{ "_3dmet": { "comment": "Website has been down since 2023/2024", "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/$1" }, "aeo": { "appears_in": [ "ehdaa2" ], "contact": { "email": "J.Bard@ed.ac.uk", "name": "Jonathan Bard" }, "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "deprecated": true, "description": "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology", "download_obo": "http://purl.obolibrary.org/obo/aeo.obo", "download_owl": "http://purl.obolibrary.org/obo/aeo.owl", "example": "0001017", "homepage": "https://github.com/obophenotype/human-developmental-anatomy-ontology/", "keywords": [ "anatomy", "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "AEO", "bartoc": "181", "biocontext": "AEO", "bioportal": "AEO", "fairsharing": "FAIRsharing.93ee19", "obofoundry": "aeo", "ols": "aeo", "ontobee": "AEO" }, "name": "Anatomical Entity Ontology", "pattern": "^\\d{7}$", "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_$1" }, "affy.probeset": { "description": "An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration.", "example": "243002_at", "homepage": "http://bio2rdf.org", "mappings": { "biocontext": "AFFY.PROBESET", "miriam": "affy.probeset", "n2t": "affy.probeset", "togoid": "AffyProbeset" }, "name": "Affymetrix Probeset", "pattern": "^\\d{4,}((_[asx])?_at)$", "preferred_prefix": "affy.probeset", "uri_format": "http://bio2rdf.org/affymetrix:$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/2024/12/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": "2024/12" }, "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=$1" }, "aftol.taxonomy": { "contact": { "email": "davem@umn.edu", "name": "David J. McLaughlin" }, "contributor_extras": [ { "email": "laylamichan@ciencias.unam.mx", "github": "lmichan", "name": "Layla Michán Aguirre", "orcid": "0000-0002-5798-662X" } ], "deprecated": true, "description": "The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species.", "example": "959", "homepage": "https://aftol.umn.edu", "mappings": { "biocontext": "AFTOL.TAXONOMY", "miriam": "aftol.taxonomy", "n2t": "aftol.taxonomy" }, "name": "Assembling the Fungal Tree of Life - Taxonomy", "pattern": "^\\d+$", "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": { "appears_in": [ "chebi", "pmc" ], "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": "IND608186955", "homepage": "http://agricola.nal.usda.gov/", "mappings": { "biocontext": "AGRICOLA", "go": "AGRICOLA_ID", "miriam": "agricola", "n2t": "agricola" }, "name": "Agricultural Online Access", "pattern": "^IND\\d+$", "preferred_prefix": "agricola", "providers": [ { "code": "usda", "description": "This endpoint no longer works but is maintained for legacy purposes", "homepage": "https://agricola.nal.usda.gov", "name": "USDA Legacy Endpoint", "uri_format": "https://agricola.nal.usda.gov/vwebv/holdingsInfo?bibId=$1" } ], "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://europepmc.org/article/AGR/$1" }, "agrkb": { "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "contributor": { "github": "sierra-moxon", "name": "Sierra Moxon", "orcid": "0000-0002-8719-7760" }, "description": "The [Alliance of Genome Resources](https://www.alliancegenome.org/about-us) creates identifiers for several biological entity types including genes, other sequence features, constructs, morpholinos, TALENs, CRISPRs, variants, alleles, genotypes, strains, environments and experiments, phenotype annotations, expression annotations, disease annotations, interactions, and variant annotations.\n\nThe Alliance of Genome Resources was founded by the following Model Organism databases and the Gene Ontology Consortium and distributes high-quality, curated knowledge about several model organisms in a single, unified location:\n\n- [ZFIN](https://zfin.org) - Zebrafish Information Network\n- [WormBase](https://wormbase.org)\n- [MGI](https://www.mgi.org) - Mouse Genome Informatics\n- [RGD](https://rgd.mcw.edu) - Rat Genome Database\n- [SGD](https://www.yeastgenome.org) - Saccharomyces Genome Database\n- [FlyBase](https://flybase.org)\n- [Xenbase](https://www.xenbase.org)", "example": "100000000000001", "github_request_issue": 359, "homepage": "https://www.alliancegenome.org", "keywords": [ "model organism database" ], "mappings": { "biolink": "AGRKB", "uniprot": "DB-0266" }, "name": "Alliance of Genome Resources Knowledge Base", "pattern": "^[1-9][0-9]{14}$", "preferred_prefix": "agrkb", "publications": [ { "doi": "10.1093/nar/gkz813", "pubmed": "31552413" } ], "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=$1" }, "aio": { "contact": { "email": "MJoachimiak@lbl.gov", "github": "realmarcin", "name": "Marcin Pawel Joachimiak", "orcid": "0000-0001-8175-045X" }, "contributor": { "email": "lindsey.anderson@pnnl.gov", "github": "lnanderson", "name": "Lindsey N. 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Girón", "orcid": "0000-0002-0851-6883" }, "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "depends_on": [ "bfo", "bspo", "caro", "pato", "ro", "uberon" ], "description": "The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research.", "download_json": "http://purl.obolibrary.org/obo/aism.json", "download_obo": "http://purl.obolibrary.org/obo/aism.obo", "download_owl": "http://purl.obolibrary.org/obo/aism.owl", "example": "0000027", "homepage": "https://github.com/insect-morphology/aism", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "AISM", "bioportal": "AISM", "obofoundry": "aism", "ols": "aism", "ontobee": "AISM" }, "name": "Ontology for the Anatomy of the Insect SkeletoMuscular system", "pattern": "^\\d{7}$", "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_$1", "version": "2025-03-18" }, "alfred": { "comment": "This resource doesn't exist on the web anymore", "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "sumirp", "name": "Sumir H Pandit", "orcid": "0000-0002-1216-4761" } ], "deprecated": true, "description": "ALFRED has been designed to make allele frequency data on anthropologically defined human population samples readily available to the scientific community and to link these polymorphism data to the molecular genetics-human genome databases.", "example": "LO362836C", "homepage": "http://alfred.med.yale.edu", "keywords": [ "classification", "genome" ], "mappings": { "prefixcommons": "alfred" }, "name": "The ALlele FREquency Database", "preferred_prefix": "alfred", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources.", "example": "1948", "homepage": "http://www.allergome.org/", "keywords": [ "allergen", "biomedical science", "health science", "life science", "medicine" ], "mappings": { "biocontext": "ALLERGOME", "fairsharing": "FAIRsharing.w6cxgb", "integbio": "nbdc01708", "miriam": "allergome", "n2t": "allergome", "prefixcommons": "allergome", "uniprot": "DB-0160" }, "name": "Allergome", "pattern": "^\\d+$", "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=$1" }, "amoebadb": { "contact": { "email": "oharb@upenn.edu", "github": "ramobrah", "name": "Omar S. 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While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", "example": "EDI_244000", "homepage": "http://amoebadb.org/amoeba/", "keywords": [ "functional genomics", "genomics", "model organism" ], "mappings": { "biocontext": "AMOEBADB", "fairsharing": "FAIRsharing.swbypy", "integbio": "nbdc01207", "miriam": "amoebadb", "n2t": "amoebadb", "prefixcommons": "amoebadb", "re3data": "r3d100012457" }, "name": "AmoebaDB", "pattern": "^EDI_\\d+$", "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_$1" }, "antifam": { "contact": { "email": "agb@ebi.ac.uk", "name": "Alex Bateman", "orcid": "0000-0002-6982-4660" }, "contributor": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "AntiFam is a database of spurious protein families that have been removed from Pfam due to incorrect hidden Markov model prediction.", "example": "ANF00001", "github_request_issue": 1523, "homepage": "https://www.ebi.ac.uk/interpro/entry/antifam", "mappings": { "uniprot": "DB-0275" }, "name": "AntiFam", "pattern": "^ANF\\d{5}$", "preferred_prefix": "antifam", "publications": [ { "doi": "10.1093/database/bas003", "pmc": "PMC3308159", "pubmed": "22434837", "title": "AntiFam: a tool to help identify spurious ORFs in protein annotation", "year": 2012 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.ebi.ac.uk/interpro/entry/antifam/$1" }, "antweb": { "description": "AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures.", "example": "casent0106247", "homepage": "http://www.antweb.org/", "keywords": [ "anatomy", "classification", "life science" ], "mappings": { "biocontext": "ANTWEB", "fairsharing": "FAIRsharing.yk38tw", "integbio": "nbdc01710", "miriam": "antweb", "n2t": "antweb", "ncbi": "AntWeb", "prefixcommons": "antweb", "wikidata": "P5299" }, "name": "AntWeb", "pattern": "^casent\\d+(\\-D\\d+)?$", "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). 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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/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). 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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/$1" }, "aspgd.locus": { "deprecated": true, "description": "The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references gene information.", "example": "ASPL0000349247", "homepage": "http://www.aspgd.org/", "mappings": { "biocontext": "ASPGD.LOCUS", "biolink": "AspGD", "go": "AspGD_LOCUS", "miriam": "aspgd.locus", "n2t": "aspgd.locus" }, "name": "Aspergillus Genome Database", "pattern": "^[A-Za-z_0-9]+$", "preferred_prefix": "aspgd.locus", "uri_format": "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$1" }, "aspgd.protein": { "deprecated": true, "description": "The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references protein information.", "example": "ASPL0000349247", "homepage": "http://www.aspgd.org/", "mappings": { "biocontext": "ASPGD.PROTEIN", "miriam": "aspgd.protein", "n2t": "aspgd.protein" }, "name": "AspGD Protein", "pattern": "^[A-Za-z_0-9]+$", "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=$1" }, "asteraceaegd.genome": { "contact": { "email": "greatchen@cdutcm.edu.cn", "name": "Wei Chen", "orcid": "0000-0002-6857-7696" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "The AGD is an integrated database resource dedicated to collecting the genomic-related data of the Asteraceae family. This collection refers to the genomic data of Asteraceae species.", "example": "0002", "github_request_issue": 1214, "homepage": "https://cbcb.cdutcm.edu.cn/AGD/", "name": "Asteraceae Genome Database", "pattern": "^\\d{4}$", "preferred_prefix": "asteraceaegd.genome", "publications": [ { "doi": "10.3389/fpls.2024.1445365", "pmc": "PMC11366637", "pubmed": "39224843", "title": "Asteraceae genome database: a comprehensive platform for Asteraceae genomics", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://cbcb.cdutcm.edu.cn/AGD/genome/details/?id=$1" }, "asteraceaegd.plant": { "contact": { "email": "greatchen@cdutcm.edu.cn", "name": "Wei Chen", "orcid": "0000-0002-6857-7696" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "The AGD is an integrated database resource dedicated to collecting the genomic-related data of the Asteraceae family. This collections refers to the broader phenotypic and genetic resources of Asteraceae plants.", "example": "0016", "github_request_issue": 1214, "homepage": "https://cbcb.cdutcm.edu.cn/AGD/", "name": "Asteraceae Genome Database", "pattern": "^\\d{4}$", "preferred_prefix": "asteraceaegd.plant", "publications": [ { "doi": "10.3389/fpls.2024.1445365", "pmc": "PMC11366637", "pubmed": "39224843", "title": "Asteraceae genome database: a comprehensive platform for Asteraceae genomics", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://cbcb.cdutcm.edu.cn/AGD/plant/details/?id=$1" }, "atc": { "contact": { "email": "whocc@fhi.no", "name": "WHO Collaborating Centre for Drug Statistics Methodology" }, "description": "The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels.", "example": "A10BA02", "homepage": "http://www.whocc.no/atc_ddd_index/", "keywords": [ "anatomical therapeutic chemical code", "approved drug", "biomedical science", "chemical", "chemical biology", "drug", "ontology", "pharmacological family classification", "pharmacology" ], "mappings": { "aberowl": "ATC", "bartoc": "449", "biocontext": "ATC", "bioportal": "ATC", "edam": "3103", "fairsharing": "FAIRsharing.1a27h8", "hl7": "2.16.840.1.113883.6.73", "miriam": "atc", "n2t": "atc", "prefixcommons": "atc", "togoid": "Atc", "wikidata": "P267" }, "name": "Anatomical Therapeutic Chemical Classification System", "pattern": "^[A-Z](\\d+([A-Z]{1,2}(\\d+)?)?)?$", "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=$1" }, "atcc": { "description": "The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences.", "example": "11303", "example_extras": [ "ccl-1", "ccl-1.4" ], "homepage": "https://www.lgcstandards-atcc.org", "keywords": [ "epidemiology", "life science", "virology" ], "mappings": { "biocontext": "ATCC", "cellosaurus": "ATCC", "fairsharing": "FAIRsharing.j0ezpm", "hl7": "2.16.840.1.113883.6.77", "miriam": "atcc", "n2t": "atcc", "ncbi": "ATCC" }, "name": "American Type Culture Collection", "pattern": "^([a-zA-Z]+-)?\\d+(\\.\\d)?$", "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=$1" }, "atfdb.family": { "description": "The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found.", "example": "CUT", "homepage": "https://guolab.wchscu.cn/AnimalTFDB4", "mappings": { "biocontext": "ATFDB.FAMILY", "miriam": "atfdb.family", "n2t": "atfdb.family" }, "name": "Animal TFDB Family", "pattern": "^\\w+$", "preferred_prefix": "atfdb.family", "uri_format": "https://guolab.wchscu.cn/AnimalTFDB4//?#/family_summary/TF/$1" }, "ato": { "contact": { "email": "david.c.blackburn@gmail.com", "name": "David Blackburn", "orcid": "0000-0002-1810-9886" }, "deprecated": true, "description": "Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource", "download_obo": "http://aber-owl.net/media/ontologies/ATO/2/ato.obo", "example": "0000000", "homepage": "http://www.amphibanat.org", "keywords": [ "obo", "ontology", "taxonomic classification", "taxonomy" ], "mappings": { "aberowl": "ATO", "biocontext": "ATO", "bioportal": "ATO", "fairsharing": "FAIRsharing.ayjdsm", "obofoundry": "ato" }, "name": "Amphibian taxonomy", "pattern": "^\\d{7}$", "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/$1" }, "bacdive": { "contact": { "email": "lorenz.reimer@dsmz.de", "name": "Lorenz Reimer", "orcid": "0000-0002-7805-0660" }, "description": "BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity.", "example": "131392", "homepage": "https://bacdive.dsmz.de/", "keywords": [ "biodiversity", "life science", "microbiology" ], "mappings": { "fairsharing": "FAIRsharing.aSszvY", "miriam": "bacdive", "n2t": "bacdive", "re3data": "r3d100013060", "wikidata": "P2946" }, "name": "BacDive", "pattern": "^[0-9]+$", "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_$1", "version": "2.8.13" }, "bartoc": { "contact": { "email": "voss@gbv.de", "github": "nichtich", "name": "Jakob Voß", "orcid": "0000-0002-7613-4123" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "email": "voss@gbv.de", "github": "nichtich", "name": "Jakob Voß", "orcid": "0000-0002-7613-4123" } ], "description": "The Basic Register of Thesauri, Ontologies & Classifications (BARTOC) is a database of Knowledge Organization Systems and KOS related registries.