbef", "homepage": "https://gdc.cancer.gov", "mappings": { "biocontext": "GDC", "miriam": "gdc", "n2t": "gdc" }, "name": "Genomic Data Commons Data Portal", "pattern": "^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$", "preferred_prefix": "gdc", "uri_format": "https://portal.gdc.cancer.gov/cases/$1" }, "gdsc": { "description": "The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed to facilitate an increased understanding of the molecular features that influence drug response in cancer cells and which will enable the design of improved cancer therapies.", "example": "1242", "homepage": "https://www.cancerrxgene.org", "mappings": { "cellosaurus": "GDSC", "miriam": "gdsc", "n2t": "gdsc" }, "name": "Genomics of Drug Sensitivity in Cancer", "pattern": "^[0-9]+$", "preferred_prefix": "gdsc", "uri_format": "https://www.cancerrxgene.org/translation/Drug/$1" }, "gear": { "contact": { "email": "jorvis@gmail.com", "github": "jorvis", "name": "Joshua Orvis", "orcid": "0000-0002-5705-5710" }, "contributor": { "email": "jorvis@gmail.com", "github": "jorvis", "name": "Joshua Orvis", "orcid": "0000-0002-5705-5710" }, "description": "The gEAR portal is a website for visualization and analysis of multi-omic data both in public and private domains.", "example": "d.a59037e8", "example_extras": [ "p.bfd178f5" ], "github_request_issue": 728, "homepage": "https://umgear.org", "license": "AGPL-3.0-only", "name": "Gene Expression Analysis Resource", "pattern": "^[dp]\\.[a-z0-9]{8}$", "preferred_prefix": "gear", "repository": "https://github.com/IGS/gEAR", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://umgear.org/p?id=$1" }, "gecko": { "contact": { "email": "rbca.jackson@gmail.com", "github": "beckyjackson", "name": "Rebecca Jackson", "orcid": "0000-0003-4871-5569" }, "description": "An ontology to represent genomics cohort attributes.", "download_owl": "http://purl.obolibrary.org/obo/gecko.owl", "example": "0000044", "homepage": "https://github.com/IHCC-cohorts/GECKO", "keywords": [ "biological sample", "experimental measurement", "genomics", "life science", "obo", "ontology", "statistics", "survey" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "GECKO", "bioportal": "GECKO", "fairsharing": "FAIRsharing.3da56b", "obofoundry": "gecko", "ols": "gecko", "ontobee": "GECKO" }, "name": "Genomics Cohorts Knowledge Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "GECKO", "rdf_uri_format": "http://purl.obolibrary.org/obo/GECKO_$1", "repository": "https://github.com/IHCC-cohorts/GECKO", "uri_format": "http://purl.obolibrary.org/obo/GECKO_$1", "version": "2021-01-18" }, "gemet": { "contact": { "email": "helpdesk@eionet.europa.eu", "name": "Eionet Helpdesk" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The European Environment Information and Observation Network (Eionet) is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries. The EEA is responsible for developing Eionet and coordinating its activities together with National Focal Points (NFPs) in the countries. This terminology supports those efforts.", "example": "627", "homepage": "https://www.eionet.europa.eu/gemet/en/themes/", "keywords": [ "biodiversity", "ecology", "environmental science" ], "mappings": { "agroportal": "GEMET", "bartoc": "16", "fairsharing": "FAIRsharing.9091d9" }, "name": "General Multilingual Environmental Thesaurus", "pattern": "^\\d+$", "preferred_prefix": "gemet", "uri_format": "https://www.eionet.europa.eu/gemet/en/concept/$1" }, "genatlas": { "description": "GenAtlas is a database containing information on human genes, markers and phenotypes.", "example": "HBB", "homepage": "http://genatlas.medecine.univ-paris5.fr/", "keywords": [ "disorder", "gene", "human", "life science" ], "mappings": { "biocontext": "GENATLAS", "fairsharing": "FAIRsharing.pmg2vd", "integbio": "nbdc00275", "miriam": "genatlas", "n2t": "genatlas", "prefixcommons": "genatlas", "uniprot": "DB-0027" }, "name": "Genatlas", "pattern": "^\\w+$", "preferred_prefix": "genatlas", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/genatlas:$1" } ], "publications": [ { "doi": "10.1016/s0764-4469(99)80021-3", "pubmed": "9835018", "title": "Genatlas database, genes and development defects", "year": 1998 }, { "doi": "10.1006/mgme.1999.2867", "pubmed": "10444337", "title": "Human genes involved in chromatin remodeling in transcription initiation, and associated diseases: An overview using the GENATLAS database", "year": 1999 } ], "uri_format": "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1" }, "genbank": { "contact": { "email": "nawrocke@ncbi.nlm.nih.gov", "github": "nawrockie", "name": "Eric P. 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/genbank:$1" } ], "publications": [ { "doi": "10.1186/s12859-020-3537-3", "pmc": "PMC7245624", "pubmed": "32448124", "title": "VADR: validation and annotation of virus sequence submissions to GenBank", "year": 2020 }, { "doi": "10.1093/nar/gkz956", "pmc": "PMC7145611", "pubmed": "31665464", "title": "GenBank", "year": 2020 }, { "doi": "10.1093/nar/gky989", "pmc": "PMC6323954", "pubmed": "30365038", "title": "GenBank", "year": 2019 }, { "doi": "10.1093/nar/gkx1094", "pmc": "PMC5753231", "pubmed": "29140468", "title": "GenBank", "year": 2018 }, { "doi": "10.1093/nar/gkw1070", "pmc": "PMC5210553", "pubmed": "27899564", "title": "GenBank", "year": 2016 }, { "doi": "10.1093/nar/gkv1276", "pmc": "PMC4702903", "pubmed": "26590407", "title": "GenBank", "year": 2015 }, { "doi": "10.1093/nar/gku1216", "pmc": "PMC4383990", "pubmed": "25414350", "title": "GenBank", "year": 2014 }, { "doi": "10.1093/nar/gkt1030", "pmc": "PMC3965104", "pubmed": "24217914", "title": "GenBank", "year": 2013 }, { "doi": "10.1093/nar/gks1195", "pmc": "PMC3531190", "pubmed": "23193287", "title": "GenBank", "year": 2012 }, { "doi": "10.1093/nar/gkr1202", "pmc": "PMC3245039", "pubmed": "22144687", "title": "GenBank", "year": 2011 }, { "doi": "10.1093/nar/gkq1079", "pmc": "PMC3013681", "pubmed": "21071399", "title": "GenBank", "year": 2010 }, { "doi": "10.1093/nar/gkn723", "pmc": "PMC2686462", "pubmed": "18940867", "title": "GenBank", "year": 2008 }, { "doi": "10.1093/nar/gkm929", "pmc": "PMC2238942", "pubmed": "18073190", "title": "GenBank", "year": 2007 }, { "doi": "10.1093/nar/gkl1031", "pmc": "PMC1781113", "pubmed": "17170002", "title": "Database resources of the National Center for Biotechnology Information", "year": 2006 } ], "uri_format": "https://www.ncbi.nlm.nih.gov/nucleotide/$1" }, "genbase": { "contact": { "email": "zhaoxuetong@big.ac.cn", "name": "Xuetong Zhao", "orcid": "0000-0002-9551-6370" }, "contributor": { "email": "shah.tanay2@northeastern.edu", "github": "tanayshah2", "name": "Tanay Shah", "orcid": "0009-0001-1912-5132" }, "description": "GenBase is a genetic sequence database that accepts user submissions (mRNA, genomic DNAs, ncRNA, or small genomes such as organelles, viruses, plasmids, phages from any organism) and integrates data from INSDC.", "example": "C_AA001108.1", "homepage": "https://ngdc.cncb.ac.cn/genbase/?lang=en", "keywords": [ "biological sample", "experimental measurement", "genomics", "life science", "statistics", "survey" ], "mappings": { "fairsharing": "FAIRsharing.3da56b", "re3data": "r3d100014353" }, "name": "GenBase", "preferred_prefix": "genbase", "uri_format": "https://ngdc.cncb.ac.cn/genbase/search/gb/$1" }, "gendis": { "comment": "This resource doesn't exist on the web anymore", "deprecated": true, "description": "Genomic Distribution of structural Superfamilies identifies and classifies evolutionary related proteins at the superfamily level in whole genome databases.", "example": "46946", "homepage": "http://caps.ncbs.res.in/gendis/home.html", "keywords": [ "classification", "genome" ], "mappings": { "prefixcommons": "gendis" }, "name": "Genomic Distribution of structural Superfamilies", "preferred_prefix": "gendis", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/jcvi.genprop:$1" } ], "uri_format": "https://www.ebi.ac.uk/interpro/genomeproperties/#$1" }, "geo": { "banana_peel": "_", "contact": { "email": "barrett@ncbi.nlm.nih.gov", "name": "Tanya Barrett", "orcid": "0000-0002-9448-8064" }, "description": "The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval.", "example": "GDS1234", "homepage": "https://www.ncbi.nlm.nih.gov/geo/", "keywords": [ "comparative genomics", "epigenomics", "gene expression", "genome", "genomics", "life science", "omics", "phenomics", "transcriptomics" ], "mappings": { "cellosaurus": "GEO", "edam": "1147", "fairsharing": "FAIRsharing.5hc8vt", "go": "GEO", "integbio": "nbdc00080", "miriam": "geo", "n2t": "geo", "prefixcommons": "geo", "re3data": "r3d100010283" }, "name": "NCBI Gene Expression Omnibus", "pattern": "^G(PL|SM|SE|DS)\\d+$", "preferred_prefix": "geo", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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This collection references ligands.", "example": "L000001", "homepage": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/", "mappings": { "biocontext": "GLIDA.LIGAND", "miriam": "glida.ligand", "n2t": "glida.ligand" }, "name": "GLIDA Ligand", "pattern": "^L\\d+$", "preferred_prefix": "glida.ligand", "uri_format": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$1" }, "glycoepitope": { "description": "GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes.", "example": "EP0311", "homepage": "https://www.glycoepitope.jp/epitopes/", "mappings": { "biocontext": "GLYCOEPITOPE", "integbio": "nbdc00087", "miriam": "glycoepitope", "n2t": "glycoepitope" }, "name": "GlycoEpitope", "pattern": "^EP\\d{4}$", "preferred_prefix": "glycoepitope", "uri_format": "https://www.glycoepitope.jp/epitopes/$1" }, "glycomapsdb": { "description": "A database of GlycoMaps containing 2585 conformational maps.", "example": "6819", "homepage": "http://www.glycosciences.de/modeling/glycomapsdb/", "keywords": [ "small molecule" ], "mappings": { "prefixcommons": "glycomapsdb" }, "name": "GlycoMapsDB", "preferred_prefix": "glycomapsdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/glycomedb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkq1014", "pmc": "PMC3013643", "pubmed": "21045056", "title": "GlycomeDB--a unified database for carbohydrate structures", "year": 2010 }, { "doi": "10.1093/glycob/cwp137", "pubmed": "19759275", "title": "Glycome-DB.org: a portal for querying across the digital world of carbohydrate sequences", "year": 2009 }, { "doi": "10.1186/1471-2105-9-384", "pmc": "PMC2567997", "pubmed": "18803830", "title": "GlycomeDB - integration of open-access carbohydrate structure databases", "year": 2008 } ], "uri_format": "https://glytoucan.org/Structures/Glycans/$1" }, "glyconavi": { "contact": { "email": "issaku@noguchi.or.jp", "name": "Issaku Yamada", "orcid": "0000-0001-9504-189X" }, "description": "GlycoNAVI is a website for carbohydrate research. It consists of the \"GlycoNAVI Database\" that provides information such as existence ratios and names of glycans, 3D structures of glycans and complex glycoconjugates, and the \"GlycoNAVI tools\" such as editing of 2D structures of glycans, glycan structure viewers, and conversion tools.", "example": "GN_G03681DA", "example_extras": [ "GN_GlyTouCan_G03681DA" ], "homepage": "https://www.noguchi.or.jp/", "keywords": [ "chemistry", "glycomics", "life science", "organic chemistry" ], "mappings": { "fairsharing": "FAIRsharing.wvp1t7", "integbio": "nbdc01174", "miriam": "glyconavi" }, "name": "GlycoNAVI", "pattern": "^GN_[A-Za-z0-9_:]+$", "preferred_prefix": "glyconavi", "repository": "https://glyconavi.github.io/doc/", "uri_format": "https://glyconavi.org/hub/?id=$1" }, "glycopost": { "description": "GlycoPOST is a mass spectrometry data repository for glycomics and glycoproteomics. 