\nThe main goal of BARTOC is to list as many Knowledge Organization Systems as possible at one place in order to achieve greater visibility, highlight their features, make them searchable and comparable, and foster knowledge sharing. BARTOC includes any kind of KOS from any subject area, in any language, any publication format, and any form of accessibility. BARTOC’s search interface is available in 20 European languages and provides two search options: Basic Search by keywords, and Advanced Search by taxonomy terms. A circle of editors has gathered around BARTOC from all across Europe and BARTOC has been approved by the International Society for Knowledge Organization (ISKO).", "example": "241", "homepage": "https://bartoc.org", "keywords": [ "knowledge and information systems", "ontology and terminology" ], "license": "PDDL 1.0", "mappings": { "bartoc": "2054", "fairsharing": "FAIRsharing.f1777e", "wikidata": "P2689" }, "name": "Basic Register of Thesauri, Ontologies & Classifications", "owners": [ { "name": "Verbundzentrale des GBV", "partnered": false, "ror": "048vdhs48" } ], "pattern": "^[1-9][0-9]*$", "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://purl.obolibrary.org/obo/BCGO_$1", "version": "2015-07-08" }, "bcio": { "contact": { "email": "srodriguez142857@gmail.com", "name": "Sergio José Rodríguez Méndez", "orcid": "0000-0001-7203-8399" }, "description": "The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation.", "download_owl": "http://humanbehaviourchange.org/ontology/bcio.owl", "example": "040000", "homepage": "https://www.humanbehaviourchange.org/", "keywords": [ "ontology" ], "mappings": { "aberowl": "BCI-O", "bioportal": "BCI-O", "ols": "bcio" }, "name": "The Behaviour Change Intervention Ontology", "pattern": "^\\d{6}$", "preferred_prefix": "bcio", "uri_format": "https://w3id.org/BCI-ontology#$1", "version": "2024-09-17" }, "bco": { "appears_in": [ "fovt" ], "contact": { "email": "rlwalls2008@gmail.com", "github": "ramonawalls", "name": "Ramona Walls", "orcid": "0000-0001-8815-0078" }, "description": "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.", "download_owl": "http://purl.obolibrary.org/obo/bco.owl", "example": "0000081", "homepage": "https://github.com/BiodiversityOntologies/bco", "keywords": [ "biodiversity", "biological sample", "biological sample annotation", "ecology", "environmental material", "metagenomics", "obo", "ontology", "taxonomic classification", "taxonomy" ], "license": "CC0-1.0", "mappings": { "aberowl": "BCO", "agroportal": "BCO", "biocontext": "BCO", "bioportal": "BCO", "ecoportal": "BCO", "fairsharing": "FAIRsharing.8ktkqy", "obofoundry": "bco", "ols": "bco", "ontobee": "BCO" }, "name": "Biological Collections Ontology", "pattern": "^\\d{7}$", "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": "https://bcrj.org.br/pesquisa/?search=$1" }, "bdgp.est": { "description": "The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI).", "example": "EY223054.1", "has_canonical": "dbest", "homepage": "https://www.ncbi.nlm.nih.gov/dbEST/index.html", "keywords": [ "genome" ], "mappings": { "biocontext": "BDGP.EST", "miriam": "bdgp.est", "n2t": "bdgp.est", "ncbi": "BDGP_EST", "prefixcommons": "flybase.est" }, "name": "Berkeley Drosophila Genome Project EST database", "pattern": "^\\w+(\\.)?(\\d+)?$", "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/$1" }, "beetlebase": { "contact": { "email": "sjbrown@ksu.edu", "name": "Susan J. Brown", "orcid": "0000-0002-7984-0445" }, "deprecated": true, "description": "BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications.", "example": "TC010103", "homepage": "http://beetlebase.org/", "keywords": [ "computational biology", "genome", "life science" ], "mappings": { "biocontext": "BEETLEBASE", "fairsharing": "FAIRsharing.h5f091", "integbio": "nbdc01820", "miriam": "beetlebase", "n2t": "beetlebase", "ncbi": "BEETLEBASE", "prefixcommons": "beetlebase", "re3data": "r3d100010921" }, "name": "Tribolium Genome Database -- Insertion", "pattern": "^TC\\d+$", "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/$1.aspx" }, "bel": { "comment": "INDRA uses bel as a catch-all for scomp/sfam", "contact": { "email": "support@bel.bio", "name": "William Hayes", "orcid": "0000-0003-0728-781X" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Biological Expression Language is a domain-specific language for describing causal, correlative, and associative relationships between a variety of biological agents.", "example": "9-1-1 Complex", "homepage": "https://biological-expression-language.github.io/", "keywords": [ "biology" ], "mappings": { "fairsharing": "FAIRsharing.dp0jvd" }, "name": "Biological Expression Language", "preferred_prefix": "bel" }, "bfo": { "appears_in": [ "ado", "agro", "aism", "cdno", "colao", "duo", "ecocore", "epio", "foodon", "fovt", "hso", "lepao", "mco", "ons", "pcl", "pco", "psdo", "rbo", "uberon", "xpo", "zp" ], "contact": { "email": "phismith@buffalo.edu", "github": "phismith", "name": "Barry Smith", "orcid": "0000-0003-1384-116X" }, "description": "The upper level ontology upon which OBO Foundry ontologies are built.", "download_obo": "http://purl.obolibrary.org/obo/bfo.obo", "download_owl": "http://purl.obolibrary.org/obo/bfo.owl", "example": "0000001", "homepage": "http://ifomis.org/bfo/", "keywords": [ "data identity and mapping", "data retrieval", "interoperability", "obo", "ontology", "subject agnostic" ], "license": "CC-BY-4.0", "logo": "https://avatars2.githubusercontent.com/u/12972134?v=3&s=200", "mappings": { "aberowl": "BFO", "agroportal": "BFO", "biocontext": "BFO", "bioportal": "BFO", "fairsharing": "FAIRsharing.wcpd6f", "go": "BFO", "obofoundry": "bfo", "ols": "bfo", "ontobee": "BFO" }, "name": "Basic Formal Ontology", "pattern": "^\\d{7}$", "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/$1" }, "bgee.organ": { "contributor_extras": [ { "github": "smoretti", "name": "Sébastien Moretti", "orcid": "0000-0003-3947-488X" } ], "deprecated": true, "description": "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. 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It published genome-scale metabolic networks into a single database with a set of standardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolites.", "example": "12dgr161", "example_extras": [ "12dgr161[c]" ], "homepage": "http://bigg.ucsd.edu/universal/metabolites", "license": "http://bigg.ucsd.edu/license#license", "mappings": { "biocontext": "BIGG.METABOLITE", "miriam": "bigg.metabolite", "n2t": "bigg.metabolite" }, "name": "BiGG Metabolite", "pattern": "^[a-z_A-Z0-9]+(\\[[c|cm|cx|e|f|g|h|i|im|l|m|mm|n|p|r|s|u|um|v|w|x|y]\\])?$", "preferred_prefix": "bigg.metabolite", "uri_format": "http://bigg.ucsd.edu/models/universal/metabolites/$1" }, "bigg.model": { "description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models.", "example": "iECABU_c1320", "homepage": "http://bigg.ucsd.edu/models", "license": "http://bigg.ucsd.edu/license#license", "mappings": { "biocontext": "BIGG.MODEL", "miriam": "bigg.model", "n2t": "bigg.model" }, "name": "BiGG Model", "pattern": "^[a-z_A-Z0-9]+$", "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. 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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/gkae1075", "pubmed": "39574417", "title": "BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data", "year": 2024 }, { "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. 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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/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=$1" }, "biodeep": { "banana": "BioDeep", "banana_peel": "_", "description": "The BioDeep database is a comprehensive database of metabolite information in living organisms: by aggregating metabolite information from multiple public databases and large-scale natural language text mining work, we have built a large scale knowledge network for biological knowledge interpretation. By using the BioDeep database, it is possible to query such large scale metabolic knowledge network.", "example": "00000000001", "homepage": "https://en.panomix.com/", "mappings": { "miriam": "biodeep" }, "name": "BioDeep Database", "pattern": "^\\d{11}$", "preferred_prefix": "biodeep", "uri_format": "https://query.biodeep.cn/metabolite/$1" }, "biodolphin": { "contact": { "email": "andrew.mcshan@chemistry.gatech.edu", "name": "Andrew C. McShan", "orcid": "0000-0002-3212-9867" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "Identifiers for lipid-protein interactions, including details about protein functions, protein families, lipid classifications, lipid-protein binding affinities, membrane association type, and atomic structures.", "example": "BD1a05-A-A-IPM1", "github_request_issue": 1327, "homepage": "https://biodolphin.chemistry.gatech.edu", "name": "BioDolphin", "pattern": "^BD\\d[a-zA-Z0-9]+-[A-Za-z]-[A-Za-z]-[A-Za-z0-9]+$", "preferred_prefix": "biodolphin", "publications": [ { "doi": "10.1038/s42004-024-01384-z", "pmc": "PMC11618342", "pubmed": "39633021", "title": "BioDolphin as a comprehensive database of lipid-protein binding interactions", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. 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stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). 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": "https://www.ddbj.nig.ac.jp/biosample", "name": "BioSample at DNA Data Bank of Japan", "uri_format": "https://ddbj.nig.ac.jp/search/entry/biosample/$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/$1" }, "biosystems": { "contact": { "email": "lewis.geer@nih.gov", "name": "Aron Marchler-Bauer", "orcid": "0000-0003-1516-0712" }, "contributor_extras": [ { "email": "egon.willighagen@gmail.com", "github": "egonw", "name": "Egon Willighagen", "orcid": "0000-0001-7542-0286" } ], "deprecated": true, "description": "The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources.", "example": "001", "homepage": "https://www.ncbi.nlm.nih.gov/Structure/biosystems/docs/biosystems_about.html", "keywords": [ "biology", "molecules", "pathways", "systems biology" ], "mappings": { "biocontext": "BIOSYSTEMS", "fairsharing": "FAIRsharing.w2eeqr", "integbio": "nbdc00379", "miriam": "biosystems", "n2t": "biosystems", "prefixcommons": "biosystems", "re3data": "r3d100011033" }, "name": "BioSystems", "pattern": "^\\d+$", "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" }, "biotop": { "contact": { "email": "stefan.schulz@medunigraz.at", "github": "steschu63", "name": "Stefan Schulz", "orcid": "0000-0001-7222-3287" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Upper-Level ontology for Biology and Medicine. Compatible with BFO, DOLCE, and the UMLS Semantic Network", "download_owl": "https://raw.githubusercontent.com/BioTopOntology/biotop/master/biotop.owl", "example": "attachedTo", "github_request_issue": 1312, "homepage": "http://purl.org/biotop", "keywords": [ "biology", "ontology" ], "license": "CC-BY-3.0", "mappings": { "lov": "biotop" }, "name": "BioTop", "preferred_prefix": "biotop", "publications": [ { "doi": "10.1093/bioinformatics/btp194", "pmc": "PMC2687948", "pubmed": "19478019", "title": "Alignment of the UMLS semantic network with BioTop: methodology and assessment", "year": 2009 }, { "doi": "10.1093/bioinformatics/btn158", "pmc": "PMC2718636", "pubmed": "18586729", "title": "The ontology of biological taxa", "year": 2008 } ], "repository": "https://github.com/BioTopOntology/biotop/", "uri_format": "http://purl.org/biotop/biotop.owl#$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:$1" }, "blastrule": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "BlastRules (identifiers starting with the “NBR” prefix) are a type of evidence for functional classification of proteins based on BLAST (Basic Local Alignment Search Tool). A BlastRule consists of one or more 'model' proteins with known biological function, and BLAST identity and coverage cutoffs. Any protein aligning to a model protein above the cutoffs is considered a BlastRule hit. [from homepage]", "example": "NBR016799", "github_request_issue": 1522, "homepage": "https://www.ncbi.nlm.nih.gov/genome/annotation_prok/evidence/", "name": "BlastRule", "pattern": "^NBR\\d+$", "preferred_prefix": "blastrule", "references": [ "https://ftp.ncbi.nlm.nih.gov/pub/blastrules/" ], "uri_format": "https://www.ncbi.nlm.nih.gov/genome/annotation_prok/evidence/$1" }, "bmrb": { "contact": { "email": "markley@nmrfam.wisc.edu", "name": "John L. Markley", "orcid": "0000-0003-1799-6134" }, "description": "BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy.", "example": "15000", "homepage": "https://bmrb.io/", "keywords": [ "structural biology" ], "mappings": { "fairsharing": "FAIRsharing.p06nme", "integbio": "nbdc00380", "miriam": "bmrb", "re3data": "r3d100010191", "uniprot": "DB-0256" }, "name": "Biological Magnetic Resonance Data Bank", "pattern": "^(bmr|bmse|bmst)?[0-9]{1,6}$", "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": "https://bmrb.io/data_library/summary/index.php?bmrbId=$1" }, "bmrb.restraint": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The NMR Restraints Grid contains the original NMR data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. In addition to the original restraints, most of the distance, dihedral angle and RDC restraint data (>85%) were parsed, and those in over 500 entries were converted and filtered. The converted and filtered data sets constitute the DOCR and FRED databases respectively.", "example": "28789", "homepage": "https://restraintsgrid.bmrb.io/NRG/MRGridServlet", "keywords": [ "chemistry", "nmr", "spectrometry" ], "name": "NMR Restraints Grid", "pattern": "^\\d+$", "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. 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/bold:$1" } ], "publications": [ { "doi": "10.1111/j.1471-8286.2007.01678.x", "pmc": "PMC1890991", "pubmed": "18784790", "title": "bold: The Barcode of Life Data System (http://www.barcodinglife.org)", "year": 2007 } ], "uri_format": "http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1" }, "bootstrep": { "contact": { "email": "vlee@ebi.ac.uk", "name": "Vivian Lee" }, "deprecated": true, "homepage": "http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html", "keywords": [ "obo", "ontology" ], "mappings": { "biocontext": "BOOTSTREP", "obofoundry": "bootstrep" }, "name": "Gene Regulation Ontology", "preferred_prefix": "BOOTSTREP", "rdf_uri_format": "http://purl.obolibrary.org/obo/BOOTSTREP_$1", "uri_format": "http://purl.obolibrary.org/obo/BOOTSTREP_$1" }, "bpdb": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Database of biopesticides maintained by the University of Hertfordshire ", "example": "2404", "homepage": "https://sitem.herts.ac.uk/aeru/bpdb/index.htm", "keywords": [ "biology", "biopesticides", "pesticides" ], "name": "Bio-Pesticides DataBase", "pattern": "^\\d+$", "preferred_prefix": "bpdb", "uri_format": "https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm" }, "brenda": { "contact": { "email": "D.Schomburg@tu-braunschweig.de", "name": "Dietmar Schomburg", "orcid": "0000-0002-3354-822X" }, "description": "BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data.", "example": "1.1.1.1", "homepage": "https://www.brenda-enzymes.org/", "keywords": [ "enzyme", "life science" ], "mappings": { "biocontext": "BRENDA", "fairsharing": "FAIRsharing.etp533", "go": "BRENDA", "miriam": "brenda", "n2t": "brenda", "pathguide": "51", "prefixcommons": "brenda", "re3data": "r3d100010616" }, "name": "BRENDA Enzyme", "pattern": "^((\\d+\\.-\\.-\\.-)|(\\d+\\.\\d+\\.-\\.-)|(\\d+\\.\\d+\\.\\d+\\.-)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$", "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. 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Gyori", "orcid": "0000-0001-9439-5346" }, "description": "The Common Coordinate Framework (CCF) Ontology is an application ontology built to support the development of the Human Reference Atlas (HRA). It unifies vocabulary for HRA construction and usage—making it possible to ingest external data sources; supporting uniform tissue sample registration that includes the spatial positioning and semantic annotations within 3D reference organs; and supporting user-formulated cross-domain queries over tissue donor properties, anatomical structures, cell types, biomarkers, and 3D space. The CCF Ontology consists of three major ontologies. The Biological Structure Ontology records anatomical structures, cell types, and biomarkers (ASCT+B) and the relationships between them. The ASCT+B tables are authored by human experts using templated Google Sheets. The biomarkers, cell types, and anatomical structures are mapped to existing ontologies (Uberon/FMA, CL, HGNC) whenever possible. 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://aber-owl.net/media/ontologies/CCF/16/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" }, "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_$1", "version": "2024-11-12" }, "cdpd": { "description": "The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN).", "example": "63250", "homepage": "https://www.canada.ca/en/health-canada/services/drugs-health-products/drug-products/drug-product-database.html", "mappings": { "biocontext": "CDPD", "miriam": "cdpd", "n2t": "cdpd" }, "name": "Canadian Drug Product Database", "pattern": "^\\d+$", "preferred_prefix": "cdpd", "uri_format": "https://health-products.canada.ca/dpd-bdpp/info?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/$1" }, "cellosaurus": { "banana": "CVCL", "banana_peel": "_", "contact": { "email": "Amos.Bairoch@sib.swiss", "github": "AmosBairoch", "name": "Amos Bairoch", "orcid": "0000-0003-2826-6444" }, "description": "The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.", "download_obo": "https://ftp.expasy.org/databases/cellosaurus/cellosaurus.obo", "example": "0440", "homepage": "https://cellosaurus.org", "keywords": [ "cell lines", "controlled vocabularies", "life science", "ontologies", "ontology", "thesaurus" ], "license": "CC-BY-4.0", "logo": "https://www.cellosaurus.org/images/cellosaurus/cellosaurus.png", "mappings": { "biocontext": "CELLOSAURUS", "cellosaurus": "Cellosaurus", "fairsharing": "FAIRsharing.hkk309", "integbio": "nbdc02180", "miriam": "cellosaurus", "n2t": "cellosaurus", "re3data": "r3d100013293", "rrid": "CVCL", "togoid": "Cellosaurus", "wikidata": "P3289" }, "mastodon": "cellosaurus@fediscience.org", "name": "Cellosaurus", "pattern": "^[A-Z0-9]{4}$", "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" }, { "code": "obo", "description": "Incorrectly encoded OBO PURL - do not use!", "homepage": "http://purl.obolibrary.org", "name": "OBO PURL", "uri_format": "http://purl.obolibrary.org/obo/Cellosaurus#CVCL_$1" }, { "code": "obo.incorrect", "description": "OBO PURL generated by incorrectly configured OBO file - this is not registered in OBO Foundry.", "homepage": "http://purl.obolibrary.org", "name": "OBO (Incorrect)", "uri_format": "http://purl.obolibrary.org/obo/Cellosaurus#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/$1" }, "cemo": { "contact": { "email": "n.queralt_rosinach@lumc.nl", "github": "NuriaQueralt", "name": "Núria Queralt Rosinach", "orcid": "0000-0003-0169-8159" }, "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. 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This prefix provides identifiers for compounds that compete with probes for binding to target proteins.", "example": "LDCM0160", "github_request_issue": 1424, "homepage": "https://chemprosquare.idrblab.net", "name": "ChemPro Competitor", "pattern": "^LDCM\\d+$", "preferred_prefix": "chempro.competitor", "publications": [ { "doi": "10.1093/nar/gkae943", "pmc": "PMC11701659", "pubmed": "39436046", "title": "Chem(Pro)2: the atlas of chemoproteomic probes labelling human proteins", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. 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This prefix provides identifiers for chemoproteomic probes used to label human proteins in living cells.", "example": "LDPC0032", "github_request_issue": 1424, "homepage": "https://chemprosquare.idrblab.net", "name": "ChemPro Probe", "pattern": "^LDPC\\d+$", "preferred_prefix": "chempro.probe", "publications": [ { "doi": "10.1093/nar/gkae943", "pmc": "PMC11701659", "pubmed": "39436046", "title": "Chem(Pro)2: the atlas of chemoproteomic probes labelling human proteins", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. 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This prefix provides identifiers for human proteins that interact with chemoproteomic probes.", "example": "LDTP03903", "github_request_issue": 1424, "homepage": "https://chemprosquare.idrblab.net", "name": "ChemPro Target", "pattern": "^LDTP\\d+$", "preferred_prefix": "chempro.target", "publications": [ { "doi": "10.1093/nar/gkae943", "pmc": "PMC11701659", "pubmed": "39436046", "title": "Chem(Pro)2: the atlas of chemoproteomic probes labelling human proteins", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://chemprosquare.idrblab.net/data/target/details/$1" }, "chemrof": { "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "CHEMROF is an ontological framework for Chemical Entities Mixtures Reactions Ontological Framework. This OWL ontology is an automated Translation of the source LinkML schema, https://w3id.org/chemrof", "download_owl": "http://aber-owl.net/media/ontologies/CHEMROF/4/chemrof.owl", "example": "FullySpecifiedAtom", "homepage": "https://chemkg.github.io/chemrof/", "keywords": [ "ontology" ], "mappings": { "aberowl": "CHEMROF", "bioportal": "CHEMROF" }, "name": "Chemical Entity Materials and Reactions Ontological Framework", "preferred_prefix": "ChEMROF", "uri_format": "https://chemkg.github.io/chemrof/$1" }, "chemspider": { "contact": { "email": "pencehe@oneonta.edu", "name": "Harry E. Pence", "orcid": "0000-0002-0412-9018" }, "description": "ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources.", "example": "56586", "homepage": "http://www.chemspider.com/", "keywords": [ "chemistry", "life science", "molecules", "structure" ], "mappings": { "biocontext": "CHEMSPIDER", "cheminf": "000405", "edam": "1173", "fairsharing": "FAIRsharing.96f3gm", "integbio": "nbdc01863", "miriam": "chemspider", "n2t": "chemspider", "prefixcommons": "chemspider", "re3data": "r3d100010205", "wikidata": "P661" }, "name": "ChemSpider", "pattern": "^\\d+$", "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" }, "chr": { "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "contributor": { "email": "jhc@lbl.gov", "github": "caufieldjh", "name": "Harry Caufield", "orcid": "0000-0001-5705-7831" }, "description": "The Chromosome Ontology is an automatically derived ontology of chromosomes and chromosome parts.", "download_json": "https://raw.githubusercontent.com/monarch-initiative/monochrom/refs/heads/master/chr.json", "download_obo": "https://raw.githubusercontent.com/monarch-initiative/monochrom/refs/heads/master/chr.obo", "download_owl": "https://raw.githubusercontent.com/monarch-initiative/monochrom/refs/heads/master/chr.owl", "example": "10090-chr10qC", "github_request_issue": 1265, "homepage": "https://github.com/monarch-initiative/monochrom", "keywords": [ "ontology" ], "license": "BSD-3", "mappings": { "aberowl": "CHR", "biocontext": "CHR", "bioportal": "CHR" }, "name": "Chromosome Ontology", "preferred_prefix": "chr", "repository": "https://github.com/monarch-initiative/monochrom", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } }, "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/$1" }, "cl": { "appears_in": [ "clo", "ecao", "ehdaa2", "go", "mco", "pcl", "uberon", "xpo" ], "banana": "CL", "contact": { "email": "addiehl@buffalo.edu", "github": "addiehl", "name": "Alexander Diehl", "orcid": "0000-0001-9990-8331" }, "contributor_extras": [ { "github": "anitacaron", "name": "Anita Caron", "orcid": "0000-0002-6523-4866" } ], "depends_on": [ "go", "ncbitaxon", "omo", "pato", "pr", "ro", "uberon" ], "description": "The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi.", "download_json": "http://purl.obolibrary.org/obo/cl.json", "download_obo": "https://github.com/obophenotype/cell-ontology/raw/master/cl.obo", "download_owl": "http://purl.obolibrary.org/obo/cl.owl", "example": "0000062", "homepage": "https://obophenotype.github.io/cell-ontology/", "keywords": [ "anatomy", "annotation", "cell", "cell biology", "life science", "morphology", "obo", "ontology" ], "license": "CC-BY-4.0", "logo": "https://obofoundry.org/images/CL-logo.jpg", "mappings": { "aberowl": "CL", "agroportal": "CL", "biocontext": "CL", "bioportal": "CL", "cellosaurus": "CL", "fairsharing": "FAIRsharing.j9y503", "go": "CL", "miriam": "cl", "n2t": "cl", "obofoundry": "cl", "ols": "cl", "ontobee": "CL", "prefixcommons": "cl", "wikidata": "P7963" }, "name": "Cell Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "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_$1", "version": "2025-02-13" }, "clao": { "contact": { "email": "lagonzalezmo@unal.edu.co", "github": "luis-gonzalez-m", "name": "Luis González-Montaña", "orcid": "0000-0002-9136-9932" }, "depends_on": [ "ro" ], "description": "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).", "download_obo": "http://purl.obolibrary.org/obo/clao.obo", "download_owl": "http://purl.obolibrary.org/obo/clao.owl", "example": "0000088", "homepage": "https://github.com/luis-gonzalez-m/Collembola", "keywords": [ "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "CLAO", "bioportal": "CLAO", "obofoundry": "clao", "ols": "clao", "ontobee": "CLAO" }, "name": "Collembola Anatomy Ontology", "pattern": "^\\d{7}$", "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", "chemont" ], "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/$1" }, "cldb": { "description": "The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories.", "example": "cl3603", "homepage": "http://bioinformatics.hsanmartino.it/hypercldb/indexes.html", "mappings": { "biocontext": "CLDB", "cellosaurus": "CLDB", "miriam": "cldb", "n2t": "cldb" }, "name": "Cell Line Database", "pattern": "^(cl|tum)\\d+$", "preferred_prefix": "cldb", "synonyms": [ "hypercldb" ], "uri_format": "http://bioinformatics.hsanmartino.it/hypercldb/$1.html" }, "clingen.affiliation": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "ClinGen is a National Institutes of Health (NIH)-funded resource that defines the clinical relevance of genes and variants for use in precision medicine and research. This prefix provides identifiers for a panel of experts performing variant pathogenecity evaluation.", "example": "40135", "github_request_issue": 1314, "homepage": "https://clinicalgenome.org/affiliation", "name": "ClinGen Clinical Genome Expert Panel", "preferred_prefix": "clingen.affiliation", "uri_format": "https://clinicalgenome.org/affiliation/$1/" }, "clingen.allele": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "github": "sierra-moxon", "name": "Sierra Moxon", "orcid": "0000-0002-8719-7760" } ], "description": "ClinGen is a National Institutes of Health (NIH)-funded resource that defines the clinical relevance of genes and variants for use in precision medicine and research. This prefix provides and maintains identifiers for alleles.", "example": "CA981206459", "homepage": "https://reg.clinicalgenome.org", "keywords": [ "alleles", "genetics", "mutations" ], "mappings": { "biolink": "CAID" }, "name": "ClinGen Allele Registry", "pattern": "^CA\\d+$", "preferred_prefix": "clingen.allele", "references": [ "https://github.com/biopragmatics/bioregistry/issues/647" ], "synonyms": [ "CAID", "clingene" ], "uri_format": "https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1" }, "clingen.curation": { "banana": "CCID", "banana_peel": ":", "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "ClinGen is a National Institutes of Health (NIH)-funded resource that defines the clinical relevance of genes and variants for use in precision medicine and research. This prefix provides identifiers for curations representing evidence aggregation and expert panel assertions based on standardized evaluation procedures", "example": "004126", "github_request_issue": 1414, "homepage": "https://search.clinicalgenome.org/kb/gene-validity", "name": "ClinGen Curation", "pattern": "^\\d{6}$", "preferred_prefix": "clingen.curation", "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://search.clinicalgenome.org/CCID:$1" }, "clinicaltrials": { "description": "ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries", "example": "NCT00222573", "homepage": "https://clinicaltrials.gov/", "keywords": [ "disease", "drug", "human" ], "license": "https://clinicaltrials.gov/about-site/terms-conditions#availability", "mappings": { "biocontext": "CLINICALTRIALS", "miriam": "clinicaltrials", "n2t": "clinicaltrials", "prefixcommons": "clinicaltrials", "wikidata": "P3098" }, "name": "ClinicalTrials.gov", "pattern": "^NCT\\d{8}$", "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/$1" }, "clo": { "appears_in": [ "mco" ], "contact": { "email": "zhengj2007@gmail.com", "github": "zhengj2007", "name": "Jie Zheng", "orcid": "0000-0002-2999-0103" }, "depends_on": [ "cl", "doid", "ncbitaxon", "uberon" ], "description": "The Cell Line Ontology is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns.", "download_owl": "http://purl.obolibrary.org/obo/clo.owl", "example": "0000091", "homepage": "https://github.com/CLO-Ontology/CLO", "keywords": [ "cell", "cell biology", "cell line", "life science", "morphology", "obo", "ontology" ], "license": "CC-BY-3.0", "logo": "https://avatars.githubusercontent.com/u/12410534", "mappings": { "aberowl": "CLO", "biocontext": "CLO", "bioportal": "CLO", "cellosaurus": "CLO", "fairsharing": "FAIRsharing.4dvtcz", "miriam": "clo", "obofoundry": "clo", "ols": "clo", "ontobee": "CLO", "prefixcommons": "clo", "wikidata": "P2158" }, "name": "Cell Line Ontology", "pattern": "^\\d{7}$", "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_$1", "version": "2020-05-29" }, "cmecs": { "contact": { "email": "kate.rose@noaa.gov", "name": "Kate Rose" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard.", "download_owl": "http://aber-owl.net/media/ontologies/CMECS/2/cmecs.owl", "example": "595", "homepage": "https://cmecscatalog.org/cmecs", "keywords": [ "ecology", "marine ecology", "ontology" ], "mappings": { "aberowl": "CMECS", "bioportal": "CMECS", "ecoportal": "CMECS" }, "name": "Costal and Marine Ecological Classification Standard", "pattern": "^\\d+$", "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_$1", "version": "2.241" }, "cmpo": { "contact": { "email": "jupp@ebi.ac.uk", "name": "Simon Jupp", "orcid": "0000-0002-0643-3144" }, "description": "CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations.", "download_owl": "http://www.ebi.ac.uk/cmpo/releases/2017-12-19/cmpo.owl", "example": "0000435", "homepage": "http://www.ebi.ac.uk/cmpo", "keywords": [ "bioimaging", "cell", "cell biology", "cellular component", "imaging", "microscopy", "ontology", "phenomics", "phenotype" ], "mappings": { "aberowl": "CMPO", "bioportal": "CMPO", "fairsharing": "FAIRsharing.knp11s", "ols": "cmpo" }, "name": "Cellular Microscopy Phenotype Ontology", "pattern": "^\\d{7}$", "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_$1", "version": "2017-12-19" }, "cncb.gwh": { "contact": { "email": "baoym@big.ac.cn", "name": "Yiming Bao", "orcid": "0000-0002-9922-9723" }, "contributor": { "email": "palayoor.n@northeastern.edu", "github": "nalikapalayoor", "name": "Nalika Palayoor", "orcid": "0009-0008-8406-631X" }, "description": "The China National Center for Bioinformation's (CNCB) Genome Warehouse (GWH) is a public repository holding genetic information for a wide range of species including humans, plants, animals, and microorganisms. Identifiers in this resource correspond to genomes of various species. The goal of the resource is to make genomic data accessible to researchers in areas like precision medicine and biotechnology.", "example": "167047", "github_request_issue": 1452, "homepage": "https://ngdc.cncb.ac.cn/gwh/browse/genome", "name": "CNCB Genome Warehouse", "pattern": "^\\d{6}$", "preferred_prefix": "cncb.gwh", "publications": [ { "doi": "10.1093/gpbjnl/qzaf010", "pubmed": "39977364", "title": "The Updated Genome Warehouse: Enhancing Data Value, Security, and Usability to Address Data Expansion", "year": 2025 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://ngdc.cncb.ac.cn/gwh/Genome/$1/show" }, "cnrs": { "comment": "Motivated to add because of appearance in ROR", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "identifier for an academic research group issued by the CNRS", "example": "UMR7315", "example_extras": [ "UPS76" ], "homepage": "https://annuaire.cnrs.fr", "mappings": { "wikidata": "P4550" }, "name": "French National Center for Scientific Research - Research Group Identifier", "pattern": "^(UMR|UMS|UMI|UPR|URA|USR|GDR|EA|FR|SNC|ERL|FRC|FRE|IFR|MOY|UPS)\\d+$", "preferred_prefix": "cnrs", "uri_format": "https://web-ast.dsi.cnrs.fr/l3c/owa/structure.infos_admin?