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This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena.", "example": "68513255-fc44-4041-bc4b-4fd2fae7541d", "homepage": "http://gmd.mpimp-golm.mpg.de/", "keywords": [ "life science", "metabolomics" ], "mappings": { "biocontext": "GMD", "fairsharing": "FAIRsharing.jykmkw", "miriam": "gmd", "n2t": "gmd", "re3data": "r3d100011046" }, "name": "Golm Metabolome Database", "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", "preferred_prefix": "gmd", "publications": [ { "doi": "10.1007/s11306-010-0198-7", "pmc": "PMC2874469", "pubmed": "20526350", "title": "Decision tree supported substructure prediction of metabolites from GC-MS profiles", "year": 2010 }, { "doi": "doi:10.1007/s11306-010-0198-7", "title": "Decision tree supported substructure prediction of metabolites from GC-MS profiles" } ], "uri_format": "http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx" }, "gmd.analyte": { "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes.", "example": "4f0fa9b6-514f-4ff4-98cc-0009bc08eb80", "homepage": "http://gmd.mpimp-golm.mpg.de/", "mappings": { "biocontext": "GMD.ANALYTE", "miriam": "gmd.analyte", "n2t": "gmd.analyte" }, "name": "Golm Metabolome Database Analyte", "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", "preferred_prefix": "gmd.analyte", "uri_format": "http://gmd.mpimp-golm.mpg.de/Analytes/$1" }, "gmd.gcms": { "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra.", "example": "53d583d8-40c6-40e1-9296-23f821cd77a5", "homepage": "http://gmd.mpimp-golm.mpg.de/", "mappings": { "biocontext": "GMD.GCMS", "miriam": "gmd.gcms", "n2t": "gmd.gcms" }, "name": "Golm Metabolome Database GC-MS spectra", "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", "preferred_prefix": "gmd.gcms", "uri_format": "http://gmd.mpimp-golm.mpg.de/Spectrums/$1" }, "gmd.profile": { "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues.", "example": "10b38aaf-b977-4950-85b8-f4775f66658d", "homepage": "http://gmd.mpimp-golm.mpg.de/", "mappings": { "biocontext": "GMD.PROFILE", "miriam": "gmd.profile", "n2t": "gmd.profile" }, "name": "Golm Metabolome Database Profile", "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", "preferred_prefix": "gmd.profile", "uri_format": "http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$1" }, "gmd.ref": { "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances.", "example": "8cf84adb-b4db-4807-ac98-0004247c35df", "homepage": "http://gmd.mpimp-golm.mpg.de/", "mappings": { "biocontext": "GMD.REF", "miriam": "gmd.ref", "n2t": "gmd.ref" }, "name": "Golm Metabolome Database Reference Substance", "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", "preferred_prefix": "gmd.ref", "uri_format": "http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1" }, "gmelin": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Gmelin database is a large database of organometallic and inorganic compounds updated quarterly. It is based on the German publication Gmelins Handbuch der anorganischen Chemie which was originally published by Leopold Gmelin in 1817; the last print edition, the 8th, appeared in the 1990s.", "example": "1466", "homepage": "https://link.springer.com/bookseries/562", "mappings": { "edam": "1004", "wikidata": "P1578" }, "name": "Gmelins Handbuch der anorganischen Chemie", "pattern": "^[1-9][0-9]{3,6}$", "preferred_prefix": "gmelin", "proprietary": true, "references": [ "https://en.wikipedia.org/wiki/Gmelin_database" ] }, "gnd": { "description": "The Gemeinsame Normdatei (Integrated Authority File) or GND is an international authority file for person names, subject headings and corporate bodies. It is used mainly for documentation in libraries and increasingly also by archives and museums. The GND is managed by the German National Library in cooperation with various regional library networks in German-speaking Europe and other partners.", "example": "117145750", "homepage": "https://lobid.org/", "keywords": [ "culture", "knowledge and information systems", "publication", "social science" ], "mappings": { "bartoc": "430", "fairsharing": "FAIRsharing.8337e2", "miriam": "gnd", "wikidata": "P227" }, "name": "GND ID", "pattern": "^[0-9X\\-]+$", "preferred_prefix": "gnd", "rdf_uri_format": "https://d-nb.info/gnd/$1", "twitter": "gndnet", "uri_format": "https://lobid.org/gnd/$1" }, "gno": { "contact": { "email": "nje5@georgetown.edu", "github": "edwardsnj", "name": "Nathan Edwards", "orcid": "0000-0001-5168-3196" }, "description": "An ontology for glycans based on GlyTouCan, but organized by subsumption.", "download_json": "http://purl.obolibrary.org/obo/gno.json", "download_obo": "http://purl.obolibrary.org/obo/gno.obo", "download_owl": "http://purl.obolibrary.org/obo/gno.owl", "example": "10004892", "example_extras": [ "G99373GG" ], "homepage": "https://gnome.glyomics.org/", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "GNO", "bioportal": "GNO", "obofoundry": "gno", "ols": "gno", "ontobee": "GNO" }, "name": "Glycan Naming and Subsumption Ontology", "pattern": "^(\\d{8}|(\\w+\\d+\\w+))$", "preferred_prefix": "GNO", "providers": [ { "code": "gno.composition", "description": "GNOme composition browser", "homepage": "https://gnome.glyomics.org/CompositionBrowser.html", "name": "GNOme Composition Browser", "uri_format": "https://gnome.glyomics.org/CompositionBrowser.html?focus=$1" }, { "code": "gno.structure", "description": "GNOme structure browser", "homepage": "https://gnome.glyomics.org/StructureBrowser.html", "name": "GNOme Structure Viewer", "uri_format": "https://gnome.glyomics.org/StructureBrowser.html?focus=$1" } ], "publications": [ { "doi": "10.5281/zenodo.6678278", "title": "GNOme - Glycan Naming and Subsumption Ontology", "year": 2021 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/GNO_$1", "repository": "https://github.com/glygen-glycan-data/GNOme", "synonyms": [ "gnome" ], "uri_format": "http://purl.obolibrary.org/obo/GNO_$1", "version": "2024-05-21" }, "gnomad": { "contact": { "email": "hrehm@mgh.harvard.edu", "github": "heidirehm", "name": "Heidi L. Rehm", "orcid": "0000-0002-6025-0015" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community (from https://gnomad.broadinstitute.org).", "example": "1-55516888-G-GA", "example_extras": [ "M-8602-T-C", "DUP_2_5708" ], "github_request_issue": 695, "homepage": "https://gnomad.broadinstitute.org", "license": "CC0-1.0", "mappings": { "integbio": "nbdc02561" }, "name": "Genome Aggregation Database", "preferred_prefix": "gnomad", "publications": [ { "doi": "10.1038/s41586-020-2308-7", "pmc": "PMC7334197", "pubmed": "32461654", "title": "The mutational constraint spectrum quantified from variation in 141,456 humans", "year": 2020 }, { "doi": "10.1038/s41586-020-2287-8", "pmc": "PMC7334194", "pubmed": "32461652", "title": "A structural variation reference for medical and population genetics", "year": 2020 } ], "uri_format": "https://gnomad.broadinstitute.org/variant/$1" }, "gnpis": { "contact": { "email": "urgi-contact@versailles.inra.fr", "name": "URGI Contact", "orcid": "0000-0003-3001-4908" }, "description": "GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest.", "example": "AY109603", "homepage": "https://urgi.versailles.inra.fr/gnpis/", "keywords": [ "life science" ], "mappings": { "biocontext": "GNPIS", "fairsharing": "FAIRsharing.dw22y3", "miriam": "gnpis", "n2t": "gnpis", "re3data": "r3d100012647" }, "name": "GnpIS", "pattern": "^[A-Za-z0-9]+$", "preferred_prefix": "gnpis", "publications": [ { "doi": "10.1093/database/bat058", "pmc": "PMC3746681", "pubmed": "23959375", "title": "GnpIS: an information system to integrate genetic and genomic data from plants and fungi", "year": 2013 } ], "uri_format": "https://urgi.versailles.inra.fr/gnpis/#result/term=$1" }, "gnps.task": { "contact": { "email": "mingxun.wang@cs.ucr.edu", "github": "mwang87", "name": "Mingxun Wang", "orcid": "0000-0001-7647-6097" }, "contributor": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "description": "GNPS is a web-based mass spectrometry ecosystem that aims to be an open-access knowledge base for community-wide organization and sharing of raw, processed, or annotated fragmentation mass spectrometry data (MS/MS)", "example": "4b848c342a4f4abc871bdf8a09a60807", "github_request_issue": 833, "homepage": "https://gnps.ucsd.edu/", "name": "Global Natural Products Social Molecular Networking Task", "pattern": "^[a-f0-9]+$", "preferred_prefix": "gnps.task", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=$1" }, "go": { "appears_in": [ "agro", "chiro", "cl", "ecocore", "ecto", "envo", "maxo", "pcl", "pco", "planp", "uberon", "xpo", "zp" ], "banana": "GO", "contact": { "email": "suzia@stanford.edu", "github": "suzialeksander", "name": "Suzi Aleksander", "orcid": "0000-0001-6787-2901" }, "contributor_extras": [ { "email": "jmcl@ebi.ac.uk", "github": "jamesamcl", "name": "James Alastair McLaughlin", "orcid": "0000-0002-8361-2795" } ], "depends_on": [ "cl", "ncbitaxon", "ro", "uberon" ], "description": "The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.", "download_json": "http://purl.obolibrary.org/obo/go.json", "download_obo": "http://purl.obolibrary.org/obo/go.obo", "download_owl": "http://purl.obolibrary.org/obo/go.owl", "example": "0032571", "homepage": "http://geneontology.org/", "keywords": [ "annotation", "biocuration", "biological process", "cellular component", "data model", "expression data", "gene", "gene functional annotation", "gene ontology enrichment", "knowledge representation", "life science", "molecular function", "obo", "ontology", "protein", "sequence annotation", "transcript" ], "license": "CC-BY-4.0", "logo": "https://obofoundry.org/images/go_logo.png", "mappings": { "aberowl": "GO", "agroportal": "GO", "bartoc": "572", "biocontext": "GO", "bioportal": "GO", "edam": "1176", "fairsharing": "FAIRsharing.6xq0ee", "go": "GO", "hl7": "2.16.840.1.113883.6.128", "integbio": "nbdc00074", "miriam": "go", "n2t": "go", "ncbi": "GO", "obofoundry": "go", "ols": "go", "ontobee": "GO", "pathguide": "272", "prefixcommons": "go", "re3data": "r3d100014165", "togoid": "Go", "uniprot": "DB-0037", "wikidata": "P686" }, "mastodon": "go@genomic.social", "name": "Gene Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "GO", "providers": [ { "code": "CURATOR_REVIEW", "description": "GO Browser", "homepage": "http://www.informatics.jax.org/searches/GO_form.shtml", "name": "GO Browser", "uri_format": "http://www.informatics.jax.org/searches/GO.cgi?id=GO:$1" }, { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/go:$1" }, { "code": "go_site", "description": "A non-PURL link through the GO site", "homepage": "http://www.geneontology.org", "name": "GO Site Link", "uri_format": "http://www.geneontology.org/GO:$1" }, { "code": "jax", "description": "The JAX endpoint for exploring GO", "homepage": "http://www.informatics.jax.org", "name": "Jackson Laboratories", "uri_format": "http://www.informatics.jax.org/vocab/gene_ontology/GO:$1" }, { "code": "miriam_obo_legacy", "description": "An old