&p_lab=$1&p_origine_appel=u" }, "co_320": { "contact": { "email": "j.detras@cgiar.org", "name": "Jeffrey A. Detras", "orcid": "0000-0002-6680-578X" }, "description": "Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping Network variables", "example": "0000618", "homepage": "https://cropontology.org/ontology/CO_320/Rice", "keywords": [ "agriculture", "botany", "food", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_320", "cropoct": "CO_320", "fairsharing": "FAIRsharing.2jkxp5", "ols": "co_320" }, "name": "Rice ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_320", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_320:$1", "version": "2019-10-09" }, "co_321": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Rosemary Shrestha", "orcid": "0000-0002-9399-8003" }, "description": "July 2018", "example": "0000449", "homepage": "https://cropontology.org/ontology/CO_321/Wheat", "keywords": [ "agriculture", "food", "life science", "phenotype" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_321", "cropoct": "CO_321", "fairsharing": "FAIRsharing.czzmpg", "ols": "co_321" }, "name": "Wheat ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_321", "publications": [ { "doi": "10.1093/aobpla/plq008", "pmc": "PMC3000699", "pubmed": "22476066", "title": "Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature", "year": 2010 } ], "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_321:$1", "version": "2019-10-09" }, "co_322": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk" }, "description": "Maize Trait Dictionary in template 5 - CIMMYT- September 2016", "example": "0000773", "homepage": "https://cropontology.org/ontology/CO_322/Maize", "keywords": [ "agriculture", "botany", "food", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_322", "cropoct": "CO_322", "fairsharing": "FAIRsharing.eeyne8", "ols": "co_322" }, "name": "Maize ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_322", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_322:$1", "version": "2019-10-09" }, "co_323": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Fawzy Nawar" }, "description": "ICARDA - TDv5 - Sept 2018", "example": "0000252", "homepage": "https://cropontology.org/ontology/CO_323/Barley", "keywords": [ "agriculture", "botany", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_323", "cropoct": "CO_323", "fairsharing": "FAIRsharing.f69084", "ols": "co_323" }, "name": "Barley ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_323", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_323:$1", "version": "2019-11-20" }, "co_324": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk" }, "description": "Sorghum TDv5 - Oct 2019", "example": "0000111", "homepage": "https://cropontology.org/ontology/CO_324/Sorghum", "keywords": [ "agriculture", "botany", "food", "phenotype" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_324", "cropoct": "CO_324", "fairsharing": "FAIRsharing.dxx0c", "ols": "co_324" }, "name": "Sorghum ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_324", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_324:$1", "version": "2019-10-09" }, "co_325": { "contact": { "email": "e.arnaud@cgiar.org", "name": "Elizabeth Arnaud", "orcid": "0000-0002-6020-5919" }, "description": "Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019", "example": "0000519", "homepage": "https://cropontology.org/ontology/CO_325/Banana", "keywords": [ "agriculture", "food", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_325", "cropoct": "CO_325", "fairsharing": "FAIRsharing.gdszhh", "ols": "co_325" }, "name": "Banana ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_325", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_325:$1", "version": "2019-10-09" }, "co_326": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk" }, "description": "Draft version", "example": "0000254", "homepage": "https://cropontology.org/ontology/CO_326/Coconut", "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_326", "cropoct": "CO_326", "ols": "co_326" }, "name": "Coconut ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_326", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_326:$1" }, "co_327": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk" }, "description": "Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016", "example": "0000095", "homepage": "http://www.cropontology.org/ontology/CO_327/Pearl%20millet", "keywords": [ "agriculture", "botany", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_327", "cropoct": "CO_327", "fairsharing": "FAIRsharing.4e3qh9", "ols": "co_327" }, "name": "Pearl millet ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_327", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_327:$1" }, "co_330": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk" }, "description": "CIP - potato ontology - december 2018", "example": "0000106", "homepage": "https://cropontology.org/ontology/CO_330/Potato", "keywords": [ "agriculture", "botany", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_330", "cropoct": "CO_330", "fairsharing": "FAIRsharing.4fa657", "ols": "co_330" }, "name": "Potato ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_330", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_330:$1", "version": "2019-10-09" }, "co_331": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Vilma Hualla Mamani", "orcid": "0000-0003-0595-5271" }, "description": "Sweet Potato Trait Dictionary in template v5 - CIP - November 2019", "example": "0000088", "homepage": "http://www.cropontology.org/ontology/CO_331/Sweet%20Potato", "keywords": [ "agriculture", "botany", "food", "life science" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_331", "cropoct": "CO_331", "fairsharing": "FAIRsharing.4g5qcw", "ols": "co_331" }, "name": "Sweet Potato ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_331", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_331:$1" }, "co_333": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk" }, "description": "This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez) - First submission in November 2017.", "example": "3000045", "homepage": "http://www.cropontology.org/ontology/CO_333/Beet%20Ontology", "keywords": [ "agriculture", "botany", "food", "life science", "phenotype", "plant breeding", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_333", "cropoct": "CO_333", "fairsharing": "FAIRsharing.af5655", "ols": "co_333" }, "name": "Beet Ontology ontology", "pattern": "^\\d+$", "preferred_prefix": "CO_333", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_333:$1" }, "co_334": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk" }, "description": "Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016", "example": "0000070", "homepage": "https://cropontology.org/ontology/CO_334/Cassava", "keywords": [ "agriculture", "botany", "food", "nutritional science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_334", "cropoct": "CO_334", "fairsharing": "FAIRsharing.v06c4q", "ols": "co_334" }, "name": "Cassava ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_334", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_334:$1", "version": "2019-10-09" }, "co_335": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk" }, "description": "CIAT Common bean trait dictionary - version August 2014", "example": "0000189", "homepage": "http://www.cropontology.org/ontology/CO_335/Common%20Bean", "keywords": [ "agriculture", "botany", "food" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_335", "cropoct": "CO_335", "fairsharing": "FAIRsharing.a14123", "ols": "co_335" }, "name": "Common Bean ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_335", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_335:$1" }, "co_336": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Elizabeth Arnaud", "orcid": "0000-0002-6020-5919" }, "description": "Soybean Trait Dictionary in template v5 - IITA - July 2015", "example": "0000339", "homepage": "https://cropontology.org/ontology/CO_336/Soybean", "keywords": [ "agriculture", "food", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_336", "cropoct": "CO_336", "fairsharing": "FAIRsharing.j75srj", "ols": "co_336" }, "name": "Soybean ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_336", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_336:$1" }, "co_337": { "contact": { "email": "tm.shah@cgiar.org", "name": "Trushar Shah", "orcid": "0000-0002-0091-7981" }, "description": "Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015", "example": "0000054", "homepage": "https://cropontology.org/ontology/CO_337/Groundnut", "keywords": [ "agriculture", "botany", "food", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_337", "cropoct": "CO_337", "fairsharing": "FAIRsharing.ge8y23", "ols": "co_337" }, "name": "Groundnut ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_337", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_337:$1", "version": "2019-10-09" }, "co_338": { "contact": { "email": "tm.shah@cgiar.org", "name": "Trushar Shah", "orcid": "0000-0002-0091-7981" }, "description": "Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015", "example": "0000138", "homepage": "https://cropontology.org/ontology/CO_338/Chickpea", "keywords": [ "agriculture", "botany", "food", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_338", "cropoct": "CO_338", "fairsharing": "FAIRsharing.js20q3", "ols": "co_338" }, "name": "Chickpea ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_338", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_338:$1", "version": "2019-10-09" }, "co_339": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk" }, "description": "Lentil Trait Dictionary in template v5 - ICARDA - July 2015", "example": "0000032", "homepage": "https://cropontology.org/ontology/CO_339/Lentil", "keywords": [ "agriculture", "botany", "food", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_339", "cropoct": "CO_339", "fairsharing": "FAIRsharing.ry1ezg", "ols": "co_339" }, "name": "Lentil ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_339", "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_339:$1", "version": "2019-10-09" }, "co_340": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk" }, "description": "Cowpea Trait Dictionary in template v5 - IITA - August 2015", "example": "0000639", "homepage": "https://cropontology.org/ontology/CO_340/Cowpea", "keywords": [ "agriculture", "botany", "food", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_340", "cropoct": "CO_340", "fairsharing": "FAIRsharing.31apg2", "ols": "co_340" }, "name": "Cowpea ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CO_340", "publications": [ { "doi": "10.3389/fphys.2012.00326", "pmc": "PMC3429094", "pubmed": "22934074", "title": "Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice", "year": 2012 } ], "repository": "https://github.com/bioversity/Crop-Ontology", "uri_format": "https://cropontology.org/rdf/CO_340:$1", "version": "2019-10-09" }, "co_341": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Elizabeth Arnaud", "orcid": "0000-0002-6020-5919" }, "description": "Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015", "example": "0000140", "homepage": "https://cropontology.org/ontology/CO_341/Pigeonpea", "keywords": [ "agriculture", "botany", "food", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_341", "cropoct": "CO_341", "fairsharing": "FAIRsharing.ehe3yp", "ols": "co_341" }, "name": "Pigeonpea ontology", "pattern": "^\\d{7}$", "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:$1", "version": "2019-10-09" }, "co_356": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Eric Duchêne" }, "description": "Grape Ontology including OIV and bioversity descriptors. INRA July 2017", "example": "4000027", "homepage": "https://cropontology.org/ontology/CO_356/Vitis", "keywords": [ "agriculture", "botany", "life science", "phenotype", "plant phenotypes and traits" ], "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_356", "cropoct": "CO_356", "fairsharing": "FAIRsharing.c7f4d7", "ols": "co_356" }, "name": "Vitis ontology", "pattern": "^\\d+$", "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:$1" }, "co_365": { "contact": { "email": "helpdesk@cropontology-curationtool.org", "name": "Crop Ontology Helpdesk" }, "description": "developed by ICARDA - Dec 2018", "example": "0000205", "homepage": "https://cropontology.org/ontology/CO_365/Fababean", "license": "CC-BY-4.0", "mappings": { "agroportal": "CO_365", "cropoct": "CO_365", "ols": "co_365" }, "name": "Fababean ontology", "pattern": "^\\d{7}$", "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_$1", "version": "2025-02-20" }, "coconut": { "comment": "@mSorok is the dev of the resource, hope I got it right!", "contributor": { "email": "adriano.rutz@ik.me", "github": "adafede", "name": "Adriano Rutz", "orcid": "0000-0003-0443-9902" }, "description": "COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source project for Natural Products (NPs) storage, search and analysis. It gathers data from over 50 open NP resources and is available free of charge and without any restriction. Each entry corresponds to a \"flat\" NP structure, and is associated, when available, to their known stereochemical forms, literature, organisms that produce them, natural geographical presence and diverse pre-computed molecular properties.", "example": "CNP0171505", "example_extras": [ "CNP0018459.2" ], "github_request_issue": 221, "homepage": "https://coconut.naturalproducts.net", "keywords": [ "chemistry", "natural producs", "organic chemistry" ], "mappings": { "re3data": "r3d100014517" }, "name": "COlleCtion of Open Natural ProdUcTs", "pattern": "^CNP\\d{7}(\\.\\d+)?$", "preferred_prefix": "coconut", "publications": [ { "doi": "10.1093/nar/gkae1063", "pubmed": "39588778", "title": "COCONUT 2.0: a comprehensive overhaul and curation of the collection of open natural products database", "year": 2024 }, { "doi": "10.1186/s13321-020-00478-9", "pmc": "PMC7798278", "pubmed": "33423696", "title": "COCONUT online: Collection of Open Natural Products database", "year": 2021 } ], "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" ] }, "coexistence": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "COEXISTENCE - Thesaurus of intersectionality and decolonial issues: black studies, gender, sexuality and feminist studies", "example": "163", "github_request_issue": 1310, "homepage": "https://mamoura.eci.ufmg.br", "name": "COEXISTENCE", "pattern": "^\\d+$", "preferred_prefix": "coexistence", "uri_format": "https://mamoura.eci.ufmg.br/tematres/vocab/index.php?tema=$1" }, "cog": { "contact": { "email": "cogs@ncbi.nlm.nih.gov", "name": "Michael Y Galperin", "orcid": "0000-0002-2265-5572" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "COGs stands for Clusters of Orthologous Genes. The database was initially created in 1997 (Tatusov et al., PMID: 9381173) followed by several updates, most recently in 2014 (Galperin et al., PMID: 25428365). The current update includes complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. The new features include ~250 updated COG annotations with corresponding references and PDB links, where available; new COGs for proteins involved in CRISPR-Cas immunity, sporulation, and photosynthesis, and the lists of COGs grouped by pathways and functional systems.", "example": "COG0001", "homepage": "https://www.ncbi.nlm.nih.gov/research/cog/", "keywords": [ "genome", "life science", "protein" ], "mappings": { "biolink": "COG", "fairsharing": "FAIRsharing.djsbw2", "go": "COG_Cluster", "miriam": "cog", "prefixcommons": "cog", "togoid": "Cog" }, "name": "Cluster of orthologous genes", "pattern": "^COG\\d+$", "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", "github_request_issue": 1145, "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. 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/cmd:$1" } ], "provides": "hgnc.symbol", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://eds.gene.le.ac.uk/home.php?select_db=$1" }, "colonatlas": { "description": "Cell line databases/resources", "example": "ALA", "homepage": "http://www.coloncanceratlas.org", "mappings": { "cellosaurus": "ColonAtlas" }, "name": "Colorectal Cancer Atlas", "preferred_prefix": "colonatlas", "uri_format": "http://www.coloncanceratlas.org/search_cell_line?cell_line=$1" }, "combine.specifications": { "description": "The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network.", "example": "sed-ml.level-1.version-1", "homepage": "https://co.mbine.org/standards/", "mappings": { "biocontext": "COMBINE.SPECIFICATIONS", "miriam": "combine.specifications", "n2t": "combine.specifications" }, "name": "COMBINE specifications", "pattern": "^\\w+(\\-|\\.|\\w)*$", "preferred_prefix": "combine.specifications", "uri_format": "https://github.com/combine-org/combine-specifications/blob/main/specifications/$1.md" }, "come": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "COMe (Co-Ordination of Metals) at the EBI represents an ontology for bioinorganic and other small molecule centres in complex proteins, using a classification system based on the concept of a bioinorganic motif.", "example": "MOL000160", "homepage": "https://www.flymine.org/come", "keywords": [ "protein" ], "mappings": { "prefixcommons": "come" }, "name": "The Bioinorganic Motif Database", "preferred_prefix": "come", "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/come:$1" } ], "synonyms": [ "COMe" ], "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/$1" }, "complexportal": { "contact": { "email": "sbalu@ebi.ac.uk", "github": "CP-SB", "name": "Sucharitha Balu", "orcid": "0000-0001-7456-0594" }, "description": "A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases.", "example": "CPX-263", "homepage": "https://www.ebi.ac.uk/complexportal", "license": "CC0-1.0", "mappings": { "biocontext": "COMPLEXPORTAL", "biolink": "ComplexPortal", "go": "ComplexPortal", "miriam": "complexportal", "n2t": "complexportal", "re3data": "r3d100013295", "uniprot": "DB-0228", "wikidata": "P7718" }, "name": "Complex Portal", "pattern": "^CPX-[0-9]+$", "preferred_prefix": "complexportal", "publications": [ { "doi": "10.1093/nar/gkae1085", "pmc": "PMC11701666", "pubmed": "39558156", "title": "Complex portal 2025: predicted human complexes and enhanced visualisation tools for the comparison of orthologous and paralogous complexes", "year": 2025 }, { "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/$1" }, "compulyeast": { "deprecated": true, "description": "Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record.", "example": "O08709", "homepage": "http://compluyeast2dpage.dacya.ucm.es/", "keywords": [ "protein" ], "mappings": { "biocontext": "COMPULYEAST", "fairsharing": "FAIRsharing.rbjs3e", "miriam": "compulyeast", "n2t": "compulyeast", "prefixcommons": "compluyeast2dpage" }, "name": "Compluyeast-2D-DB", "pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$", "preferred_prefix": "compulyeast", "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/compluyeast2dpage:$1" } ], "provides": "uniprot", "uri_format": "http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1" }, "conference": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The conference-ontology is a new self-contained ontology for modelleing knowledge about conferences. The conference-ontology adopts best ontology design practices (e.g., Ontology Design Patterns, ontology reuse and interlinking) and guarantees interoperability