URI style for MIRIAM + GO", "homepage": "https://identifiers.org/", "name": "MIRIAM OBO Legacy", "uri_format": "http://identifiers.org/obo.go/GO:$1" }, { "code": "nextprot", "description": "The neXtProt endpoint for exploring GO", "homepage": "https://www.nextprot.org/", "name": "neXtProt GO Browser", "uri_format": "https://www.nextprot.org/term/GO:$1" }, { "code": "pantherdb", "description": "GO Browser in PantherDB", "homepage": "http://www.pantherdb.org/panther", "name": "PatherDB", "uri_format": "http://www.pantherdb.org/panther/category.do?categoryAcc=GO:$1" }, { "code": "quickgo", "description": "Gene Ontology browser from the EBI", "homepage": "https://www.ebi.ac.uk/QuickGO/", "name": "QuickGO", "uri_format": "https://www.ebi.ac.uk/QuickGO/term/GO:$1" }, { "code": "quickgo.legacy", "description": "QuickGO (Gene Ontology browser)", "homepage": "https://www.ebi.ac.uk/QuickGO/", "name": "QuickGO (Legacy URL)", "uri_format": "https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:$1" } ], "publications": [ { "doi": "10.1093/nar/gkaa1113", "pmc": "PMC7779012", "pubmed": "33290552", "title": "The Gene Ontology resource: enriching a GOld mine", "year": 2021 }, { "doi": "10.1093/nar/gky1055", "pmc": "PMC6323945", "pubmed": "30395331", "title": "The Gene Ontology Resource: 20 years and still GOing strong", "year": 2019 }, { "doi": "10.1093/nar/gku1179", "pmc": "PMC4383973", "pubmed": "25428369", "title": "Gene Ontology Consortium: going forward", "year": 2014 }, { "doi": "10.1186/1471-2164-14-513", "pmc": "PMC3733925", "pubmed": "23895341", "title": "Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology", "year": 2013 }, { "doi": "10.1093/nar/gks1050", "pmc": "PMC3531070", "pubmed": "23161678", "title": "Gene Ontology annotations and resources", "year": 2012 }, { "doi": "10.1093/nar/gkr1028", "pmc": "PMC3245151", "pubmed": "22102568", "title": "The Gene Ontology: enhancements for 2011", "year": 2011 }, { "doi": "10.1093/nar/gkp1018", "pmc": "PMC2808930", "pubmed": "19920128", "title": "The Gene Ontology in 2010: extensions and refinements", "year": 2009 }, { "doi": "10.1093/nar/gkh036", "pmc": "PMC308770", "pubmed": "14681407", "title": "The Gene Ontology (GO) database and informatics resource", "year": 2004 }, { "doi": "10.1038/75556", "pmc": "PMC3037419", "pubmed": "10802651", "title": "Gene ontology: tool for the unification of biology. The Gene Ontology Consortium", "year": 2000 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/GO_$1", "repository": "https://github.com/geneontology/go-ontology", "synonyms": [ "gobp", "gobpid", "gocc", "goccid", "gomf", "gomfid" ], "twitter": "news4go", "uri_format": "http://purl.obolibrary.org/obo/GO_$1", "version": "2024-06-17" }, "go.gpi": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "github": "sierra-moxon", "name": "Sierra Moxon", "orcid": "0000-0002-8719-7760" } ], "description": "This describes the metadata schema for the Gene Product Information (GPI) files in the Gene Ontology, i.e., the local unique identifiers in this identifier space refer to the columns in GPI files.", "example": "db-object-id", "homepage": "http://geneontology.org/docs/gene-product-information-gpi-format/#db-object-id", "mappings": { "biolink": "gpi" }, "name": "Gene Product Information Schema", "preferred_prefix": "go.gpi", "uri_format": "http://geneontology.org/docs/gene-product-information-gpi-format/#$1" }, "go.model": { "description": "GO-Causal Activity Models (GO-CAMs) use a defined “grammar” for linking multiple GO annotations into larger models of biological function (such as “pathways”) in a semantically structured manner. GO-CAMs are created by expert biocurators from the GO Consortium, using the Noctua Curation Platform.", "example": "5fce9b7300001250", "homepage": "http://www.geneontology.org/gocam", "mappings": { "go": "gomodel" }, "name": "Gene Ontology Causal Assembly Model", "preferred_prefix": "go.model", "uri_format": "http://noctua.geneontology.org/editor/graph/gomodel:$1" }, "go.ref": { "banana": "GO_REF", "description": "The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of \"GO content\" meetings at which substantial changes in the ontologies are discussed and made.", "example": "0000041", "homepage": "http://www.geneontology.org/cgi-bin/references.cgi", "mappings": { "biocontext": "GO_REF", "go": "GO_REF", "miriam": "go_ref", "n2t": "go.ref" }, "name": "Gene Ontology Database references", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "go.ref", "uri_format": "https://github.com/geneontology/go-site/blob/master/metadata/gorefs/README.md#goref$1" }, "go.resource": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A database-specific registry supporting curation in the Gene Ontology", "example": "CHEBI", "homepage": "http://geneontology.org/", "name": "Gene Ontology Registry", "preferred_prefix": "go.resource", "uri_format": "https://bioregistry.io/metaregistry/go/$1" }, "go.rule": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "GO Rules are a way of documenting the set of filters and reports that should apply to GAF annotation data. Some rules are expressed as SPARQL on a triplestore, some are code in the GAF parsing software, ontobio.", "example": "0000004", "homepage": "https://github.com/geneontology/go-site/tree/master/metadata/rules", "name": "Gene Ontology Rules", "part_of": "go", "pattern": "^\\d{7}$", "preferred_prefix": "GORULE", "uri_format": "https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-$1.md" }, "goa": { "contact": { "email": "r.huntley@ucl.ac.uk", "github": "rachhuntley", "name": "Rachael P. Huntley", "orcid": "0000-0001-6718-3559" }, "description": "The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups.", "example": "P12345", "homepage": "https://www.ebi.ac.uk/GOA/", "keywords": [ "biology", "gene", "life science", "ontology", "protein" ], "mappings": { "biocontext": "GOA", "fairsharing": "FAIRsharing.7zffgc", "integbio": "nbdc00468", "miriam": "goa", "n2t": "goa", "ncbi": "GOA", "prefixcommons": "goa" }, "name": "Gene Ontology Annotation Database", "pattern": "^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$", "preferred_prefix": "goa", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/goa:$1" } ], "provides": "uniprot", "publications": [ { "doi": "10.1093/nar/gku1113", "pmc": "PMC4383930", "pubmed": "25378336", "title": "The GOA database: gene Ontology annotation updates for 2015", "year": 2014 }, { "doi": "10.1093/nar/gkn803", "pmc": "PMC2686469", "pubmed": "18957448", "title": "The GOA database in 2009--an integrated Gene Ontology Annotation resource", "year": 2008 } ], "uri_format": "https://www.ebi.ac.uk/QuickGO/GProtein?ac=$1" }, "goche": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Represent chemical entities having particular CHEBI roles", "download_owl": "https://raw.githubusercontent.com/geneontology/go-ontology/master/src/ontology/imports/chebi_roles.owl", "example": "25512", "homepage": "https://github.com/geneontology/go-ontology", "keywords": [ "ontology" ], "name": "GO Chemicals", "pattern": "^\\d+$", "preferred_prefix": "GOCHE", "rdf_uri_format": "http://purl.obolibrary.org/obo/GOCHE_$1", "references": [ "https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638472847049400", "https://github.com/geneontology/go-ontology/issues/19535" ], "repository": "https://github.com/geneontology/go-ontology", "synonyms": [ "go.chebi", "go.chemical", "go.chemicals" ], "uri_format": "https://biopragmatics.github.io/providers/goche/$1" }, "goeco": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A GO annotation is a statement about the function of a particular gene. Each annotation includes an evidence code to indicate how the annotation to a particular term is supported.", "example": "IPI", "homepage": "http://geneontology.org/docs/guide-go-evidence-codes/", "name": "GO Evidence Code", "preferred_prefix": "goeco" }, "gold": { "contact": { "email": "tbreddy@lbl.gov", "github": "TBKReddy", "name": "TBK Reddy", "orcid": "0000-0002-0871-5567" }, "description": "The Genomes OnLine Database (GOLD) catalogues genome and metagenome sequencing projects from around the world, along with their associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project.", "example": "Gs0000008", "homepage": "https://gold.jgi.doe.gov/", "keywords": [ "genome", "genomics", "metabolomics", "metagenomics", "ontology and terminology", "phylogenetics" ], "mappings": { "fairsharing": "FAIRsharing.5q1p14", "integbio": "nbdc00483", "miriam": "gold", "prefixcommons": "gold", "re3data": "r3d100010808" }, "name": "Genomes Online Database", "pattern": "^[A-Z][a-z][0-9]+$", "preferred_prefix": "gold", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/gold:$1" } ], "publications": [ { "doi": "10.1093/nar/gkaa983", "pmc": "PMC7778979", "pubmed": "33152092", "title": "Genomes OnLine Database (GOLD) v.8: overview and updates", "year": 2021 }, { "doi": "10.1093/nar/gky977", "pmc": "PMC6323969", "pubmed": "30357420", "title": "Genomes OnLine database (GOLD) v.7: updates and new features", "year": 2019 }, { "doi": "10.1093/nar/gkp848", "pmc": "PMC2808860", "pubmed": "19914934", "title": "The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata", "year": 2009 }, { "doi": "10.1093/nar/gkm884", "pmc": "PMC2238992", "pubmed": "17981842", "title": "The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata", "year": 2007 }, { "doi": "10.1093/nar/29.1.126", "pmc": "PMC29859", "pubmed": "11125068", "title": "Genomes OnLine Database (GOLD): a monitor of genome projects world-wide", "year": 2001 }, { "doi": "10.1093/bioinformatics/15.9.773", "pubmed": "10498782", "title": "Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide", "year": 1999 }, { "doi": "11125068", "title": "Genomes OnLine Database (GOLD): a monitor of genome projects world-wide." } ], "uri_format": "https://gold.jgi.doe.gov/resolver?id=$1" }, "gold.genome": { "description": "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace.\n\nThe GOLD (Genomes OnLine Database)is a resource for centralised monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes.", "example": "Gi07796", "homepage": "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi", "mappings": { "biocontext": "GOLD.GENOME", "miriam": "gold.genome", "n2t": "gold.genome" }, "name": "GOLD genome", "pattern": "^(Gi|Gc)\\d+$", "preferred_prefix": "gold.genome", "uri_format": "http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$1" }, "gold.meta": { "description": "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. \n\nThe GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples.", "example": "Gm00047", "has_canonical": "gold", "homepage": "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi", "mappings": { "biocontext": "GOLD.META", "miriam": "gold.meta", "n2t": "gold.meta" }, "name": "GOLD metadata", "pattern": "^Gm\\d+$", "preferred_prefix": "gold.meta", "uri_format": "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1" }, "goldbook": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Compendium is popularly referred to as the \"Gold Book\", in recognition of the contribution of the late Victor Gold, who initiated work on the first edition. It is one of the series of IUPAC \"Colour Books\" on chemical nomenclature, terminology, symbols and units (see the list of source documents), and collects together terminology definitions from IUPAC recommendations already published in Pure and Applied Chemistry and in the other Colour Books.\n\nTerminology definitions published by IUPAC are drafted by international committees of experts in the appropriate chemistry sub-disciplines, and ratified by IUPAC's Interdivisional Committee on Terminology, Nomenclature and Symbols (ICTNS). In this edition of the Compendium these IUPAC-approved definitions are supplemented with some definitions from ISO and from the International Vocabulary of Basic and General Terms in Metrology; both these sources are recognised by IUPAC as authoritative. The result is a collection of nearly 7000 terms, with authoritative definitions, spanning the whole range of chemistry.", "example": "G02681", "homepage": "https://goldbook.iupac.org", "license": "CC BY 4.0-NC-ND", "mappings": { "bartoc": "1884", "wikidata": "P4732" }, "name": "IUPAC Gold Book Compendium of Chemical Terminology", "pattern": "^[A-Z]{1,2}\\d{5}$", "preferred_prefix": "goldbook", "rdf_uri_format": "http://dx.doi.org/10.1351/goldbook.$1", "uri_format": "https://goldbook.iupac.org/terms/view/$1" }, "google.book": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Search the world's most comprehensive index of full-text books.", "example": "qafeQTWIWmcC", "github_request_issue": 511, "homepage": "https://books.google.com", "mappings": { "wikidata": "P675" }, "name": "Google Books", "preferred_prefix": "google.book", "uri_format": "https://books.google.com/books?id=$1" }, "google.patent": { "contributor_extras": [ { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" } ], "description": "Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date.", "example": "US4145692", "example_extras": [ "USRE38117E1" ], "homepage": "https://www.google.com/patents/", "mappings": { "biocontext": "GOOGLE.PATENT", "cellosaurus": "Patent", "miriam": "google.patent", "n2t": "google.patent" }, "name": "Google Patents", "pattern": "^[A-Z]{2,4}\\d+([A-Z])?([0-9])?$", "preferred_prefix": "google.patent", "synonyms": [ "patent" ], "uri_format": "https://www.google.com/patents/$1" }, "google.scholar": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Google Scholar provides a simple way to broadly search for scholarly literature. You can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites.", "example": "PjrpzUIAAAAJ", "homepage": "https://scholar.google.com/", "mappings": { "biolink": "GSID", "wikidata": "P1960" }, "name": "Google Scholar Researcher", "pattern": "^[-_0-9A-Za-z]{12}$", "preferred_prefix": "google.scholar", "uri_format": "https://scholar.google.com/citations?user=$1" }, "gorel": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO.", "download_owl": "ftp://ftp.geneontology.org/pub/go/ontology/extensions/gorel.owl", "example": "0002005", "homepage": "http://geneontology.org/docs/ontology-relations/", "keywords": [ "ontology" ], "mappings": { "biolink": "GOREL", "go": "GOREL" }, "name": "GO Relations", "pattern": "^\\d{7}$", "preferred_prefix": "gorel", "providers": [ { "code": "obo.legacy", "description": "Legacy OBO PURLs", "homepage": "http://purl.obolibrary.org/obo/gorel.owl", "name": "Legacy OBO", "uri_format": "http://purl.obolibrary.org/obo/GOREL_$1" } ], "uri_format": "http://purl.obolibrary.org/obo/GOREL_$1" }, "gpcrdb": { "contact": { "email": "david.gloriam@sund.ku.dk", "name": "David Gloriam", "orcid": "0000-0002-4299-7561" }, "description": "The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models.", "example": "RL3R1_HUMAN", "homepage": "http://www.gpcrdb.org/", "keywords": [ "life science", "molecular biology", "protein", "small molecule" ], "mappings": { "biocontext": "GPCRDB", "fairsharing": "FAIRsharing.e4n3an", "integbio": "nbdc00484", "miriam": "gpcrdb", "n2t": "gpcrdb", "prefixcommons": "gpcrdb", "uniprot": "DB-0038" }, "name": "G protein-coupled receptor database", "pattern": "^\\w+$", "preferred_prefix": "gpcrdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/gpcrdb:$1" } ], "publications": [ { "doi": "10.1093/nar/26.1.275", "pmc": "PMC147194", "pubmed": "9399852", "title": "GPCRDB: an information system for G protein-coupled receptors", "year": 1998 }, { "doi": "10.1093/nar/gkaa1080", "pmc": "PMC7778909", "pubmed": "33270898", "title": "GPCRdb in 2021: integrating GPCR sequence, structure and function", "year": 2021 }, { "doi": "10.1093/nar/gkx1109", "pmc": "PMC5753179", "pubmed": "29155946", "title": "GPCRdb in 2018: adding GPCR structure models and ligands", "year": 2018 }, { "doi": "10.1111/bph.13509", "pmc": "PMC4919580", "pubmed": "27155948", "title": "GPCRdb: the G protein-coupled receptor database - an introduction", "year": 2016 }, { "doi": "10.1093/nar/gkv1178", "pmc": "PMC4702843", "pubmed": "26582914", "title": "GPCRdb: an information system for G protein-coupled receptors", "year": 2015 }, { "doi": "10.1093/nar/gkt1255", "pmc": "PMC3965068", "pubmed": "24304901", "title": "GPCRDB: an information system for G protein-coupled receptors", "year": 2013 }, { "doi": "10.1093/nar/gkq1009", "pmc": "PMC3013641", "pubmed": "21045054", "title": "GPCRDB: information system for G protein-coupled receptors", "year": 2010 }, { "doi": "10.1093/nar/gkg103", "pmc": "PMC165550", "pubmed": "12520006", "title": "GPCRDB information system for G protein-coupled receptors", "year": 2003 }, { "doi": "10.1093/nar/29.1.346", "pmc": "PMC29816", "pubmed": "11125133", "title": "Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems", "year": 2001 } ], "twitter": "gpcrdb", "uri_format": "https://gpcrdb.org/protein/$1" }, "gpcrnava": { "description": "The GPCR NaVa database describes sequence variants within the family of human G Protein-Coupled Receptors (GPCRs). GPCRs regulate many physiological functions and are the targets for most of today's medicines. The acronym NaVa stands for Natural Variant, which means any (non-artificial) variant that occurs in humans.", "example": "1150", "homepage": "http://nava.liacs.nl/", "keywords": [ "pathway", "protein" ], "mappings": { "prefixcommons": "gnd" }, "name": "GPCR Natural Variants database", "preferred_prefix": "gpcrnava", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/gnd:$1" } ], "uri_format": "http://nava.liacs.nl/cgi-bin/nava.py?id=$1" }, "gpmdb": { "contact": { "email": "rbeavis@thegpm.org", "github": "RonBeavis", "name": "Ronald C. 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It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene.", "example": "GR:0080039", "homepage": "http://www.gramene.org/", "mappings": { "biocontext": "GRAMENE.GENE", "go": "GR_GENE", "miriam": "gramene.gene", "n2t": "gramene.gene" }, "name": "Gramene Gene", "pattern": "^GR\\:\\d+$", "preferred_prefix": "gramene.gene", "synonyms": [ "GR_GENE" ], "uri_format": "http://www.gramene.org/db/genes/search_gene?acc=$1" }, "gramene.growthstage": { "banana": "GRO", "contact": { "email": "po-discuss@plantontology.org", "name": "Plant Ontology Administrators" }, "deprecated": true, "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene.", "example": "0007133", "homepage": "http://www.gramene.org/plant_ontology/", "keywords": [ "anatomy", "obo", "ontology" ], "mappings": { "biocontext": "GRAMENE.GROWTHSTAGE", "bioportal": "GRO-CPGA", "miriam": "gro", "n2t": "gramene.growthstage", "obofoundry": "gro", "prefixcommons": "gramene.po" }, "name": "Gramene Growth Stage Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "GRO", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/gramene.po:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/GRO_$1", "synonyms": [ "cpga", "gro-cpga" ], "uri_format": "http://www.gramene.org/db/ontology/search?id=GRO:$1" }, "gramene.protein": { "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene.", "example": "78073", "homepage": "http://www.gramene.org/", "mappings": { "biocontext": "GRAMENE.PROTEIN", "go": "GR_PROTEIN", "miriam": "gramene.protein", "n2t": "gramene.protein" }, "name": "Gramene protein", "pattern": "^\\d+$", "preferred_prefix": "gramene.protein", "synonyms": [ "GR_PROTEIN" ], "uri_format": "http://www.gramene.org/db/protein/protein_search?protein_id=$1" }, "gramene.qtl": { "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene.", "example": "CQG5", "homepage": "http://www.gramene.org/", "mappings": { "biocontext": "GRAMENE.QTL", "go": "GR_QTL", "miriam": "gramene.qtl", "n2t": "gramene.qtl" }, "name": "Gramene QTL", "pattern": "^\\w+$", "preferred_prefix": "gramene.qtl", "synonyms": [ "GR_QTL" ], "uri_format": "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1" }, "gramene.reference": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Literature references in Gramene", "example": "6200", "homepage": "http://www.gramene.org", "name": "Gramene Reference", "pattern": "^\\d+$", "preferred_prefix": "gramene.reference", "synonyms": [ "gramene.ref" ], "uri_format": "http://www.gramene.org/db/literature/pub_search?ref_id=$1" }, "gramene.taxonomy": { "banana": "GR_tax", "banana_peel": ":", "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene.", "example": "013681", "homepage": "http://www.gramene.org/", "mappings": { "biocontext": "GRAMENE.TAXONOMY", "miriam": "gramene.taxonomy", "n2t": "gramene.taxonomy" }, "name": "Gramene Taxonomy", "pattern": "^\\d+$", "preferred_prefix": "gramene.taxonomy", "uri_format": "https://archive.gramene.org/db/ontology/search?id=GR_tax:$1" }, "grassbase": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "GrassBase provides an interactive guide to nomenclature for the whole grass family. It provides lists of over 60,000 names for any given genus, geographical region or genus within a geographical region, helps find the accepted name, synonyms and distribution for any given name, and gives a desription for each species.", "example": "imp10873", "github_request_issue": 218, "homepage": "https://www.kew.org/data/grasses-syn/index.htm", "mappings": { "wikidata": "P1832" }, "name": "GrassBase", "pattern": "^(imp|gen)\\d{5}$", "preferred_prefix": "grassbase", "uri_format": "https://www.kew.org/data/grasses-db/www/$1" }, "greengenes": { "contact": { "email": "GLAndersen@lbl.gov", "name": "Gary L Andersen", "orcid": "0000-0002-1618-9827" }, "description": "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.", "example": "100000", "homepage": "http://greengenes.lbl.gov/", "keywords": [ "genetics", "life science", "rna" ], "mappings": { "biocontext": "GREENGENES", "fairsharing": "FAIRsharing.bpxgb6", "integbio": "nbdc01824", "miriam": "greengenes", "n2t": "greengenes", "ncbi": "Greengenes", "prefixcommons": "greengenes", "re3data": "r3d100010549" }, "name": "16S rRNA gene database", "pattern": "^\\d+$", "preferred_prefix": "greengenes", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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"https://catalog.hathitrust.org/Record/$1" }, "hba": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A controlled vocabulary to support the study of transcription in the human brain", "download_obo": "https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-hba.obo", "example": "4005", "example_extras": [ "265504410" ], "homepage": "https://human.brain-map.org", "keywords": [ "ontology" ], "name": "Human Brain Atlas", "pattern": "^\\d+$", "preferred_prefix": "HBA", "uri_format": "https://biopragmatics.github.io/providers/hba/$1" }, "hbvar": { "description": "This is a relational database of information about hemoglobin variants and mutations