with SWC ontology and all other pertinent vocabularies. (from homepage)", "download_owl": "https://w3id.org/scholarlydata/ontology/conference-ontology.owl", "example": "isDocumentRelatedTo", "homepage": "http://www.scholarlydata.org/ontology/doc/", "keywords": [ "ontology" ], "license": "CC-BY-3.0", "name": "Conference Ontology", "preferred_prefix": "conference", "uri_format": "https://w3id.org/scholarlydata/ontology/conference-ontology.owl#$1" }, "confident.event": { "contact": { "email": "Philip.Stroemert@tib.eu", "github": "StroemPhi", "name": "Philip Strömert", "orcid": "0000-0002-1595-3213" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating.", "example": "37af84f2-bfd7-4653-b608-eaff44febba6", "github_request_issue": 519, "homepage": "https://www.confident-conference.org/index.php/Category:Event", "keywords": [ "conferences", "meetings", "metascience" ], "name": "ConfIDent Event", "pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$", "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, and discovery tools in the conopeptide database", "year": 2011 }, { "doi": "10.1016/j.toxicon.2010.03.002", "pubmed": "20211197", "title": "Conopeptide characterization and classifications: an analysis using ConoServer", "year": 2010 }, { "doi": "10.1093/bioinformatics/btm596", "pubmed": "18065428", "title": "ConoServer, a database for conopeptide sequences and structures", "year": 2007 }, { "doi": "10.1021/cb700091j", "pubmed": "17649970", "title": "Chemical modification of conotoxins to improve stability and activity", "year": 2007 }, { "doi": "10.1152/physrev.00020.2003", "pubmed": "14715910", "title": "Conus venoms: a rich source of novel ion channel-targeted peptides", "year": 2004 } ], "uri_format": "http://www.conoserver.org/?page=card&table=protein&id=$1" }, "conso": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology describing phenomena encountered in the literature surrounding neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, tauopathies, and related protein aggregation diseases.", "example": "CONSO00010", "homepage": "https://pharmacome.github.io/conso/", "keywords": [ "biology", "life science", "neurodegeneration", "neuroscience", "ontology" ], "name": "Curation of Neurodegeneration Supporting Ontology", "pattern": "^CONSO\\d{5}$", "preferred_prefix": "conso", "uri_format": "https://pharmacome.github.io/conso/$1" }, "cordis.article": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020).", "example": "436605", "homepage": "https://cordis.europa.eu/", "name": "CORDIS Article", "pattern": "^\\d+$", "preferred_prefix": "cordis.article", "uri_format": "https://cordis.europa.eu/article/id/$1" }, "cordis.project": { "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020).", "example": "817732", "github_request_issue": 450, "homepage": "https://cordis.europa.eu/", "name": "CORDIS Project", "pattern": "^\\d+$", "preferred_prefix": "cordis.project", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://cordis.europa.eu/project/id/$1" }, "coriell": { "description": "The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world.", "example": "GM17027", "homepage": "http://ccr.coriell.org/", "mappings": { "biocontext": "Coriell", "cellosaurus": "Coriell", "go": "CORIELL", "miriam": "coriell", "n2t": "coriell" }, "name": "Coriell Institute for Medical Research", "pattern": "^[A-Z]{2}\\d+$", "preferred_prefix": "coriell", "uri_format": "http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1" }, "corrdb": { "contact": { "email": "zhu@iastate.edu", "name": "Zhiliang Hu", "orcid": "0000-0002-6704-7538" }, "description": "A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies.", "example": "37232", "homepage": "https://www.animalgenome.org", "keywords": [ "animal genetics", "genetics", "life science", "systems biology" ], "mappings": { "fairsharing": "FAIRsharing.IziuCK", "miriam": "corrdb", "re3data": "r3d100011496" }, "name": "CorrDB", "pattern": "^[0-9]+$", "preferred_prefix": "corrdb", "uri_format": "https://www.animalgenome.org/CorrDB/q/?id=CorrID:$1" }, "corum": { "contact": { "email": "andreas.ruepp@helmholtz-muenchen.de", "name": "Andreas Ruepp", "orcid": "0000-0003-1705-3515" }, "description": "The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded.", "example": "100", "homepage": "https://mips.helmholtz-muenchen.de/corum", "keywords": [ "bioinformatics", "biology", "protein" ], "mappings": { "biocontext": "CORUM", "fairsharing": "FAIRsharing.ohbpNw", "go": "CORUM", "miriam": "corum", "n2t": "corum", "pathguide": "322", "prefixcommons": "corum", "uniprot": "DB-0224" }, "name": "Comprehensive Resource of Mammalian protein complexes", "pattern": "^\\d+$", "preferred_prefix": "corum", "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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[Description taken from this site](https://www.aapc.com/codes/cpt-codes-range/)]", "example": "00103", "github_request_issue": 357, "homepage": "https://www.aapc.com", "keywords": [ "biomedical science", "health science", "medicine", "ontology" ], "mappings": { "aberowl": "CPT", "biolink": "CPT", "bioportal": "CPT", "fairsharing": "FAIRsharing.wpxab1" }, "name": "Current Procedural Terminology", "pattern": "^\\d+$", "preferred_prefix": "cpt", "publications": [ { "doi": "10.1136/neurintsurg-2014-011156", "pubmed": "24589819", "title": "Current procedural terminology; a primer", "year": 2014 }, { "doi": "10.1016/j.jacr.2007.10.004", "pubmed": "18359442", "title": "CPT: an open system that describes all that you do", "year": 2008 } ], "references": [ "https://github.com/biopragmatics/bioregistry/pull/358", "https://github.com/biolink/biolink-model/pull/993" ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "ama-cpt" ], "uri_format": "https://www.aapc.com/codes/cpt-codes/$1" }, "cran": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Repository of packages for the R programming language", "example": "ggplot2", "homepage": "https://cran.r-project.org/", "mappings": { "wikidata": "P5565" }, "name": "The Comprehensive R Archive Network", "preferred_prefix": "cran", "uri_format": "https://cran.r-project.org/web/packages/$1" }, "crates": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A repository of software packages written in Rust.", "example": "curies", "homepage": "https://crates.io", "name": "Crates.io", "preferred_prefix": "crates", "uri_format": "https://crates.io/crates/$1" }, "creativebiolabs.antibody": { "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "Creative Biolabs Antigen provides identifiers for antibody-based entities such as recombinant, functional, engineered, and format-specific antibodies as well as antibody processing tools, which are essential for applications in diagnostics, therapeutics, and immunology.", "example": "TAB-884", "github_request_issue": 1257, "homepage": "https://www.creativebiolabs.net", "name": "Creative Biolabs", "pattern": "^[a-zA-Z]+-[a-zA-Z0-9()]+(-[a-zA-Z0-9]*)?$", "preferred_prefix": "creativebiolabs.antibody", "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. 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CRISP contains over 8,000 preferred terms that are grouped hierarchically into 11 domains. Note that while still available and included in Unified Medical Language System (UMLS), it has not been updated since 2006.", "example": "2004-2820", "homepage": "https://web.archive.org/web/20091223034048/http://crisp.cit.nih.gov/Thesaurus/index.htm", "keywords": [ "anatomy", "biology", "biomedical science", "chemical biology", "disease", "food", "medicine", "ontology", "social science" ], "mappings": { "aberowl": "CRISP", "bioportal": "CRISP", "fairsharing": "FAIRsharing.1evfpc", "hl7": "2.16.840.1.113883.6.120", "pathguide": "192" }, "name": "Computer Retrieval of Information on Science Projects Thesaurus", "preferred_prefix": "csp", "publications": [ { "pubmed": "8718842", "title": "Taking a bite out of CRISP. Strategies on using and conducting searches in the Computer Retrieval of Information on Scientific Projects database", "year": 1996 } ], "synonyms": [ "CRISP", "CRISP Thesaurus", "CRISP Thesaurus, 2006", "CSP2005" ], "uri_format": "http://purl.bioontology.org/ontology/CSP/$1" }, "cst": { "description": "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways.", "example": "Akt_PKB", "homepage": "http://www.cellsignal.com/pathways/index.html", "keywords": [ "biomedical science", "life science" ], "mappings": { "biocontext": "CST", "fairsharing": "FAIRsharing.n8pxvx", "hl7": "2.16.840.1.113883.6.62", "miriam": "cst", "n2t": "cst", "pathguide": "193" }, "name": "Cell Signaling Technology Pathways", "pattern": "^[A-Za-z0-9_-]+$", "preferred_prefix": "cst", "uri_format": "http://www.cellsignal.com/reference/pathway/$1.html" }, "cst.ab": { "description": "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products.", "example": "3305", "homepage": "http://www.cellsignal.com/catalog/index.html", "keywords": [ "pathway" ], "mappings": { "biocontext": "CST.AB", "miriam": "cst.ab", "n2t": "cst.ab", "prefixcommons": "cst" }, "name": "Cell Signaling Technology Antibody", "pattern": "^\\d+$", "preferred_prefix": "cst.ab", "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/cst:$1" } ], "uri_format": "http://www.cellsignal.com/products/$1.html" }, "cstr": { "description": "CSTR is an identifier for Common Science and Technology Resources, to provide persistent identification services for the positioning, traceability, citation, statistics and evaluation of science and technology resources. ", "example": "31253.11.sciencedb.j00001.00123", "homepage": "https://www.cstr.cn/en/", "mappings": { "miriam": "cstr" }, "name": "Common Science and Technology Resources", "pattern": "^\\w{5}\\.\\d{2}\\..*$", "preferred_prefix": "cstr", "uri_format": "https://cstr.cn/$1" }, "ctcae": { "appears_in": [ "oae" ], "contact": { "email": "ncictcaehelp@mail.nih.gov", "name": "CTCAE Help" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "description": "The Common Terminology Criteria for Adverse Events (CTCAE),[1] formerly called the Common Toxicity Criteria (CTC or NCI-CTC), are a set of criteria for the standardized classification of adverse effects of drugs used in cancer therapy. The CTCAE system is a product of the US National Cancer Institute (NCI).", "download_owl": "http://aber-owl.net/media/ontologies/CTCAE/2/ctcae.owl", "example": "E12768", "homepage": "https://evs.nci.nih.gov/ftp1/CTCAE/About.html", "keywords": [ "ontology" ], "mappings": { "aberowl": "CTCAE", "bioportal": "CTCAE" }, "name": "Common Terminology Criteria for Adverse Events", "pattern": "^E\\d+$", "preferred_prefix": "ctcae", "publications": [ { "pmc": "PMC5977606", "pubmed": "29854250", "title": "Towards precision informatics of pharmacovigilance: OAE-CTCAE mapping and OAE-based representation and analysis of adverse events in patients treated with cancer drugs", "year": 2018 } ], "references": [ "https://github.com/OAE-ontology/OAE/issues/8", "https://en.wikipedia.org/wiki/Common_Terminology_Criteria_for_Adverse_Events" ], "synonyms": [ "CTCAE" ] }, "ctd.chemical": { "description": "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.", "example": "D001151", "homepage": "http://ctdbase.org/", "mappings": { "biocontext": "CTD.CHEMICAL", "biolink": "CTD.CHEMICAL", "miriam": "ctd.chemical", "n2t": "ctd.chemical" }, "name": "CTD Chemical", "part_of": "ctd", "pattern": "^[CD]\\d+$", "preferred_prefix": "ctd.chemical", "provides": "mesh", "uri_format": "http://ctdbase.org/detail.go?type=chem&acc=$1" }, "ctd.disease": { "description": "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.", "example": "D053716", "homepage": "http://ctdbase.org/", "mappings": { "biocontext": "CTD.DISEASE", "biolink": "CTD.DISEASE", "miriam": "ctd.disease", "n2t": "ctd.disease" }, "name": "CTD Disease", "part_of": "ctd", "pattern": "^D\\d+$", "preferred_prefix": "ctd.disease", "provides": "mesh", "uri_format": "http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1" }, "ctd.gene": { "contact": { "email": "apdavis3@ncsu.edu", "name": "Allan Peter Davis", "orcid": "0000-0002-5741-7128" }, "description": "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.", "example": "101", "homepage": "http://ctdbase.org/", "mappings": { "biocontext": "CTD.GENE", "biolink": "CTD.GENE", "miriam": "ctd.gene", "n2t": "ctd.gene", "uniprot": "DB-0140" }, "name": "CTD Gene", "part_of": "ctd", "pattern": "^\\d+$", "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", "publications": [ { "pubmed": "35992013", "title": "CTO: a Community-Based Clinical Trial Ontology and its Applications in PubChemRDF and SCAIView", "year": 2020 } ], "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" }, "daml.pt": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A representation of the periodic table of the elements in OWL, with both elements and a hierarchical classification. This is from the DARPA Agent Markup Language (DAML) project, which has been inactive since the mid 2000's.", "download_owl": "https://www.daml.org/2003/01/periodictable/PeriodicTable.owl", "example": "Be", "example_extras": [ "Metallic", "Non-metallic" ], "github_request_issue": 1419, "homepage": "https://www.daml.org/2003/01/periodictable/", "keywords": [ "ontology" ], "name": "DAML Periodic Table of the Elements", "preferred_prefix": "daml.pt", "uri_format": "http://www.daml.org/2003/01/periodictable/PeriodicTable#$1" }, "dandi": { "contact": { "email": "yoh@dartmouth.edu", "name": "Yaroslav Halchenko", "orcid": "0000-0003-3456-2493" }, "description": "DANDI works with BICCN and other BRAIN Initiative awardees to curate data using community data standards such as NWB and BIDS, and to make data and software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable, and Reusable).\nDANDI references electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data.\nThese data will help scientists uncover and understand cellular level mechanisms of brain function. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders.", "example": "000017", "homepage": "https://dandiarchive.org/", "keywords": [ "neurophysiology" ], "mappings": { "fairsharing": "FAIRsharing.f2c119", "miriam": "dandi", "re3data": "r3d100013638" }, "name": "Distributed Archives for Neurophysiology Data Integration", "pattern": "^\\d{6}(\\/\\d+\\.\\d+\\.\\d+)?$", "preferred_prefix": "dandi", "repository": "https://github.com/dandi/dandiarchive", "twitter": "dandiarchive", "uri_format": "https://dandiarchive.org/dandiset/$1" }, "darc": { "contact": { "email": "daniel.wilson@uni-hamburg.de", "name": "Daniel N. Wilson", "orcid": "0000-0003-3816-3828" }, "deprecated": true, "description": "DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors.", "example": "1250", "homepage": "http://darcsite.genzentrum.lmu.de/darc/index.php", "keywords": [ "life science" ], "mappings": { "biocontext": "DARC", "fairsharing": "FAIRsharing.evfe2s", "miriam": "darc", "n2t": "darc" }, "name": "Database of Aligned Ribosomal Complexes", "pattern": "^\\d+$", "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", "synonyms": [ "dcid" ], "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" }, "dbpedia": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A semi-automatically generated knowledgebase", "example": "Grenada", "github_request_issue": 1315, "homepage": "https://dbpedia.org", "mappings": { "re3data": "r3d100011713" }, "name": "DBPedia", "preferred_prefix": "dbpedia", "uri_format": "http://dbpedia.org/resource/$1" }, "dbpedia.property": { "appears_in": [ "fovt" ], "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Properties in DBPedia.", "example": "insertion", "github_request_issue": 1420, "homepage": "http://dbpedia.org/property", "name": "DBPedia Property", "part_of": "dbpedia", "preferred_prefix": "dbpedia.property", "uri_format": "http://dbpedia.org/property/$1" }, "dbprobe": { "deprecated": true, "description": "The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.", "example": "1000000", "homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe", "keywords": [ "nucleotide" ], "mappings": { "biocontext": "DBPROBE", "edam": "2719", "miriam": "dbprobe", "n2t": "dbprobe", "ncbi": "dbProbe", "prefixcommons": "dbprobe" }, "name": "NCBI Probe database Public registry of nucleic acid reagents", "pattern": "^\\d+$", "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. 