that cause thalassemia.", "example": "2526", "homepage": "http://globin.cse.psu.edu/globin/hbvar", "keywords": [ "protein" ], "mappings": { "prefixcommons": "hbvar" }, "name": "A Database of Human Hemoglobin Variants and 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/hbvar:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=$1" }, "hc.din": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A Drug Identification Number (DIN) is a computer-generated eight digit number assigned by Health Canada to a drug product prior to being marketed in Canada. It uniquely identifies all drug products sold in a dosage form in Canada and is located on the label of prescription and over-the-counter drug products that have been evaluated and authorized for sale in Canada.", "example": "02069237", "homepage": "https://www.canada.ca/en/health-canada/services/drugs-health-products/drug-products/fact-sheets/drug-identification-number.html", "mappings": { "hl7": "2.16.840.1.113883.5.1105" }, "name": "Health Canada Drug Identification Number", "pattern": "^\\d{8}$", "preferred_prefix": "hc.din", "references": [ "http://www.hc-sc.gc.ca/dhp-mps/prodpharma/databasdon/index-eng.php" ] }, "hc.npn": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Licensed Natural Health Products Database contains information about natural health products that have been issued a product licence by Health Canada.", "example": "18125", "homepage": "http://webprod.hc-sc.gc.ca/nhpid-bdipsn/search-rechercheReq.do?lang=eng", "mappings": { "hl7": "2.16.840.1.113883.5.1107" }, "name": "Health Canada Natural Product Number", "pattern": "^\\d+$", "preferred_prefix": "hc.npn", "references": [ "https://www.canada.ca/en/health-canada/services/drugs-health-products/natural-non-prescription/applications-submissions/product-licensing/licensed-natural-health-products-database.html" ], "uri_format": "http://webprod.hc-sc.gc.ca/nhpid-bdipsn/ingredReq.do?id=$1" }, "hc.trial": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Health Canada, through its Clinical Trials Database, is providing to the public a listing of specific information relating to phase I, II and III clinical trials in patients. The database is managed by Health Canada and provides a source of information about Canadian clinical trials involving human pharmaceutical and biological drugs. [from website]", "example": "239287", "homepage": "https://health-products.canada.ca/ctdb-bdec", "name": "Health Canada Clinical Trials Database", "pattern": "^\\d+$", "preferred_prefix": "hc.trial", "uri_format": "https://health-products.canada.ca/ctdb-bdec/brand/?submissionNo=$1" }, "hcao": { "description": "Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas.", "download_owl": "http://ontology.data.humancellatlas.org/ontologies/hcao/releases/2023-05-16/hcao.owl", "homepage": "https://www.humancellatlas.org", "keywords": [ "ontology" ], "mappings": { "ols": "hcao" }, "name": "Human Cell Atlas Ontology", "no_own_terms": true, "preferred_prefix": "hcao" }, "hco": { "description": "The Human Chromosome Ontology (HCO) provides simple and stable URIs for human reference genome versions to semantically identify human chromosomes.", "example": "MT", "homepage": "https://dbcls.rois.ac.jp/", "mappings": { "miriam": "hco" }, "name": "Human Chromosome Ontology", "pattern": "^.+$", "preferred_prefix": "hco", "uri_format": "http://biohackathon.org/resource/hco#$1" }, "hcpcs": { "contact": { "email": "Cynthia.Hake@cms.hhs.gov", "name": "Cynthia Hake" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "HCPCS is a collection of standardized codes that represent medical procedures, supplies, products and services. The codes are used to facilitate the processing of health insurance claims by Medicare and other insurers.", "example": "G8944", "homepage": "https://www.cms.gov/Medicare/Coding/MedHCPCSGenInfo", "keywords": [ "biomedical science", "business administration", "ontology" ], "mappings": { "aberowl": "HCPCS", "biolink": "HCPCS", "bioportal": "HCPCS", "fairsharing": "FAIRsharing.x81wz8" }, "name": "Healthcare Common Procedure Coding System", "preferred_prefix": "hcpcs", "uri_format": "http://purl.bioontology.org/ontology/HCPCS/$1" }, "hcvdb": { "description": "the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses.", "example": "M58335", "homepage": "http://euhcvdb.ibcp.fr/euHCVdb/", "keywords": [ "gene" ], "mappings": { "biocontext": "HCVDB", "miriam": "hcvdb", "n2t": "hcvdb", "prefixcommons": "hcv" }, "name": "Hepatitis C Virus Database Project", "pattern": "^M\\d{5}$", "preferred_prefix": "hcvdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/hcv:$1" } ], "uri_format": "https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1" }, "hdl": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Welcome to the web site of the Handle.Net Registry (HNR), run by Corporation for National Research Initiatives (CNRI). CNRI is a Multi-Primary Administrator (MPA) of the Global Handle Registry (GHR), authorized by the DONA Foundation to allot prefixes to users of the Handle System. The DONA Foundation is a non-profit organization based in Geneva that has taken over responsibility for the evolution of CNRI's Digital Object (DO) Architecture including outreach around the world. One of the Foundation's responsibilities is to administer and maintain the overall operation of the GHR, a task that was previously performed by CNRI. (from website)", "example": "2381/12775", "example_extras": [ "391/00-0000-0000-0009-3C7E-F" ], "homepage": "https://www.handle.net/", "keywords": [ "centrally registered identifier", "subject agnostic" ], "mappings": { "fairsharing": "FAIRsharing.0b7e54" }, "name": "Handle", "pattern": "^\\d+/.+$", "preferred_prefix": "hdl", "synonyms": [ "handle" ], "uri_format": "http://hdl.handle.net/$1" }, "hdr": { "description": "The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders.", "example": "63", "homepage": "http://research.nhgri.nih.gov/apps/homeodomain/web/", "keywords": [ "genome" ], "mappings": { "biocontext": "HDR", "miriam": "hdr", "n2t": "hdr", "pathguide": "307", "prefixcommons": "hdr" }, "name": "Homeodomain Research", "pattern": "^\\d+$", "preferred_prefix": "hdr", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/hdr:$1" } ], "uri_format": "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=$1" }, "hemonc": { "comment": "It is unclear if identifiers can be resolved on the website but a spreadsheet of the terminology is available via the NCI at https://evs.nci.nih.gov/ftp1/HemOnc/HemOnc_Terminology.xls", "contributor": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "HemOnc.org is the largest freely available medical wiki of interventions, regimens, and general information relevant to the fields of hematology and oncology.", "example": "15543", "github_request_issue": 1149, "homepage": "https://hemonc.org/", "name": "HemOnc Terminology", "pattern": "^\\d+$", "preferred_prefix": "hemonc", "publications": [ { "doi": "10.1016/j.jbi.2019.103239", "pmc": "PMC6697579", "pubmed": "31238109", "title": "HemOnc: A new standard vocabulary for chemotherapy regimen representation in the OMOP common data model", "year": 2019 } ], "reviewer": { "github": "callahantiff", "name": "Tiffany J. Callahan", "orcid": "0000-0002-8169-9049" } }, "hepro": { "contact": { "email": "paul.fabry@usherbrooke.ca", "github": "pfabry", "name": "Paul Fabry", "orcid": "0000-0002-3336-2476" }, "contributor": { "email": "paul.fabry@usherbrooke.ca", "github": "pfabry", "name": "Paul Fabry", "orcid": "0000-0002-3336-2476" }, "description": "HEPRO is an ontology of informational entities and processes related to health procedures and health activities.", "download_json": "https://github.com/OpenLHS/HEPRO/raw/main/HEPRO.json", "download_owl": "https://github.com/OpenLHS/HEPRO/raw/main/HEPRO.owl", "example": "0000001", "github_request_issue": 810, "homepage": "https://openlhs.github.io/HEPRO/", "keywords": [ "ontology" ], "license": "CC-BY-4.0", "name": "Health Procedure Ontology", "owners": [ { "name": "Université de Sherbrooke", "partnered": false, "ror": "00kybxq39" } ], "pattern": "^\\d{7}$", "preferred_prefix": "HEPRO", "repository": "https://github.com/OpenLHS/HEPRO", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://purl.obolibrary.org/obo/HEPRO_$1" }, "hesa": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An identifier for institutions in the United Kingdom, used in GRID and ROR.", "example": "0154", "homepage": "https://www.hesa.ac.uk", "keywords": [ "bibliometrics", "institution" ], "name": "UK Higher Education Statistics Agency", "pattern": "^\\d+$", "preferred_prefix": "hesa" }, "hgmd": { "description": "The Human Gene Mutation Database (HGMD) collates data on germ-line mutations in nuclear genes associated with human inherited disease. It includes information on single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation entry is unique, and includes cDNA reference sequences for most genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases.", "example": "CALM1", "homepage": "http://www.hgmd.cf.ac.uk/ac/index.php", "mappings": { "biocontext": "HGMD", "edam": "3265", "integbio": "nbdc00097", "miriam": "hgmd", "n2t": "hgmd" }, "name": "Human Gene Mutation Database", "pattern": "^[A-Z_0-9]+$", "preferred_prefix": "hgmd", "uri_format": "http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1" }, "hgnc": { "contact": { "email": "elspeth@genenames.org", "name": "Elspeth Bruford", "orcid": "0000-0002-8380-5247" }, "description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database.", "download_owl": "http://aber-owl.net/media/ontologies/HGNC/1/hgnc.owl", "example": "16793", "homepage": "http://www.genenames.org", "keywords": [ "classification", "gene", "gene name", "life science", "non-coding rna", "ontology", "protein", "pseudogene" ], "license": "CC0-1.0", "mappings": { "aberowl": "HGNC", "biocontext": "HGNC", "bioportal": "HGNC", "cellosaurus": "HGNC", "edam": "2298", "fairsharing": "FAIRsharing.amcv1e", "go": "HGNC", "hl7": "2.16.840.1.113883.6.281", "miriam": "hgnc", "n2t": "hgnc", "ncbi": "HGNC", "prefixcommons": "hgnc", "togoid": "Hgnc", "uniprot": "DB-0042", "wikidata": "P354" }, "name": "HUGO Gene Nomenclature Committee", "pattern": "^\\d{1,5}$", "preferred_prefix": "hgnc", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/hgnc:$1" }, { "code": "gencc", "description": "The GenCC DB provides information pertaining to the validity of gene-disease relationships, with a current focus on Mendelian diseases. Curated gene-disease relationships are submitted by GenCC member organizations. The GenCC comprises organizations that currently provide online resources (e.g. ClinGen, DECIPHER, Genomics England PanelApp, OMIM, Orphanet, PanelApp Australia, TGMI’s G2P), as well as diagnostic laboratories that have committed to sharing their internal curated gene-level knowledge (e.g. Ambry, Illumina, Invitae, Myriad Women’s Health, Mass General Brigham Laboratory for Molecular Medicine).", "homepage": "https://thegencc.org", "name": "The Gene Curation Coalition", "uri_format": "https://search.thegencc.org/genes/HGNC:$1" }, { "code": "indra", "description": "A large scale database of biomedical statements.", "homepage": "https://db.indra.bio", "name": "INDRA Database", "uri_format": "https://db.indra.bio/statements/from_agents?