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/dbprobe:$1" } ], "uri_format": "https://www.ncbi.nlm.nih.gov/probe/?term=$1" }, "dbsnp": { "contact": { "email": "pruitt@ncbi.nlm.nih.gov", "name": "Kim Dixon Pruitt", "orcid": "0000-0001-7950-1374" }, "description": "The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms.", "example": "rs121909098", "homepage": "https://www.ncbi.nlm.nih.gov/snp/", "keywords": [ "genome", "life science" ], "mappings": { "biocontext": "dbSNP", "cellosaurus": "dbSNP", "edam": "1106", "fairsharing": "FAIRsharing.edxb58", "go": "dbSNP", "hl7": "2.16.840.1.113883.6.284", "integbio": "nbdc00206", "miriam": "dbsnp", "n2t": "dbsnp", "ncbi": "dbSNP", "prefixcommons": "dbsnp", "re3data": "r3d100010652", "togoid": "Dbsnp", "uniprot": "DB-0013", "wikidata": "P6861" }, "name": "dbSNP Reference SNP number", "pattern": "^rs\\d+$", "preferred_prefix": "dbsnp", "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/dbsnp:$1" }, { "code": "sib", "description": "SNP2TFBS", "homepage": "https://epd.expasy.org/", "name": "SNP2TFBS", "uri_format": "https://epd.expasy.org/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", "dcelem", "elements" ], "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#$1" }, "dcterms": { "contact": { "email": "futo@stanford.edu", "name": "Michelle Futornick" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes.", "download_owl": "http://aber-owl.net/media/ontologies/dcterms/1/dcterms.owl", "download_rdf": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/dublin_core_terms.rdf", "example": "title", "homepage": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/", "keywords": [ "metadata", "metadata standardization", "ontology", "resource metadata", "subject agnostic" ], "mappings": { "aberowl": "dcterms", "biocontext": "dcterms", "biolink": "dct", "bioportal": "DCTERMS", "fairsharing": "FAIRsharing.9vtwjs", "lov": "dcterms", "ols": "dcterms", "zazuko": "dcterms" }, "name": "Dublin Core Metadata Initiative Terms", "preferred_prefix": "dcterms", "synonyms": [ 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Highly related to CCLE Cells.", "example": "ACH-000001", "homepage": "https://depmap.org/portal", "license": "CC-BY-4.0", "mappings": { "cellosaurus": "DepMap" }, "name": "DepMap Cell Lines", "pattern": "^ACH-\\d+$", "preferred_prefix": "depmap", "uri_format": "https://depmap.org/portal/cell_line/$1" }, "depod": { "contact": { "email": "depod@embl.de", "name": "General Enquiries", "orcid": "0000-0003-3562-7869" }, "description": "The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources.", "example": "PTPN1", "homepage": "http://www.depod.bioss.uni-freiburg.de", "keywords": [ "life science" ], "mappings": { "biocontext": "DEPOD", "fairsharing": "FAIRsharing.q9j2e3", "miriam": "depod", "n2t": "depod", "pathguide": "584", "re3data": "r3d100011936", "uniprot": "DB-0190" }, "name": "Human Dephosphorylation Database", "pattern": "^[A-Z0-9]+$", "preferred_prefix": "depod", "provides": "hgnc.symbol", "publications": [ { "doi": "10.1093/database/baz133", "pmc": "PMC6911163", "pubmed": "31836896", "title": "The human DEPhOsphorylation Database DEPOD: 2019 update", "year": 2019 }, { "doi": "10.1093/nar/gku1009", "pmc": "PMC4383878", "pubmed": "25332398", "title": "The human DEPhOsphorylation database DEPOD: a 2015 update", "year": 2014 }, { "doi": "10.1126/scisignal.2003203", "pubmed": "23674824", "title": "Elucidating human phosphatase-substrate networks", "year": 2013 } ], "uri_format": "http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1" }, "dermo": { "contact": { "email": "pns12@hermes.cam.ac.uk", "github": "PaulNSchofield", "name": "Paul Schofield", "orcid": "0000-0002-5111-7263" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders", "download_obo": "http://aber-owl.net/media/ontologies/DERMO/10/dermo.obo", "example": "0000000", "homepage": "https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0085-x", "keywords": [ "dermatology", "disease", "ontology" ], "mappings": { "aberowl": "DERMO", "bioportal": "DERMO", "fairsharing": "FAIRsharing.k008w7" }, "name": "Human Dermatological Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "dermo", "publications": [ { "doi": "10.1186/s13326-016-0085-x", "pmc": "PMC4907256", "pubmed": "27296450", "title": "DermO; an ontology for the description of dermatologic disease", "year": 2016 } ], "repository": "https://github.com/dermatology-ontology/dermatology", "uri_format": "http://purl.obolibrary.org/obo/DERMO_$1" }, "dev.ga4ghdos": { "description": "Assists in resolving data across cloud resources.", "example": "23fa7b4b-9d68-429b-aece-658b11124bb3#2017-03-24T18:43:16.886826-05:00", "homepage": "http://github.com/ga4gh/data-object-service-schemas", "mappings": { "biocontext": "DEV.GA4GHDOS", "miriam": "dev.ga4ghdos", "n2t": "dev.ga4ghdos" }, "name": "Development Data Object Service", "pattern": "^[a-zA-Z0-9\\-:#\\.]+$", "preferred_prefix": "dev.ga4ghdos", "uri_format": "https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/$1" }, "devtox": { "contact": { "email": "rupert.kellner@item.fraunhofer.de", "name": "Rupert Kellner", "orcid": "0000-0002-6807-8731" }, "contributor": { "github": "bgyori", "name": "Benjamin M. 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Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org", "example": "00077f1c-c45a-47ba-8e6c-1bf6b6b43fce", "homepage": "https://gen3.theanvil.io", "mappings": { "miriam": "dg.anv0" }, "name": "Anvil", "pattern": "^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$", "preferred_prefix": "dg.anv0", "uri_format": "https://gen3.theanvil.io/ga4gh/drs/v1/objects/$1" }, "dg.f82a1a": { "description": "Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. 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The data commons supports cross-project analyses by harmonizing data from different projects through the collaborative development of a data dictionary, providing an API for data queries and download, and providing a cloud-based analysis workspace with rich tools and resources.", "example": "00000d53-99bc-4d3e-8ed7-6dc358baccb7", "homepage": "https://data.bloodpac.org/.", "mappings": { "miriam": "dg.5b0d" }, "name": "BloodPAC", "pattern": "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$", "preferred_prefix": "dg5b0d", "uri_format": "https://data.bloodpac.org/ga4gh/drs/v1/objects/$1" }, "dggr": { "description": "Organism supplier which collects Drosophila stocks from laboratories all over the world, maintains them, and provides them to researchers upon request. 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"https://dialnet.unirioja.es", "mappings": { "wikidata": "P1608" }, "name": "Dialnet book ID", "preferred_prefix": "dialnet.book", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1171" ], "uri_format": "https://dialnet.unirioja.es/servlet/libro?codigo=$1" }, "dialnet.journal": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "identifier of a journal in Dialnet", "example": "1119", "homepage": "http://dialnet.unirioja.es", "mappings": { "wikidata": "P1609" }, "name": "Dialnet journal ID", "pattern": "^[1-9]\\d{0,6}$", "preferred_prefix": "dialnet.journal", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1171" ], "uri_format": "https://dialnet.unirioja.es/servlet/revista?codigo=$1" }, "dicom": { "contact": { "email": "dclunie@dclunie.com", "name": "David Clunie", "orcid": "0000-0002-2406-1145" }, "description": "DICOM Controlled Terminology", 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This collection refers to DNA sequence information.", "example": "3hB06", "homepage": "http://www.antirrhinum.net/", "mappings": { "biocontext": "DRAGONDB.DNA", "miriam": "dragondb.dna", "n2t": "dragondb.dna" }, "name": "DragonDB DNA", "part_of": "dragondb", "pattern": "^\\d\\w+$", "preferred_prefix": "dragondb.dna", "uri_format": "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=DNA" }, "dragondb.locus": { "comment": "Deprecated because the website is dead", "deprecated": true, "description": "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information.", "example": "DEF", "homepage": "http://www.antirrhinum.net/", "mappings": { "biocontext": "DRAGONDB.LOCUS", "miriam": "dragondb.locus", "n2t": "dragondb.locus" }, "name": "DragonDB Locus", "part_of": "dragondb", "pattern": "^\\w+$", "preferred_prefix": "dragondb.locus", "uri_format": "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Locus" }, "dragondb.protein": { "comment": "Deprecated because the website is dead", "deprecated": true, "description": "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information.", "example": "AMDEFA", "homepage": "http://www.antirrhinum.net/", "mappings": { "biocontext": "DRAGONDB.PROTEIN", "miriam": "dragondb.protein", "n2t": "dragondb.protein" }, "name": "DragonDB Protein", "part_of": "dragondb", "pattern": "^\\w+$", "preferred_prefix": "dragondb.protein", "uri_format": "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide" }, "drc.filenumber": { "contributor": { "email": "egon.willighagen@maastrichtuniversity.nl", "github": "egonw", "name": "Egon Willighagen", "orcid": "0000-0001-7542-0286" }, "description": "Dutch Research Council file numbers are used for approved grants.", "example": "osf232097", "github_request_issue": 1460, "homepage": "https://www.nwo.nl/en/", "name": "Dutch Research Council File Number", "preferred_prefix": "drc.filenumber", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.nwo.nl/en/projects/$1" }, "drduke": { "description": "identifier for chemicals linked to information on occurrence in plants", "example": "19", "homepage": "https://phytochem.nal.usda.gov/phytochem/search/list", "mappings": { "wikidata": "P10074" }, "name": "Dr. Duke's Phytochemical and Ethnobotanical Databases chemical", "preferred_prefix": "drduke", "uri_format": "https://phytochem.nal.usda.gov/phytochem/chemicals/show/$1" }, "drks": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The German Clinical Trials Register (DRKS) is the German WHO primary registry. It is competent for the registration of all patient-oriented clinical trials conducted in Germany. The DRKS now contains well over 14,000 studies. Currently, around 2,000 studies are added annually. (from website)", "example": "DRKS00031815", "homepage": "http://drks.de", "name": "German Clinical Trials Register", "pattern": "^DRKS\\d+$", "preferred_prefix": "drks", "providers": [ { "code": "alt1", "description": "German Language Provider", "first_party": true, "homepage": "http://drks.de", "name": "German Language Provider", "uri_format": "https://drks.de/search/de/trial/$1" }, { "code": "alt2", "description": "Legacy Provider", "first_party": true, "homepage": "http://drks.de", "name": "Legacy Provider", "uri_format": "http://drks.de/en/trial/$1" } ], "uri_format": "https://drks.de/search/en/trial/$1" }, "dron": { "appears_in": [ "scdo" ], "contact": { "email": "hoganwr@gmail.com", "github": "hoganwr", "name": "William Hogan", "orcid": "0000-0002-9881-1017" }, "description": "An ontology to support comparative effectiveness researchers studying claims data.", "download_json": "http://purl.obolibrary.org/obo/dron.json", "download_obo": "http://purl.obolibrary.org/obo/dron.obo", "download_owl": "http://purl.obolibrary.org/obo/dron.owl", "example": "00023232", "homepage": "https://github.com/ufbmi/dron", "keywords": [ "approved drug", "biomedical science", "drug", "obo", "ontology", "small molecule" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "DRON", "biocontext": "DRON", "bioportal": "DRON", "fairsharing": "FAIRsharing.w5ntfd", "obofoundry": "dron", "ols": "dron", "ontobee": "DRON" }, "name": "The Drug Ontology", "pattern": "^\\d{8}$", "preferred_prefix": "DRON", "publications": [ { "doi": "10.1186/s13326-017-0121-5", "pmc": "PMC5335794", "pubmed": "28253937", "title": "Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request", "year": 2017 }, { "doi": "10.1186/s13326-016-0048-2", "pmc": "PMC4836073", "pubmed": "27096073", "title": "An accurate and precise representation of drug ingredients", "year": 2016 }, { "doi": "10.1186/2041-1480-4-44", "pmc": "PMC3931349", "pubmed": "24345026", "title": "Building a drug ontology based on RxNorm and other sources", "year": 2013 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/DRON_$1", "repository": "https://github.com/ufbmi/dron", "uri_format": "http://purl.obolibrary.org/obo/DRON_$1", "version": "2024-12-20" }, "drsanv0": { "description": "This namespace is used for GA4GH Data Repository Service (DRS) access to the USA National Institutes of Health (NIH), National Human Genome Research Institute (NHGRI), Genomic Analysis, Visualization and Informatics Lab-space (AnVIL) program data. AnVIL is a cloud-based genomic data sharing and analysis platform which facilitates integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by the National Institutes of Health (NIH) or by other agencies that support human genomics research. ", "example": "v2_1b0f158a-86e2-3887-b990-89e3cf2d9082", "homepage": "https://www.genome.gov/", "mappings": { "miriam": "drs.anv0" }, "name": "AnVIL DRS", "pattern": "^v2_[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$", "preferred_prefix": "drsanv0", "uri_format": "https://data.terra.bio/ga4gh/drs/v1/objects/$1" }, "drsc": { "description": "The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene.", "example": "DRSC05221", "homepage": "http://flyrnai.org/", "mappings": { "biocontext": "DRSC", "miriam": "drsc", "n2t": "drsc" }, "name": "Drosophila RNAi Screening Center", "pattern": "^DRSC\\d+$", "preferred_prefix": "drsc", "uri_format": "http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1" }, "drugbank": { "contact": { "email": "david.wishart@ualberta.ca", "name": "David Wishart", "orcid": "0000-0002-3207-2434" }, "description": "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information.", "example": "DB14938", "homepage": "http://www.drugbank.ca", "keywords": [ "biomedical science", "drug", "life science", "protein" ], "mappings": { "bartoc": "18377", "biocontext": "DrugBank", "cellosaurus": "DrugBank", "cheminf": "000406", "edam": "2326", "fairsharing": "FAIRsharing.353yat", "integbio": "nbdc01071", "miriam": "drugbank", "n2t": "drugbank", "pathguide": "221", "prefixcommons": "drugbank", "re3data": "r3d100010544", "togoid": "Drugbank", "uniprot": "DB-0019", "wikidata": "P715" }, "name": "DrugBank", "pattern": "^DB\\d{5}$", "preferred_prefix": "drugbank", "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/drugbank:$1" } ], "publications": [ { "doi": "10.1093/nar/gkad976", "pubmed": "37953279" }, { "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://go.drugbank.com/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}$", "preferred_prefix": "dsm5", "references": [ "https://archive.org/details/diagnosticstatis0005unse" ], "synonyms": [ "dsm-v" ] }, "dsmz": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Leibniz Institute DSMZ is the most diverse biological resource center in the world and one of the largest collections of microorganisms and cell cultures worldwide (bacteria, archaea, protists, yeasts, fungi, bacteriophages, plant viruses, genomic bacterial DNA as well as human and animal cell lines). The following designations are used as part of local unique identifiers:\n\n- `PC`: positive control\n- `NC`: negative control\n- `AS`: antiserum\n- `PV`: plant viruses\n- `RT`: recommended test\n- `ACC`: human or animal cell line\n- `DSM`: microorganism cell line", "example": "ACC-1", "example_extras": [ "AS-0753", "DSM-2", "PC-0754", "PV-0998", "RT-0753" ], "homepage": "https://www.dsmz.de", "mappings": { "cellosaurus": "DSMZCellDive", "re3data": "r3d100010219" }, "name": "Deutsche Sammlung von Mikroorganismen und Zellkulturen", "pattern": "^(ACC|DSM|NC|PC|RT|AS|PV)-\\d+$", "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" }, "dwc": { "contact": { "email": "gtuco.btuco@gmail.com", "github": "tucotuco", "name": "John Wieczorek", "orcid": "0000-0003-1144-0290" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Darwin Core is a vocabulary standard for transmitting information about biodiversity. This document lists all terms in namespaces currently used in the vocabulary.", "example": "Dataset", "github_request_issue": 1316, "homepage": "https://dwc.tdwg.org/list/", "keywords": [ "biodiversity", "biological sample annotation", "geographical location", "life science", "taxonomic classification" ], "mappings": { "fairsharing": "FAIRsharing.xvf5y3" }, "name": "Darwin Core Terms", "preferred_prefix": "dwc", "publications": [ { "doi": "10.1371/journal.pone.0102623", "pubmed": "25099149", "title": "The GBIF integrated publishing toolkit: facilitating the efficient publishing of biodiversity data on the internet", "year": 2014 }, { "doi": "10.3897/bdj.2.e1039", "pubmed": "24723785", "title": "Linking multiple biodiversity informatics platforms with Darwin Core Archives", "year": 2014 }, { "doi": "10.1371/journal.pone.0029715", "pubmed": "22238640", "title": "Darwin Core: an evolving community-developed biodiversity data standard", "year": 2012 } ], "repository": "https://github.com/tdwg/dwc", "uri_format": "http://rs.tdwg.org/dwc/terms/$1" }, "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" }, "ec": { "comment": "The Nomenclature Committee website does not yet contain an official policy regarding the use of dashes in the hierarchical categorization of enzymes, so the Bioregistry's regular expression is permissive and accepts both EC identifiers with dashes (e.g. 2.3.-.-) and without dashes (e.g., 2.3). This means you may have to do post-processing of EC identifiers in data integration scenarios.", "contact": { "email": "kristian.axelsen@sib.swiss", "github": "kaxelsen", "name": "Kristian Axelsen", "orcid": "0000-0003-3889-2879" }, "description": "The Enzyme Nomenclature (also known as the Enzyme Commission Code) is a species-agnostic controlled vocabulary for specific enzymes and an associated hierarchical classification into 7 main categories.\n\nThe Enzyme Nomenclature is maintained by the [Nomenclature Committee](https://iubmb.org/about/committees/nomenclature-committee/) of the International Union of Biochemistry and Molecular Biology (IUBMB). A detailed history of the nomenclature since the 1950s can be found [here](https://iubmb.qmul.ac.uk/enzyme/history.html).\n\nThere are few notable resources providing access to the Enzyme Nomenclature:\n\n