&format=html&agent0=$1@HGNC" } ], "publications": [ { "doi": "10.1093/nar/gkaa980", "pmc": "PMC7779007", "pubmed": "33152070", "title": "Genenames.org: the HGNC and VGNC resources in 2021", "year": 2021 }, { "doi": "10.1093/nar/gky930", "pmc": "PMC6324057", "pubmed": "30304474", "title": "Genenames.org: the HGNC and VGNC resources in 2019", "year": 2019 }, { "doi": "10.1159/000131404", "pubmed": "295268", "title": "International system for human gene nomenclature (1979) ISGN (1979)", "year": 1979 } ], "uri_format": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1" }, "hgnc.genefamily": { "description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families.", "example": "2029", "has_canonical": "hgnc.genegroup", "homepage": "http://www.genenames.org", "mappings": { "biocontext": "HGNC.GENEFAMILY", "miriam": "hgnc.genefamily", "n2t": "hgnc.genefamily" }, "name": "HGNC gene family", "pattern": "^\\d+$", "preferred_prefix": "hgnc.genefamily", "synonyms": [ "GFAM", "HGNC_GROUP", "hgnc.family" ], "uri_format": "https://www.genenames.org/cgi-bin/genefamilies/set/$1" }, "hgnc.genegroup": { "description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families.", "example": "141", "homepage": "https://www.genenames.org", "mappings": { "miriam": "hgnc.genegroup" }, "name": "HGNC Gene Group", "pattern": "^\\d+$", "preferred_prefix": "hgnc.genegroup", "uri_format": "https://www.genenames.org/data/genegroup/#!/group/$1" }, "hgnc.symbol": { "description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol.", "example": "DAPK1", "homepage": "https://www.genenames.org/", "mappings": { "biocontext": "HGNC.SYMBOL", "miriam": "hgnc.symbol", "n2t": "hgnc.symbol", "togoid": "HgncSymbol", "wikidata": "P353" }, "name": "HGNC gene symbol", "pattern": "^[A-Za-z-0-9_]+(\\@)?$", "preferred_prefix": "hgnc.symbol", "providers": [ { "code": "depmap", "description": "DepMap summary of the given gene", "homepage": "https://depmap.org", "name": "DepMap Gene Summary", "uri_format": "https://depmap.org/portal/gene/$1" }, { "code": "oncomx", "description": "Mutation profiles for a gene", "homepage": "https://oncomx.org", "name": "OncoMX", "uri_format": "https://oncomx.org/searchview/?gene=$1" }, { "code": "pathwaycommons", "description": "Interactions between a given gene and other molecular entities", "homepage": "https://www.pathwaycommons.org/", "name": "Pathway Commons Gene Interations", "uri_format": "https://apps.pathwaycommons.org/interactions?source=$1" } ], "uri_format": "https://www.genenames.org/data/gene-symbol-report/#!/symbol/$1" }, "hgvs": { "contact": { "email": "reecehart@gmail.com", "github": "reece", "name": "Reece Hart", "orcid": "0000-0003-3463-0775" }, "contributor": { "email": "miseming@sfu.ca", "github": "miseminger", "name": "Madeline Iseminger", "orcid": "0000-0002-0548-891X" }, "description": "The HGVS Nomenclature is an internationally-recognized standard for the description of DNA, RNA and protein sequence variants. It is used to convey variants in clinical reports and to share variants in publications and databases. The HGVS Nomenclature is administered by the [HGVS Variant Nomenclature Committee (HVNC)](https://hgvs-nomenclature.org/stable/hvnc/) under the auspices of the [Human Genome Organization (HUGO)](https://hugo-int.org/).", "example": "NP_003997.1:p.Trp24Cys", "example_extras": [ "NG_012337.3(NM_003002.4):c.274G>T", "NG_012337.3(NM_003002.4):r.(274g>u)", "NC_000011.10:g.112088970del", "NC_000011.10(NM_001276503.2):c.169+998del", "GRCh38(chr11):g.112088970del" ], "github_request_issue": 1032, "homepage": "https://hgvs-nomenclature.org/stable/background/simple/", "mappings": { "hl7": "2.16.840.1.113883.6.282", "wikidata": "P3331" }, "name": "Human Genome Variation Society Nomenclature", "preferred_prefix": "hgvs", "providers": [ { "code": "mutalyzer", "description": " The Mutalyzer tool suite is designed to be of help when working with HGVS sequence variant nomenclature descriptions.", "homepage": "https://mutalyzer.nl", "name": "LUMC Mutalyzer 3", "uri_format": "https://mutalyzer.nl/api/description_to_model/$1" } ], "publications": [ { "doi": "10.1002/humu.22981", "pubmed": "26931183", "title": "HGVS Recommendations for the Description of Sequence Variants: 2016 Update", "year": 2016 }, { "doi": "10.1093/bioinformatics/btu630", "pmc": "PMC4287946", "pubmed": "25273102", "title": "A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature", "year": 2014 } ], "references": [ "https://github.com/biopragmatics/bioregistry/issues/460" ], "repository": "https://github.com/HGVSnomenclature/hgvs-nomenclature", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://reg.clinicalgenome.org/allele?hgvs=$1" }, "hinv.locus": { "description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view.", "example": "HIX0004394", "homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp", "mappings": { "biocontext": "HINV.LOCUS", "miriam": "hinv.locus", "n2t": "hinv.locus" }, "name": "H-InvDb Locus", "pattern": "^HIX\\d{7}(\\.\\d+)?$", "preferred_prefix": "hinv.locus", "uri_format": "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1" }, "hinv.protein": { "description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view.", "example": "HIP000030660", "homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp", "mappings": { "biocontext": "HINV.PROTEIN", "miriam": "hinv.protein", "n2t": "hinv.protein" }, "name": "H-InvDb Protein", "pattern": "^HIP\\d{9}(\\.\\d+)?$", "preferred_prefix": "hinv.protein", "uri_format": "http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1" }, "hinv.transcript": { "description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view.", "example": "HIT000195363", "homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp", "mappings": { "biocontext": "HINV.TRANSCRIPT", "miriam": "hinv.transcript", "n2t": "hinv.transcript" }, "name": "H-InvDb Transcript", "pattern": "^HIT\\d{9}(\\.\\d+)?$", "preferred_prefix": "hinv.transcript", "uri_format": "http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1" }, "hipsci": { "description": "Cell line databases/resources", "example": "HPSI0114i-bezi_1", "homepage": "https://www.hipsci.org", "mappings": { "cellosaurus": "HipSci" }, "name": "Human Induced Pluripotent Stem Cells Initiative", "preferred_prefix": "hipsci", "uri_format": "https://www.hipsci.org/lines/#/lines/$1" }, "hivreagentprogram": { "description": "Cell line collections (Providers)", "example": "ARP-1513", "homepage": "https://www.hivreagentprogram.org/", "mappings": { "cellosaurus": "HIVReagentProgram" }, "name": "NIH HIV Reagent Program", "preferred_prefix": "hivreagentprogram", "uri_format": "https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx" }, "hl7.v2codesystem": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR.", "example": "0778", "homepage": "https://terminology.hl7.org/codesystems-v2.html", "name": "HL7 V2 Code Systems", "pattern": "^\\d+$", "preferred_prefix": "hl7.v2codesystem", "uri_format": "http://terminology.hl7.org/CodeSystem/v2-$1" }, "hl7.v3codesystem": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR.", "example": "AcknowledgementCondition", "homepage": "https://terminology.hl7.org/codesystems-v2.html", "name": "HL7 V2 Code Systems", "pattern": "^\\w+$", "preferred_prefix": "hl7.v3codesystem", "uri_format": "https://terminology.hl7.org/CodeSystem-v3-$1" }, "hmdb": { "contact": { "email": "david.wishart@ualberta.ca", "github": "DavidWishartLab", "name": "David S. Wishart", "orcid": "0000-0002-3207-2434" }, "description": "The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.", "example": "HMDB00001", "homepage": "http://www.hmdb.ca/", "keywords": [ "biochemistry", "bioinformatics", "chemical", "human", "life science", "metabolite", "metabolomics", "molecular biology", "omics", "phenomics", "proteomics" ], "mappings": { "biocontext": "HMDB", "cheminf": "000408", "edam": "2622", "fairsharing": "FAIRsharing.sye5js", "integbio": "nbdc00909", "miriam": "hmdb", "n2t": "hmdb", "pathguide": "244", "prefixcommons": "hmdb", "re3data": "r3d100011285", "togoid": "Hmdb", "wikidata": "P2057" }, "name": "Human Metabolome Database", "pattern": "^HMDB\\d+$", "preferred_prefix": "hmdb", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/hmdb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkab1062", "pmc": "PMC8728138", "pubmed": "34986597", "title": "HMDB 5.0: the Human Metabolome Database for 2022", "year": 2022 }, { "doi": "10.1093/nar/gkx1089", "pmc": "PMC5753273", "pubmed": "29140435", "title": "HMDB 4.0: the human metabolome database for 2018", "year": 2018 }, { "doi": "10.1093/nar/gks1065", "pmc": "PMC3531200", "pubmed": "23161693", "title": "HMDB 3.0--The Human Metabolome Database in 2013", "year": 2012 }, { "doi": "10.1093/nar/gkl923", "pmc": "PMC1899095", "pubmed": "17202168", "title": "HMDB: the Human Metabolome Database", "year": 2007 }, { "doi": "10.1093/nar/gkn810", "title": "HMDB: a knowledgebase for the human metabolome" } ], "synonyms": [ "HMDB" ], "twitter": "WishartLab", "uri_format": "http://www.hmdb.ca/metabolites/$1" }, "hms.lincs.antibody": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols.", "example": "80001", "homepage": "https://lincs.hms.harvard.edu/db/antibodies/", "name": "HMS Library of Integrated Network-based Cellular Signatures Antibodies", "pattern": "^8\\d{4}$", "preferred_prefix": "hms.lincs.antibody", "uri_format": "https://lincs.hms.harvard.edu/db/antibodies/$1" }, "hms.lincs.cell": { "comment": "this is NOT the same as lincs.cell. On https://lincs.hms.harvard.edu/db/cells/?search=MCF-10A&extra_form_shown=&dataset_types=, you can see there's a mapping to the other resource.", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols.", "example": "50583", "homepage": "https://lincs.hms.harvard.edu/db/cell/", "name": "HMS LINCS Cell", "pattern": "^5\\d{4}$", "preferred_prefix": "hms.lincs.cell", "references": [ "https://github.com/identifiers-org/identifiers-org.github.io/issues/223" ], "uri_format": "https://lincs.hms.harvard.edu/db/cells/$1" }, "hms.lincs.compound": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols.", "example": "10001-101", "example_extras": [ "11996-999" ], "homepage": "https://lincs.hms.harvard.edu/db/sm/", "name": "HMS LINCS Compound", "pattern": "^1\\d{4}-\\d{3}$", "preferred_prefix": "hms.lincs.compound", "synonyms": [ "HMS-LINCS", "hmsl_id" ], "uri_format": "https://lincs.hms.harvard.edu/db/sm/$1" }, "hms.lincs.dataset": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "example": "20003", "homepage": "https://lincs.hms.harvard.edu/db/datasets/", "name": "HMS Library of Integrated Network-based Cellular Signatures Datasets", "pattern": "^2\\d{4}$", "preferred_prefix": "hms.lincs.dataset", "uri_format": "https://lincs.hms.harvard.edu/db/datasets/$1" }, "hoelzel": { "contact": { "email": "info@hoelzel.de", "name": "Carsten Linder", "orcid": "0009-0009-3816-8777" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Hölzel is a life science reagent vendor based in Cologne, Germany. As a distributor, they offer products suitable for many kinds of research areas such as oncology, neuroscience, immunology, and more. Their portfolio consists of antibodies, recombinant proteins, inhibitors, ELISA-kits as well as other assays, arrays and kits. Their inhibitor portfolio can be easily accessed via the CAS-register catalog.", "example": "40592-R001-100", "homepage": "https://www.hoelzel-biotech.com", "keywords": [ "antibodies", "assays", "biologics", "elisa-kits", "inhibitors", "life sciences", "proteins", "vendor" ], "logo": "https://www.hoelzel-biotech.com/skin/frontend/ultimo/custom/images/logo.png", "name": "Hölzel Diagnostika", "preferred_prefix": "hoelzel", "synonyms": [ "hölzel" ], "uri_format": "https://www.hoelzel-biotech.com/de/catalogsearch/result/?q=$1" }, "hog": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Documentation of HOGS (Homologous Organs Groups). Contains links to HOGs download, HOGs onthology, HOGs creation, composition, etc.", "download_obo": "ftp://ftp.bgee.org/general/ontologies/HOG.obo", "example": "0000255", "homepage": "https://bgee.org/bgee/bgee?page=documentation#sectionHomologyRelationships", "keywords": [ "ontology" ], "name": "Homologous Organ Groups", "pattern": "^\\d{7}$", "preferred_prefix": "hog", "uri_format": "https://biopragmatics.github.io/providers/hog/$1" }, "hogenom": { "contact": { "email": "perriere@biomserv.univ-lyon1.fr", "name": "Guy Perrière", "orcid": "0000-0002-6850-6265" }, "description": "HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier.", "example": "HBG284870", "homepage": "http://pbil.univ-lyon1.fr/databases/hogenom/", "keywords": [ "classification", "life science", "phylogenetics", "phylogeny", "sequence" ], "mappings": { "biocontext": "HOGENOM", "fairsharing": "FAIRsharing.qe8tz8", "integbio": "nbdc01858", "miriam": "hogenom", "n2t": "hogenom", "prefixcommons": "hogenom", "uniprot": "DB-0044" }, "name": "Database of Complete Genome Homologous Genes Families", "pattern": "^\\w+$", "preferred_prefix": "hogenom", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/hogenom:$1" } ], "publications": [ { "doi": "10.1186/1471-2105-10-s6-s3", "pmc": "PMC2697650", "pubmed": "19534752", "title": "Databases of homologous gene families for comparative genomics", "year": 2009 }, { "doi": "10.1101/gr.10.3.379", "pmc": "PMC311423", "pubmed": "10720578", "title": "HOBACGEN: database system for comparative genomics in bacteria", "year": 2000 }, { "doi": "10.1186/1471-2105-10-S6-S3", "title": "Databases of homologous gene families for comparative genomics." } ], "uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1" }, "hoip": { "contact": { "email": "yuki.yamagata@riken.jp", "github": "yuki-yamagata", "name": "Yuki Yamagata", "orcid": "0000-0002-9673-1283" }, "contributor": { "email": "j.harry.caufield@gmail.com", "github": "caufieldjh", "name": "Harry Caufield", "orcid": "0000-0001-5705-7831" }, "description": "An ontology of processes triggered by homeostatic imbalance, with a focus on COVID-19 infectious processes.", "download_owl": "https://github.com/yuki-yamagata/hoip/raw/master/hoip_0308.owl", "example": "0040379", "github_request_issue": 668, "homepage": "https://knowledge.brc.riken.jp/bioresource/ontology/HOIP", "keywords": [ "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "HOIP", "bioportal": "HOIP" }, "name": "Homeostasis imbalance process ontology", "pattern": "^\\d{7}$", "preferred_prefix": "hoip", "repository": "https://github.com/yuki-yamagata/hoip", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://purl.bioontology.org/ontology/HOIP/HOIP_$1" }, "hom": { "contact": { "email": "bgee@sib.swiss", "github": "fbastian", "name": "Frederic Bastian", "orcid": "0000-0002-9415-5104" }, "description": "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.", "download_owl": "http://purl.obolibrary.org/obo/hom.owl", "example": "0000049", "homepage": "https://github.com/BgeeDB/homology-ontology", "keywords": [ "anatomy", "homologous", "life cycle stage", "life science", "molecular entity", "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "HOM", "biocontext": "HOM", "bioportal": "HOM", "fairsharing": "FAIRsharing.efv7gw", "obofoundry": "hom", "ols": "hom", "ontobee": "HOM" }, "name": "Homology Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "HOM", "publications": [ { "doi": "10.1016/j.tig.2009.12.012", "pubmed": "20116127", "title": "An ontology to clarify homology-related concepts", "year": 2010 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/HOM_$1", "repository": "https://github.com/BgeeDB/homology-ontology", "uri_format": "http://purl.obolibrary.org/obo/HOM_$1", "version": "2015-01-07" }, "homd.seq": { "contact": { "email": "tchen@forsyth.org", "github": "tsute", "name": "Tsute Chen", "orcid": "0000-0001-6689-317X" }, "description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information.", "example": "SEQF1003", "homepage": "http://www.homd.org/index.php", "keywords": [ "genome", "microbial" ], "mappings": { "biocontext": "HOMD.SEQ", "miriam": "homd.seq", "n2t": "homd.seq", "prefixcommons": "homd.seq" }, "name": "HOMD Sequence Metainformation", "pattern": "^SEQF\\d+$", "preferred_prefix": "homd.seq", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/homd.seq:$1" } ], "publications": [ { "doi": "10.1093/database/baq013", "pmc": "PMC2911848", "pubmed": "20624719", "title": "The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information", "year": 2010 } ], "uri_format": "http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1" }, "homd.taxon": { "contact": { "email": "tchen@forsyth.org", "github": "tsute", "name": "Tsute Chen", "orcid": "0000-0001-6689-317X" }, "description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information.", "example": "811", "homepage": "http://www.homd.org/index.php", "keywords": [ "microbial", "taxonomy" ], "mappings": { "biocontext": "HOMD.TAXON", "miriam": "homd.taxon", "n2t": "homd.taxon", "ncbi": "HOMD", "prefixcommons": "homd.taxon" }, "name": "Human Oral Microbiome Database", "pattern": "^\\d+$", "preferred_prefix": "homd.taxon", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/homd.taxon:$1" } ], "publications": [ { "doi": "10.1093/database/baq013", "pmc": "PMC2911848", "pubmed": "20624719", "title": "The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information", "year": 2010 } ], "uri_format": "http://www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=$1" }, "homologene": { "contact": { "email": "sayers@ncbi.nlm.nih.gov", "name": "Eric W. Sayers", "orcid": "0000-0001-8394-3802" }, "description": "HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.", "example": "1000", "homepage": "https://www.ncbi.nlm.nih.gov/homologene/", "keywords": [ "gene", "genome", "life science" ], "mappings": { "biocontext": "HOMOLOGENE", "fairsharing": "FAIRsharing.mzc066", "integbio": "nbdc00101", "miriam": "homologene", "n2t": "homologene", "prefixcommons": "homologene", "togoid": "Homologene", "wikidata": "P593" }, "name": "HomoloGene", "pattern": "^\\d+$", "preferred_prefix": "homologene", "providers": [ { "code": "CURATOR_REVIEW", "description": "Bio2RDF", "homepage": "http://homologene.bio2rdf.org/fct", "name": "Bio2RDF", "uri_format": "http://homologene.bio2rdf.org/describe/?url=http://bio2rdf.org/homologene:$1" }, { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/homologene:$1" } ], "publications": [ { "doi": "10.1093/nar/gkq1172", "pmc": "PMC3013733", "pubmed": "21097890", "title": "Database resources of the National Center for Biotechnology Information", "year": 2010 } ], "uri_format": "https://www.ncbi.nlm.nih.gov/homologene/$1" }, "horizon_discovery": { "description": "Cell line collections (Providers)", "example": "HD+118-001", "homepage": "https://horizondiscovery.com/", "mappings": { "cellosaurus": "Horizon_Discovery" }, "name": "Horizon Discovery cell line collection", "preferred_prefix": "horizon_discovery", "uri_format": "https://horizondiscovery.com/en/search?searchterm=$1" }, "hoso": { "contact": { "email": "paul.fabry@usherbrooke.ca", "github": "pfabry", "name": "Paul Fabry", "orcid": "0000-0002-3336-2476" }, "contributor": { "email": "paul.fabry@usherbrooke.ca", "github": "pfabry", "name": "Paul Fabry", "orcid": "0000-0002-3336-2476" }, "description": "HOSO is an ontology of informational entities and processes related to healthcare organizations and services.", "example": "0000001", "github_request_issue": 813, "homepage": "https://openlhs.github.io/HOSO/", "license": "CC-BY-4.0", "name": "Healthcare Organizations and Services Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "hoso", "repository": "https://github.com/OpenLHS/HOSO", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } }, "hovergen": { "contact": { "email": "duret@biomserv.univ-lyon1.fr", "name": "Laurent Duret", "orcid": "0000-0003-2836-3463" }, "description": "HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.", "example": "HBG004341", "homepage": "https://pbil.univ-lyon1.fr/databases/hovergen.php", "keywords": [ "dna", "gene", "life science", "protein" ], "mappings": { "biocontext": "HOVERGEN", "fairsharing": "FAIRsharing.dg1f0e", "integbio": "nbdc00284", "miriam": "hovergen", "n2t": "hovergen", "prefixcommons": "hovergen" }, "name": "Homologous Vertebrate Genes Database", "pattern": "^HBG\\d+$", "preferred_prefix": "hovergen", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/hovergen:$1" } ], "publications": [ { "doi": "10.1093/bioinformatics/bti325", "pubmed": "15713731", "title": "Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases", "year": 2005 } ], "uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN" }, "hp": { "appears_in": [ "chiro", "maxo", "scdo" ], "banana": "HP", "contact": { "email": "dr.sebastian.koehler@gmail.com", "github": "drseb", "name": "Sebastian Koehler", "orcid": "0000-0002-5316-1399" }, "description": "The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM.", "download_json": "http://purl.obolibrary.org/obo/hp.json", "download_obo": "http://purl.obolibrary.org/obo/hp.obo", "download_owl": "http://purl.obolibrary.org/obo/hp.owl", "example": "0011140", "homepage": "http://www.human-phenotype-ontology.org/", "keywords": [ "biomedical science", "disease", "genetics", "industry", "obo", "ontology", "phenomics", "phenotype", "preclinical studies" ], "license": "hpo", "logo": "https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/logo/HPO-logo-black_small.png", "mappings": { "aberowl": "HP_O", "bartoc": "1937", "biocontext": "HPO", "bioportal": "HP_O", "fairsharing": "FAIRsharing.kbtt7f", "hl7": "2.16.840.1.113883.6.339", "integbio": "nbdc02559", "lov": "hpo", "miriam": "hp", "n2t": "hp", "obofoundry": "hp", "ols": "hp", "ontobee": "HP", "wikidata": "P3841" }, "mastodon": "hpo@masto.ai", "name": "Human Phenotype Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "HP", "publications": [ { "doi": "10.1093/nar/gky1105", "pmc": "PMC6324074", "pubmed": "30476213", "title": "Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources", "year": 2019 }, { "doi": "10.1093/nar/gkw1039", "pmc": "PMC5210535", "pubmed": "27899602", "title": "The Human Phenotype Ontology in 2017", "year": 2016 }, { "doi": "10.1016/j.ajhg.2015.05.020", "pmc": "PMC4572507", "pubmed": "26119816", "title": "The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease", "year": 2015 }, { "doi": "10.1093/nar/gkt1026", "pmc": "PMC3965098", "pubmed": "24217912", "title": "The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data", "year": 2013 }, { "doi": "10.1111/j.1399-0004.2010.01436.x", "pubmed": "20412080", "title": "The human phenotype ontology", "year": 2010 }, { "doi": "10.1016/j.ajhg.2008.09.017", "pmc": "PMC2668030", "pubmed": "18950739", "title": "The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease", "year": 2008 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/HP_$1", "repository": "https://github.com/obophenotype/human-phenotype-ontology", "synonyms": [ "hpo" ], "twitter": "hp_ontology", "uri_format": "http://purl.obolibrary.org/obo/HP_$1", "version": "2024-08-13" }, "hpa": { "contact": { "email": "mathias.uhlen@scilifelab.se", "name": "Mathias Uhlen", "orcid": "0000-0002-4858-8056" }, "description": "The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers.", "example": "ENSG00000026508", "homepage": "http://www.proteinatlas.org/", "keywords": [ "biomedical science", "protein", "proteomics", "structure", "systems biology", "transcriptomics" ], "mappings": { "biocontext": "HPA", "fairsharing": "FAIRsharing.j0t0pe", "go": "HPA", "miriam": "hpa", "n2t": "hpa", "prefixcommons": "hpa", "re3data": "r3d100010931", "uniprot": "DB-0046" }, "name": "Human Protein Atlas tissue profile information", "pattern": "^ENSG\\d{11}$", "preferred_prefix": "hpa", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/hpa:$1" } ], "publications": [ { "doi": "10.1126/science.aan2507", "pubmed": "28818916", "title": "A pathology atlas of the human cancer transcriptome", "year": 2017 }, { "doi": "10.1126/science.aal3321", "pubmed": "28495876", "title": "A subcellular map of the human proteome", "year": 2017 }, { "doi": "10.15252/msb.20155865", "pmc": "PMC4848759", "pubmed": "27044256", "title": "Transcriptomics resources of human tissues and organs", "year": 2016 }, { "doi": "10.1126/science.1260419", "pubmed": "25613900", "title": "Proteomics. Tissue-based map of the human proteome", "year": 2015 }, { "doi": "10.1038/nbt1210-1248", "pubmed": "21139605", "title": "Towards a knowledge-based Human Protein Atlas", "year": 2010 }, { "doi": "10.1002/path.2440", "pubmed": "18853439", "title": "The Human Protein Atlas--a tool for pathology", "year": 2008 }, { "doi": "10.1074/mcp.r800013-mcp200", "pubmed": "18669619", "title": "A genecentric Human Protein Atlas for expression profiles based on antibodies", "year": 2008 }, { "doi": "10.1074/mcp.m500279-mcp200", "pubmed": "16127175", "title": "A human protein atlas for normal and cancer tissues based on antibody proteomics", "year": 2005 }, { "doi": "eaal3321", "title": "A subcellular map of the human proteome." }, { "doi": "10.1074/mcp.R800013-MCP200", "title": "A genecentric Human Protein Atlas for expression profiles based on antibodies." }, { "doi": "10.1074/mcp.M500279-MCP200", "title": "A human protein atlas for normal and cancer tissues based on antibody proteomics." } ], "twitter": "ProteinAtlas", "uri_format": "http://www.proteinatlas.org/$1" }, "hpath": { "comment": "This ontology used to be available in OLS3, but is no longer available in OLS4.\n\nThe URI format string in this resource takes the form of an OBO PURL, but it is not itself registered with the OBO Foundry, and terms therefore redirect into http://ontologies.berkeleybop.org. This happens because the data is curated natively in the OBO Flat File Format from which CURIEs are automatically assumed to expand to OBO PURLs", "contact": { "email": "carlo.ravagli@novartis.com", "github": "carloravagli", "name": "Carlo Ravagli", "orcid": "0000-0001-8372-8387" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology of histopathological morphologies used by pathologists to classify/categorise animal lesions observed histologically during regulatory toxicology studies. The ontology was developed using real data from over 6000 regulatory toxicology studies donated by 13 companies spanning nine species.\n\nThe original structure of the histopathology ontology was designed ab initio when the [INHAND](http://www.goreni.org/) manuscripts were not available. However, the ontology has been repetitively reviewed and updated to align with the subsequently published INHAND manuscripts. During this process cross references to INHAND lesion identifiers were added to the ontology. [from GitHub]", "download_obo": "https://raw.githubusercontent.com/Novartis/hpath/master/src/hpath.obo", "example": "2000191", "homepage": "https://github.com/Novartis/hpath", "keywords": [ "ontology" ], "name": "Histopathology Ontology", "pattern": "^\\d+$", "preferred_prefix": "hpath", "references": [ "https://github.com/biopragmatics/bioregistry/issues/927" ], "repository": "https://github.com/Novartis/hpath", "synonyms": [ "MC" ], "uri_format": "http://purl.obolibrary.org/obo/MC_$1" }, "hpm.peptide": { "description": "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra.", "example": "9606117", "homepage": "http://www.humanproteomemap.org/index.php", "mappings": { "biocontext": "HPM.PEPTIDE", "miriam": "hpm.peptide", "n2t": "hpm.peptide" }, "name": "Human Proteome Map Peptide", "pattern": "^\\d+$", "preferred_prefix": "hpm.peptide", "uri_format": "http://www.humanproteomemap.org/spectrum.php?pep_id=$1" }, "hpm.protein": { "description": "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins.", "example": "1968", "homepage": "http://www.humanproteomemap.org/index.php", "mappings": { "biocontext": "HPM.PROTEIN", "miriam": "hpm.protein", "n2t": "hpm.protein", "ncbi": "HPM" }, "name": "Human Proteome Map", "pattern": "^\\d+$", "preferred_prefix": "hpm.protein", "uri_format": "http://www.humanproteomemap.org/protein.php?hpm_id=$1" }, "hprd": { "contact": { "email": "pandey@jhmi.edu", "name": "Akhilesh Pandey", "orcid": "0000-0001-9943-6127" }, "description": "The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.", "example": "00001", "homepage": "http://www.hprd.org/", "keywords": [ "protein", "structure" ], "mappings": { "biocontext": "HPRD", "fairsharing": "FAIRsharing.y2qws7", "integbio": "nbdc00103", "miriam": "hprd", "n2t": "hprd", "pathguide": "14", "prefixcommons": "hprd", "re3data": "r3d100010978" }, "name": "Human Protein Reference Database", "pattern": "^\\d+$", "preferred_prefix": "hprd", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", "homepage": "https://bio2rdf.org", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/hprd:$1" } ], "publications": [ { "doi": "10.1093/nar/gkn892", "pmc": "PMC2686490", "pubmed": "18988627", "title": "Human Protein Reference Database--2009 update", "year": 2008 } ], "uri_format": "http://www.hprd.org/protein/$1" }, "hpscreg": { "contact": { "email": "stefanie.seltmann@ibmt.fraunhofer.de", "name": "Stefanie Seltmann", "orcid": "0000-0002-8411-3226" }, "description": "hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines).", "example": "BCRTi001-A", "homepage": "https://hpscreg.eu/", "keywords": [ "biomedical science", "life science" ], "mappings": { "cellosaurus": "hPSCreg", "fairsharing": "FAIRsharing.7C0aVE", "miriam": "hpscreg", "n2t": "hpscreg", "re3data": "r3d100012863" }, "name": "Human Pluripotent Stem Cell Registry", "pattern": "^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$", "preferred_prefix": "hpscreg", "publications": [ { "doi": "10.1016/j.scr.2020.101887", "pubmed": "32707486", "title": "Access to stem cell data and registration of pluripotent cell lines: The Human Pluripotent Stem Cell Registry (hPSCreg)", "year": 2020 }, { "doi": "10.1016/j.stemcr.2020.06.014", "pmc": "PMC7419703", "pubmed": "32679065", "title": "A Manually Curated Database on Clinical Studies Involving Cell Products Derived from Human Pluripotent Stem Cells", "year": 2020 }, { "doi": "10.1016/j.scr.2019.101539", "pubmed": "31450190", "title": "A pathway for attesting ethical provenance of cell lines: Lessons from the European human pluripotent stem cell registry (hPSC", "year": 2019 }, { "doi": "10.1016/j.stemcr.2017.12.002", "pmc": "PMC5768986", "pubmed": "29320760", "title": "A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells", "year": 2018 }, { "doi": "10.1093/nar/gkv963", "pmc": "PMC4702942", "pubmed": "26400179", "title": "hPSCreg--the human pluripotent stem cell registry", "year": 2015 }, { "doi": "S2213-6711(20)30235-6", "title": "A Manually Curated Database on Clinical Studies Involving Cell Products Derived from Human Pluripotent Stem Cells." }, { "doi": "S2213-6711(17)30531-3", "title": "A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells." }, { "doi": "S1873-5061(20)30188-4", "title": "Access to stem cell data and registration of pluripotent cell lines: The Human Pluripotent Stem Cell Registry (hPSCreg)." }, { "doi": "S1873-5061(19)30169-2", "title": "A pathway for attesting ethical provenance of cell lines: Lessons from the European human pluripotent stem cell registry (hPSC(reg))." } ], "uri_format": "https://hpscreg.eu/cell-line/$1" }, "hsapdv": { "appears_in": [ "scdo" ], "contact": { "email": "frederic.bastian@unil.ch", "github": "fbastian", "name": "Frédéric Bastian", "orcid": "0000-0002-9415-5104" }, "description": "Life cycle stages for Human", "download_obo": "http://purl.obolibrary.org/obo/hsapdv.obo", "download_owl": "http://purl.obolibrary.org/obo/hsapdv.owl", "example": "0000194", "homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv", "keywords": [ "anatomy", "developmental biology", "life cycle stage", "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "HSAPDV", "biocontext": "HSAPDV", "biolink": "HsapDv", "bioportal": "HSAPDV", "fairsharing": "FAIRsharing.c6vhm3", "obofoundry": "hsapdv", "ols": "hsapdv", "ontobee": "HsapDv" }, "name": "Human Developmental Stages", "pattern": "^\\d{7}$", "preferred_prefix": "HsapDv", "rdf_uri_format": "http://purl.obolibrary.org/obo/HsapDv_$1", "repository": "https://github.com/obophenotype/developmental-stage-ontologies", "synonyms": [ "HsapDv" ], "uri_format": "http://purl.obolibrary.org/obo/HsapDv_$1" }, "hsdb": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas.", "example": "5621", "homepage": "https://pubchem.ncbi.nlm.nih.gov/source/hsdb", "mappings": { "integbio": "nbdc00930", "wikidata": "P2062" }, "name": "Hazardous Substances Data Bank", "pattern": "^\\d+$", "preferred_prefix": "hsdb", "uri_format": "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1" }, "hso": { "contact": { "email": "fernanda.dorea@sva.se", "github": "nandadorea", "name": "Fernanda Dorea", "orcid": "0000-0001-8638-8525" }, "depends_on": [ "bfo", "ncbitaxon", "obi", "ro", "uberon" ], "description": "The health Surveillance Ontology (HSO) focuses on \"surveillance system level data\", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance.", "download_owl": "http://purl.obolibrary.org/obo/hso.owl", "example": "0000062", "homepage": "https://w3id.org/hso", "keywords": [ "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "HSO", "bioportal": "HSO", "obofoundry": "hso", "ols": "hso", "ontobee": "HSO" }, "name": "Health Surveillance Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "HSO", "providers": [ { "code": "hso.legacy", "description": "An incorrect encoding of OBO purls", "homepage": "http://purl.obolibrary.org/obo/hso", "name": "HSO Hash", "uri_format": "http://purl.obolibrary.org/obo/hso.owl#HSO_$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/HSO_$1", "repository": "https://github.com/SVA-SE/HSO", "uri_format": "http://purl.obolibrary.org/obo/HSO_$1", "version": "2021-12-13" }, "hssp": { "contact": { "email": "chris@sanderlab.org", "name": "Chris Sander", "orcid": "0000-0001-6059-6270" }, "description": "HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein.", "example": "102l", "homepage": "http://swift.cmbi.kun.nl/swift/hssp/", "keywords": [ "clustering", "protein", "sequence" ], "mappings": {