WebsiteHomepageNotes
ExplorEnzhttps://www.enzyme-database.orgThis is the resources officially recommended by IUBMB
IUBMB (via by Queen Mary)https://iubmb.qmul.ac.uk/enzymeThis is a web-based version of the 1992 publication.
IntEnzhttps://www.ebi.ac.uk/intenz
ExPaSyhttps://enzyme.expasy.org
", "example": "1.1.1.1", "example_decoys": [ "100", "2.", "2.n1", "2.3.", "2.3.n1", "2.3.1.", "2.3.1.n", "2.3.4.1.", "2.-.-", "2.-", "2.3.4.1.-" ], "example_extras": [ "2", "2.-.-.-", "2.3", "2.3.-.-", "2.3.1", "2.3.1.-", "2.3.1.n12", "3.1.26.n2", "3.4.24.B15" ], "homepage": "https://www.enzyme-database.org/", "keywords": [ "biochemistry", "centrally registered identifier", "classification", "enzyme", "enzyme commission number", "enzymology" ], "license": "CC-BY-4.0", "mappings": { "bartoc": "671", "biocontext": "EC-CODE", "edam": "1011", "fairsharing": "FAIRsharing.rfLD2u", "go": "EC", "integbio": "nbdc00508", "miriam": "ec-code", "n2t": "ec-code", "pathguide": "106", "prefixcommons": "intenz", "re3data": "r3d100010803", "togoid": "Ec", "uniprot": "DB-0024", "wikidata": "P591" }, "name": "Enzyme Nomenclature", "owners": [ { "name": "International Union of Biochemistry and Molecular Biology", "partnered": false, "ror": "00910ay07" } ], "pattern": "^\\d{1,2}(((\\.\\d{1,3}){1,3})|(\\.\\d+){2}\\.[nB]\\d{1,3}|\\.-\\.-\\.-|\\.\\d{1,3}\\.-\\.-|\\.\\d{1,3}\\.\\d{1,3}\\.-)?$", "preferred_prefix": "EC", "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/intenz:$1" }, { "code": "expasy", "description": "Enzyme nomenclature database, ExPASy (Expert Protein Analysis System)", "homepage": "https://enzyme.expasy.org/", "name": "Enzyme nomenclature database, ExPASy (Expert Protein Analysis System)", "uri_format": "https://enzyme.expasy.org/EC/$1" }, { "code": "expenz", "description": "ExploreEnz at Trinity College", "homepage": "http://www.enzyme-database.org/", "name": "ExploreEnz at Trinity College", "uri_format": "http://www.enzyme-database.org/query.php?ec=$1" } ], "publications": [ { "doi": "10.1093/nar/28.1.304", "pmc": "PMC102465", "pubmed": "10592255", "title": "The ENZYME database in 2000", "year": 2000 } ], "references": [ "https://github.com/biopragmatics/bioregistry/issues/681" ], "synonyms": [ "EC", "EC number", "EC-CODE", "ECCODE", "EC_CODE", "ec-code", "eccode", "intenz" ], "uri_format": "https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1" }, "ecacc": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The European Collection of Authenticated Cell Cultures (ECACC) is one of four Culture Collections of Public Health England. We supply authenticated and quality controlled cell lines, nucleic acids and induced Pluripotent Stem Cells (iPSCs).", "example": "90062901", "homepage": "https://www.phe-culturecollections.org.uk/collections/ecacc.aspx", "mappings": { "cellosaurus": "ECACC" }, "name": "European Collection of Authenticated Cell Culture", "pattern": "^\\d+$", "preferred_prefix": "ecacc", "uri_format": "https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId=$1" }, "ecao": { "contact": { "email": "ettensohn@cmu.edu", "github": "ettensohn", "name": "Charles Ettensohn", "orcid": "0000-0002-3625-0955" }, "depends_on": [ "cl", "ro", "uberon" ], "description": "None", "download_obo": "http://purl.obolibrary.org/obo/ecao.obo", "download_owl": "http://purl.obolibrary.org/obo/ecao.owl", "example": "0107180", "homepage": "https://github.com/echinoderm-ontology/ecao_ontology", "keywords": [ "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "ECAO", "bioportal": "ECAO", "obofoundry": "ecao", "ols": "ecao", "ontobee": "ECAO" }, "name": "The Echinoderm Anatomy and Development Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "ECAO", "rdf_uri_format": "http://purl.obolibrary.org/obo/ECAO_$1", "repository": "https://github.com/echinoderm-ontology/ecao_ontology", "uri_format": "http://purl.obolibrary.org/obo/ECAO_$1", "version": "2024-08-22" }, "ecg": { "contact": { "email": "rwinslow@jhu.edu", "name": "Raimond Winslow", "orcid": "0000-0003-1719-1651" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms.", "download_owl": "http://aber-owl.net/media/ontologies/ECG/12/ecg.owl", "example": "000000159", "homepage": "https://bioportal.bioontology.org/ontologies/ECG", "keywords": [ "biomedical science", "electrocardiography", "heart", "ontology" ], "mappings": { "aberowl": "ECG", "bioportal": "ECG", "fairsharing": "FAIRsharing.azr389" }, "name": "Electrocardiogram Ontology", "pattern": "^\\d+$", "preferred_prefix": "ecg", "publications": [ { "doi": "10.1016/j.jbi.2010.08.007", "pubmed": "20800107", "title": "Using an ECG reference ontology for semantic interoperability of ECG data", "year": 2010 } ], "synonyms": [ "ECGOntology" ], "uri_format": "http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_$1" }, "echinobase": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Echinobase supports the international research community by providing a centralized, integrated and easy to use web based resource to access the diverse and rich, functional genomics data of echinoderm species.", "example": "23159291", "homepage": "https://www.echinobase.org", "mappings": { "integbio": "nbdc01512" }, "name": "Echinobase", "pattern": "^\\d+$", "preferred_prefix": "echinobase", "uri_format": "https://www.echinobase.org/entry/gene/showgene.do?method=display&geneId=$1" }, "echobase": { "contact": { "email": "gavin.thomas@york.ac.uk", "github": "ghthomas", "name": "Gavin H. Thomas", "orcid": "0000-0002-9763-1313" }, "description": "EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products.", "example": "EB0170", "homepage": "http://www.york.ac.uk/", "keywords": [ "gene", "gene expression" ], "mappings": { "biocontext": "ECHOBASE", "go": "EchoBASE", "miriam": "echobase", "n2t": "echobase", "prefixcommons": "echobase", "re3data": "r3d100011646", "uniprot": "DB-0020" }, "name": "EchoBASE post-genomic database for Escherichia coli", "pattern": "^EB\\d+$", "preferred_prefix": "echobase", "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/echobase:$1" } ], "publications": [ { "doi": "10.1093/nar/gki028", "pmc": "PMC539982", "pubmed": "15608209", "title": "EchoBASE: an integrated post-genomic database for Escherichia coli", "year": 2005 } ], "uri_format": "http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1" }, "ecmdb": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The ECMDB is an expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655). This database includes significant quantities of “original” data compiled by members of the Wishart laboratory as well as additional material derived from hundreds of textbooks, scientific journals, metabolic reconstructions and other electronic databases. Each metabolite is linked to more than 100 data fields describing the compound, its ontology, physical properties, reactions, pathways, references, external links and associated proteins or enzymes.", "example": "ECMDB00005", "homepage": "https://ecmdb.ca", "mappings": { "pathguide": "386" }, "name": "E. coli Metabolite Database", "pattern": "^ECMDB\\d+$", "preferred_prefix": "ecmdb", "synonyms": [ "ECMDB" ], "uri_format": "http://ecmdb.ca/compounds/$1" }, "ecn": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "identifier for a chemical compound per EINECS or ELINCS", "example": "200-003-9", "homepage": "https://echa.europa.eu/information-on-chemicals", "mappings": { "cheminf": "000447", "wikidata": "P232" }, "name": "EC number", "pattern": "^\\d{3}-\\d{3}-\\d$", "preferred_prefix": "ecn", "references": [ "https://github.com/biopragmatics/bioregistry/issues/257", "https://en.wikipedia.org/wiki/European_Community_number" ] }, "eco": { "banana": "ECO", "contact": { "email": "mgiglio@som.umaryland.edu", "github": "mgiglio99", "name": "Michelle Giglio", "orcid": "0000-0001-7628-5565" }, "contributor_extras": [ { "github": "curtisim0", "name": "Curtis Ross", "orcid": "0000-0003-3035-6940" } ], "description": "Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity.", "download_obo": "http://purl.obolibrary.org/obo/eco.obo", "download_owl": "http://purl.obolibrary.org/obo/eco.owl", "example": "0007807", "homepage": "https://www.evidenceontology.org", "keywords": [ "assay", "biocuration", "biological sample annotation", "computational biology", "curated information", "digital curation", "evidence", "life science", "literature curation", "obo", "ontology", "resource metadata", "study design", "text mining" ], "license": "CC0-1.0", "logo": "https://avatars1.githubusercontent.com/u/12802432", "mappings": { "aberowl": "ECO", "bartoc": "1028", "biocontext": "ECO", "bioportal": "ECO", "fairsharing": "FAIRsharing.wvpgwn", "go": "ECO", "miriam": "eco", "n2t": "eco", "obofoundry": "eco", "ols": "eco", "ontobee": "ECO", "prefixcommons": "eco", "wikidata": "P3811" }, "name": "Evidence and Conclusion Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "ECO", "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/eco:$1" }, { "code": "quickgo", "description": "QuickGO's portal includes ECO terms", "homepage": "https://www.ebi.ac.uk/QuickGO", "name": "QuickGO", "uri_format": "https://www.ebi.ac.uk/QuickGO/term/ECO:$1" } ], "publications": [ { "doi": "10.1093/nar/gkab1025", "pmc": "PMC8728134", "pubmed": "34986598", "title": "ECO: the Evidence and Conclusion Ontology, an update for 2022", "year": 2022 }, { "doi": "10.1093/nar/gky1036", "pmc": "PMC6323956", "pubmed": "30407590", "title": "ECO, the Evidence & Conclusion Ontology: community standard for evidence information", "year": 2019 }, { "doi": "10.1007/978-1-4939-3743-1_18", "pmc": "PMC6377151", "pubmed": "27812948", "title": "The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations", "year": 2017 }, { "doi": "10.1093/database/bau075", "pmc": "PMC4105709", "pubmed": "25052702", "title": "Standardized description of scientific evidence using the Evidence Ontology (ECO)", "year": 2014 }, { "doi": "10.1142/9789812704856_0019", "pubmed": "14992503", "title": "An evidence ontology for use in pathway/genome databases", "year": 2004 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/ECO_$1", "repository": "https://github.com/evidenceontology/evidenceontology", "uri_format": "http://purl.obolibrary.org/obo/ECO_$1", "version": "2024-07-19" }, "ecocore": { "contact": { "email": "p.buttigieg@gmail.com", "github": "pbuttigieg", "name": "Pier Luigi Buttigieg", "orcid": "0000-0002-4366-3088" }, "depends_on": [ "bfo", "chebi", "envo", "go", "iao", "pato", "pco", "po", "ro", "uberon" ], "description": "Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms.", "download_obo": "http://purl.obolibrary.org/obo/ecocore.obo", "download_owl": "http://purl.obolibrary.org/obo/ecocore.owl", "example": "00000001", "homepage": "https://github.com/EcologicalSemantics/ecocore", "keywords": [ "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "ECOCORE", "biocontext": "ECOCORE", "bioportal": "ECOCORE", "obofoundry": "ecocore", "ols": "ecocore", "ontobee": "ECOCORE" }, "name": "An ontology of core ecological entities", "pattern": "^\\d+$", "preferred_prefix": "ECOCORE", "rdf_uri_format": "http://purl.obolibrary.org/obo/ECOCORE_$1", "repository": "https://github.com/EcologicalSemantics/ecocore", "uri_format": "http://purl.obolibrary.org/obo/ECOCORE_$1", "version": "2022-03-09" }, "ecocyc": { "contact": { "email": "pkarp@ai.sri.com", "github": "pkarp111", "name": "Peter Karp", "orcid": "0000-0002-5876-6418" }, "contributor_extras": [ { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" } ], "description": "EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of its genome, and of transcriptional regulation, transporters, and metabolic pathways.", "example": "AICARTRANSIMPCYCLO-CPLX", "homepage": "https://ecocyc.org/", "keywords": [ "biology" ], "mappings": { "fairsharing": "FAIRsharing.65dmtr", "go": "EcoCyc", "integbio": "nbdc00262", "ncbi": "ECOCYC", "pathguide": "9", "re3data": "r3d100011277" }, "name": "EcoCyc", "preferred_prefix": "ecocyc", "publications": [ { "doi": "10.3389/fmicb.2021.711077", "pmc": "PMC8357350", "pubmed": "34394059", "title": "The EcoCyc Database in 2021", "year": 2021 }, { "doi": "10.1093/nar/gkw1003", "pmc": "PMC5210515", "pubmed": "27899573", "title": "The EcoCyc database: reflecting new knowledge about Escherichia coli K-12", "year": 2016 }, { "doi": "10.1128/ecosalplus.esp-0009-2013", "pmc": "PMC4243172", "pubmed": "26442933", "title": "The EcoCyc Database", "year": 2014 }, { "doi": "10.1093/nar/gks1027", "pmc": "PMC3531154", "pubmed": "23143106", "title": "EcoCyc: fusing model organism databases with systems biology", "year": 2012 }, { "doi": "10.1128/ecosalplus.ESP-0009-2013", "title": "The EcoCyc Database." } ], "uri_format": "https://ecocyc.org/gene?id=$1" }, "ecogene": { "deprecated": true, "description": "The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites.", "example": "EG10173", "homepage": "http://ecogene.org/", "keywords": [ "genome", "protein" ], "mappings": { "biocontext": "EcoGene", "fairsharing": "FAIRsharing.3q3kvn", "miriam": "ecogene", "n2t": "ecogene", "ncbi": "EcoGene", "prefixcommons": "ecogene", "re3data": "r3d100010546" }, "name": "Database of Escherichia coli Sequence and Function", "pattern": "^EG\\d+$", "preferred_prefix": "ecogene", "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/ecogene:$1" } ], "publications": [ { "doi": "10.1093/nar/28.1.60", "pmc": "PMC102481", "pubmed": "10592181", "title": "EcoGene: a genome sequence database for Escherichia coli K-12", "year": 2000 } ], "uri_format": "http://www.ecogene.org/gene/$1" }, "ecolexicon": { "comment": "No resolution - everything is in a single page app", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "EcoLexicon represents the conceptual structure of the specialized domain of the Environment in the form of a visual thesaurus. This thesaurus has been elaborated according to the theoretical premises of Frame-Based Terminology.", "example": "canal", "homepage": "http://ecolexicon.ugr.es/en/index.htm", "keywords": [ "ecology", "environmental science" ], "name": "EcoLexicon", "preferred_prefix": "ecolexicon" }, "ecoliwiki": { "contact": { "email": "pkarp@ai.sri.com", "github": "pkarp111", "name": "Peter D. Karp", "orcid": "0000-0002-5876-6418" }, "deprecated": true, "description": "EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes.", "example": "aaeA", "homepage": "http://ecoliwiki.net/colipedia/", "keywords": [ "bioinformatics", "genomics", "life science", "ontology and terminology" ], "mappings": { "biocontext": "ECOLIWIKI", "fairsharing": "FAIRsharing.tx95wa", "go": "EcoliWiki", "integbio": "nbdc02041", "miriam": "ecoliwiki", "n2t": "ecoliwiki" }, "name": "EcoliWiki from EcoliHub", "pattern": "^[A-Za-z0-9-]+$", "preferred_prefix": "ecoliwiki", "publications": [ { "doi": "10.1016/j.tim.2009.04.004", "pmc": "PMC3575750", "pubmed": "19576778", "title": "What we can learn about Escherichia coli through application of Gene Ontology", "year": 2009 } ], "uri_format": "http://ecoliwiki.net/colipedia/index.php/$1:Gene" }, "ecso": { "contact": { "email": "brycemecum@gmail.com", "github": "amoeba", "name": "Bryce Mecum", "orcid": "0000-0002-0381-3766" }, "description": "DataONE ontology of Carbon Flux measurements for MsTMIP and LTER Use Cases", "download_owl": "https://raw.githubusercontent.com/DataONEorg/sem-prov-ontologies/run4/observation/d1-ECSO.owl", "example": "00000532", "homepage": "http://bioportal.bioontology.org/ontologies/ECSO", "keywords": [ "earth science", "ecosystem", "ecosystem science", "ontology" ], "mappings": { "aberowl": "ECSO", "bioportal": "ECSO", "ecoportal": "ECSO", "fairsharing": "FAIRsharing.a4ww64" }, "name": "The Ecosystem Ontology", "pattern": "^\\d+$", "preferred_prefix": "ecso", "repository": "https://github.com/DataONEorg/sem-prov-ontologies", "uri_format": "http://purl.dataone.org/odo/ECSO_$1" }, "ecto": { "contact": { "email": "annethessen@gmail.com", "github": "diatomsRcool", "name": "Anne Thessen", "orcid": "0000-0002-2908-3327" }, "depends_on": [ "chebi", "envo", "exo", "go", "iao", "maxo", "nbo", "ncbitaxon", "ncit", "pato", "ro", "uberon", "xco" ], "description": "ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology).", "download_json": "http://purl.obolibrary.org/obo/ecto.json", "download_obo": "http://purl.obolibrary.org/obo/ecto.obo", "download_owl": "http://purl.obolibrary.org/obo/ecto.owl", "example": "0000001", "homepage": "https://github.com/EnvironmentOntology/environmental-exposure-ontology", "keywords": [ "diet", "environmental science", "exposure", "obo", "ontology" ], "license": "CC0-1.0", "logo": "https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/ecto-logos/ecto-logo_black-banner.png", "mappings": { "aberowl": "ECTO", "agroportal": "ECTO", "biolink": "ECTO", "bioportal": "ECTO", "fairsharing": "FAIRsharing.6b77ac", "obofoundry": "ecto", "ols": "ecto", "ontobee": "ECTO" }, "name": "Environmental conditions, treatments and exposures ontology", "pattern": "^\\d{7}$", "preferred_prefix": "ECTO", "publications": [ { "doi": "10.1186/s13326-023-00283-x", "pubmed": "36823605", "title": "The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond", "year": 2023 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/ECTO_$1", "repository": "https://github.com/EnvironmentOntology/environmental-exposure-ontology", "uri_format": "http://purl.obolibrary.org/obo/ECTO_$1", "version": "2023-02-14" }, "ecyano.entity": { "description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities.", "example": "23", "homepage": "http://www.e-cyanobacterium.org/bcs/entity/", "mappings": { "biocontext": "ECYANO.ENTITY", "miriam": "ecyano.entity", "n2t": "ecyano.entity" }, "name": "E-cyanobacterium entity", "part_of": "ecyano", "pattern": "^\\d+$", "preferred_prefix": "ecyano.entity", "uri_format": "https://www.e-cyanobacterium.org/bcs/entity/$1" }, "ecyano.experiment": { "description": "E-cyanobacterium experiments is a repository of wet-lab experiments related to cyanobacteria. The emphasis is placed on annotation via mapping to local database of biological knowledge and mathematical models along with the complete experimental setup supporting the reproducibility of the experiments.", "example": "18", "homepage": "https://www.e-cyanobacterium.org/experiments-repository/", "mappings": { "miriam": "ecyano.experiment" }, "name": "E-cyanobacterium Experimental Data", "part_of": "ecyano", "pattern": "^\\d+$", "preferred_prefix": "ecyano.experiment", "uri_format": "https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id=$1" }, "ecyano.model": { "description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models.", "example": "26", "homepage": "http://e-cyanobacterium.org/models/", "mappings": { "biocontext": "ECYANO.MODEL", "miriam": "ecyano.model", "n2t": "ecyano.model" }, "name": "E-cyanobacterium model", "pattern": "^\\d+$", "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/$1" }, "edam": { "contact": { "email": "matus.kalas@uib.no", "github": "matuskalas", "name": "Matúš Kalaš", "orcid": "0000-0002-1509-4981" }, "description": "EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications).", "download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo", "download_owl": "http://edamontology.org/1.25-20240924T0027Z-unstable(1.26)", "example": "data_1664", "homepage": "http://edamontology.org", "keywords": [ "analysis", "bioinformatics", "data acquisition", "data transformation", "life science", "obo", "omics", "omics data analysis", "ontology" ], "mappings": { "aberowl": "EDAM", "agroportal": "EDAM", "biocontext": "EDAM", "bioportal": "EDAM", "fairsharing": "FAIRsharing.a6r7zs", "miriam": "edam", "n2t": "edam", "ols": "edam", "ontobee": "EDAM", "prefixcommons": "edam" }, "name": "EDAM Ontology", "pattern": "^(data|topic|operation|format)\\_\\d{4}$", "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/$1", "version": "1.25-20240924T0027Z-unstable(1.26)" }, "edam.data": { "contact": { "email": "matus.kalas@uib.no", "github": "matuskalas", "name": "Matúš Kalaš", "orcid": "0000-0002-1509-4981" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output.", "download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo", "example": "1664", "homepage": "http://edamontology.org", "keywords": [ "ontology" ], "mappings": { "biolink": "EDAM-DATA" }, "name": "EDAM Data", "part_of": "edam", "pattern": "^\\d+$", "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#$1" }, "efo": { "contact": { "email": "plwhetzel@gmail.com", "github": "twhetzel", "name": "Trish Whetzel", "orcid": "0000-0002-3458-4839" }, "description": "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team.", "download_obo": "http://www.ebi.ac.uk/efo/efo.obo", "download_owl": "http://www.ebi.ac.uk/efo/efo.owl", "example": "0005147", "homepage": "http://www.ebi.ac.uk/efo", "keywords": [ "assay", "experimental condition", "experimental measurement", "genome-wide association study", "genomics", "independent variable", "omics", "ontology", "proteomics", "study design" ], "license": "Apache-2.0", "logo": "https://upload.wikimedia.org/wikipedia/en/d/d8/Logo_of_the_Experimental_Factor_Ontlogy.gif", "mappings": { "aberowl": "EFO", "agroportal": "EFO", "biocontext": "EFO", "biolink": "EFO", "bioportal": "EFO", "cellosaurus": "EFO", "fairsharing": "FAIRsharing.1gr4tz", "miriam": "efo", "n2t": "efo", "ols": "efo", "ontobee": "EFO", "wikidata": "P11956" }, "name": "Experimental Factor Ontology", "owners": [ { "name": "European Bioinformatics Institute", "partnered": false, "ror": "02catss52" } ], "pattern": "^\\d{7}$", "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" }, { "code": "ols.curie", "description": "OLS via CURIE", "homepage": "https://www.ebi.ac.uk/ols", "name": "OLS", "uri_format": "http://www.ebi.ac.uk/ols/ontologies/efo/terms?short_form=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_$1", "version": "3.76.1" }, "ega.dataset": { "contact": { "email": "tk2@ebi.ac.uk", "github": "tk2", "name": "Thomas Keane", "orcid": "0000-0001-7532-6898" }, "description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'.", "example": "EGAD00000000001", "homepage": "https://ega-archive.org/", "keywords": [ "biology", "biomedical science", "clinical studies", "genomics", "phenomics" ], "mappings": { "biocontext": "EGA.DATASET", "fairsharing": "FAIRsharing.mya1ff", "miriam": "ega.dataset", "n2t": "ega.dataset", "re3data": "r3d100011242" }, "name": "European Genome-phenome Archive Dataset", "owners": [ { "name": "European Bioinformatics Institute", "partnered": false, "ror": "02catss52" } ], "pattern": "^EGAD\\d{11}$", "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. 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/ehdaa:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/EHDAA_$1", "uri_format": "http://purl.obolibrary.org/obo/EHDAA_$1" }, "ehdaa2": { "contact": { "email": "J.Bard@ed.ac.uk", "name": "Jonathan Bard" }, "depends_on": [ "aeo", "caro", "cl" ], "deprecated": true, "description": "A structured controlled vocabulary of stage-specific anatomical structures of the developing human.", "download_obo": "http://purl.obolibrary.org/obo/ehdaa2.obo", "download_owl": "http://purl.obolibrary.org/obo/ehdaa2.owl", "example": "0000000", "homepage": "https://github.com/obophenotype/human-developmental-anatomy-ontology", "keywords": [ "anatomy", "animal organ development", "biomedical science", "life cycle stage", "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "EHDAA2", "biocontext": "EHDAA2", "bioportal": "EHDAA2", "fairsharing": "FAIRsharing.7zxrs6", "obofoundry": "ehdaa2", "ols": "ehdaa2", "ontobee": "EHDAA2" }, "name": "Human developmental anatomy, abstract", "pattern": "^\\d{7}$", "preferred_prefix": "EHDAA2", "publications": [ { "doi": "10.1111/j.1469-7580.2012.01566.x", "pmc": "PMC3482348", "pubmed": "22973865", "title": "A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1-20)", "year": 2012 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/EHDAA2_$1", "repository": "https://github.com/obophenotype/human-developmental-anatomy-ontology", "synonyms": [ "EHDAA2_RETIRED", "HDAA2", "RETIRED_EHDAA2" ], "uri_format": "http://purl.obolibrary.org/obo/EHDAA2_$1", "version": "2013-07-04" }, "elm": { "contact": { "email": "toby.gibson@embl.de", "name": "Toby J Gibson", "orcid": "0000-0003-0657-5166" }, "description": "Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances.", "example": "CLV_MEL_PAP_1", "homepage": "http://elm.eu.org/", "keywords": [ "life science" ], "mappings": { "biocontext": "ELM", "fairsharing": "FAIRsharing.rj3kj5", "miriam": "elm", "n2t": "elm", "uniprot": "DB-0223" }, "name": "Eukaryotic Linear Motif Resource", "pattern": "^[A-Za-z_0-9]+$", "preferred_prefix": "elm", "publications": [ { "doi": "10.1093/nar/gkab975", "pubmed": "34718738" }, { "doi": "10.1093/nar/gkz1030", "pmc": "PMC7145657", "pubmed": "31680160", "title": "ELM-the eukaryotic linear motif resource in 2020", "year": 2020 }, { "doi": "10.1093/nar/gkv1291", "pmc": "PMC4702912", "pubmed": "26615199", "title": "ELM 2016--data update and new functionality of the eukaryotic linear motif resource", "year": 2015 }, { "doi": "10.1093/nar/gkr1064", "pmc": "PMC3245074", "pubmed": "22110040", "title": "ELM--the database of eukaryotic linear motifs", "year": 2011 }, { "doi": "10.1093/nar/gkg545", "pmc": "PMC168952", "pubmed": "12824381", "title": "ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins", "year": 2003 } ], "uri_format": "http://elm.eu.org/elms/elmPages/$1.html" }, "emap": { "contact": { "email": "Terry.Hayamizu@jax.org", "github": "tfhayamizu", "name": "Terry Hayamizu", "orcid": "0000-0002-0956-8634" }, "deprecated": true, "description": "A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus).", "download_owl": "http://purl.obolibrary.org/obo/emap.owl", "example": "1", "homepage": "http://emouseatlas.org", "keywords": [ "anatomy", "development", "mouse", "obo", "ontology" ], "mappings": { "biocontext": "EMAP", "bioportal": "EMAP", "obofoundry": "emap", "ols": "emap", "prefixcommons": "emap.ontology" }, "name": "Mouse gross anatomy and development, timed", "pattern": "^\\d+$", "preferred_prefix": "EMAP", "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/emap.ontology:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/EMAP_$1", "uri_format": "http://purl.obolibrary.org/obo/EMAP_$1", "version": "2020-04-13" }, "emapa": { "contact": { "email": "Terry.Hayamizu@jax.org", "github": "tfhayamizu", "name": "Terry Hayamizu", "orcid": "0000-0002-0956-8634" }, "description": "An ontology for mouse anatomy covering embryonic development and postnatal stages.", "download_obo": "http://purl.obolibrary.org/obo/emapa.obo", "download_owl": "http://purl.obolibrary.org/obo/emapa.owl", "example": "26753", "homepage": "http://www.informatics.jax.org/expression.shtml", "keywords": [ "anatomy", "developmental biology", "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "EMAPA", "bartoc": "549", "biocontext": "EMAPA", "bioportal": "EMAPA", "fairsharing": "FAIRsharing.j0fa1d", "go": "EMAPA", "obofoundry": "emapa", "ols": "emapa", "ontobee": "EMAPA" }, "name": "Mouse Developmental Anatomy Ontology", "pattern": "^\\d+$", "preferred_prefix": "EMAPA", "publications": [ { "doi": "10.1016/s0925-4773(98)00069-0", "pubmed": "9651497", "title": "An internet-accessible database of mouse developmental anatomy based on a systematic nomenclature", "year": 1998 }, { "doi": "10.1007/s00335-015-9584-9", "pmc": "PMC4602063", "pubmed": "26208972", "title": "Mouse anatomy ontologies: enhancements and tools for exploring and integrating biomedical data", "year": 2015 }, { "doi": "10.1186/2041-1480-4-15", "pmc": "PMC3851555", "pubmed": "23972281", "title": "EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update", "year": 2013 }, { "doi": "10.1016/b978-0-12-800043-4.00023-3", "title": "Textual Anatomics", "year": 2016 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/EMAPA_$1", "repository": "https://github.com/obophenotype/mouse-anatomy-ontology", "synonyms": [ "EMAPA_RETIRED" ], "uri_format": "http://purl.obolibrary.org/obo/EMAPA_$1", "version": "2023-11-14" }, "emaps": { "contact": { "email": "Terry.Hayamizu@jax.org", "github": "tfhayamizu", "name": "Terry Hayamizu", "orcid": "0000-0002-0956-8634" }, "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "depends_on": [ "emapa" ], "description": "EMAPA identifiers refer to developmental stage-independent mouse anatomical features, for instance, EMAPA:35178 resolves to the MGI's Mouse Developmental Anatomy Browser. EMAPS is an extension to EMAPA which introduces terms for different developmental stages of this generic EMAPA entry. EMAPS identifiers are constructed such that they are a concatenation of the EMAPA ID and a Theiler Stage (TS) number. For instance, EMAPA:35178 in TS 23 becomes EMAPS:3517823", "example": "3517823", "github_request_issue": 747, "homepage": "https://www.informatics.jax.org/vocab/gxd/anatomy/", "name": "Mouse Developmental Anatomy Ontology with Theiler Stage", "pattern": "^\\d+$", "preferred_prefix": "EMAPS", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.informatics.jax.org/vocab/gxd/anatomy/EMAPS:$1" }, "emdb": { "contact": { "email": "help@emdatabank.org", "name": "Ardan Patwardhan", "orcid": "0000-0001-7663-9028" }, "description": "The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community.", "example": "EMD-1001", "homepage": "https://www.ebi.ac.uk/pdbe/emdb/", "keywords": [ "epidemiology", "structural biology", "virology" ], "mappings": { "biocontext": "EMDB", "edam": "1146", "fairsharing": "FAIRsharing.651n9j", "miriam": "emdb", "n2t": "emdb", "re3data": "r3d100010562", "uniprot": "DB-0272" }, "name": "Electron Microscopy Data Bank", "owners": [ { "name": "European Bioinformatics Institute", "partnered": false, "ror": "02catss52" } ], "pattern": "^EMD-\\d{4,5}$", "preferred_prefix": "emdb", "publications": [ { "doi": "10.1093/nar/gkv1126", "pmc": "PMC4702818", "pubmed": "26578576", "title": "EMDataBank unified data resource for 3DEM", "year": 2015 }, { "doi": "10.1093/nar/gkq880", "pmc": "PMC3013769", "pubmed": "20935055", "title": "EMDataBank.org: unified data resource for CryoEM", "year": 2010 }, { "doi": "10.1016/s0968-0004(02)02176-x", "pubmed": "12417136", "title": "New electron microscopy database and deposition system", "year": 2002 }, { "doi": "10.1016/S0968-0004(02)02176-X", "title": "New electron microscopy database and deposition system" } ], "uri_format": "https://www.ebi.ac.uk/pdbe/entry/emdb/$1" }, "emea": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Product number for the European Medicines Agency", "example": "EMEA/H/C/000181", "homepage": "https://www.ema.europa.eu/en/medicines", "name": "European Medicines Evaluation Agency", "preferred_prefix": "emea" }, "emi": { "contact": { "email": "Tarcisio.Mendes@sib.swiss", "github": "tarcisiotmf", "name": "Tarcisio Mendes de Farias", "orcid": "0000-0002-3175-5372" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The EMI ontology is used to structure spectrum annotation provenance by reusing the PROV-O ontology (a W3C recommendation) and sample and observation data by applying the SOSA ontology. EMI reuses the SOSA ontology as a data schema for struturing the Sample and Observation data. SOSA (Sensor, Observation, Sample, and Actuator) is a subset of SSN (Semantic Sensor Network Ontology) that is a W3C recommendation. [from homepage]", "download_rdf": "https://github.com/digital-botanical-gardens-initiative/earth_metabolome_ontology/blob/main/emi.ttl", "example": "ChemicalStructure", "github_request_issue": 1516, "homepage": "https://www.dbgi.org/earth_metabolome_ontology/", "license": "CC0-1.0", "name": "Earth Metabolome Ontology", "preferred_prefix": "emi", "rdf_uri_format": " https://purl.org/emi#$1", "repository": "https://github.com/digital-botanical-gardens-initiative/earth_metabolome_ontology", "uri_format": "https://www.dbgi.org/earth_metabolome_ontology/#$1" }, "emmo": { "banana": "EMMO", "banana_peel": "_", "contact": { "email": "jesper.friis@sintef.no", "github": "jesper-friis", "name": "Jesper Friis", "orcid": "0000-0002-1560-809X" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "EMMO is a multidisciplinary effort to develop a standard representational framework (the ontology) for applied sciences. It is based on physics, analytical philosophy and information and communication technologies. It has been instigated by materials science to provide a framework for knowledge capture that is consistent with scientific principles and methodologies. (from GitHub)", "download_rdf": "https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl", "example": "03212fd7_abfd_4828_9c8e_62c293052d4b", "homepage": "https://emmo-repo.github.io", "keywords": [ "communication science", "industry", "philosophy", "physics" ], "license": "CC-BY-4.0", "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBdmtEIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--69489934048fba98feded162d24a8e3b36c9d370/EMMO.jpg?disposition=inline", "mappings": { "fairsharing": "FAIRsharing.1bdf3c", "lov": "emmo" }, "name": "Elementary Multiperspective Material Ontology", "preferred_prefix": "emmo", "repository": "https://github.com/emmo-repo/EMMO", "uri_format": "http://emmo.info/emmo#EMMO_$1" }, "emmo.cif": { "contact": { "email": "jesper.friis@sintef.no", "github": "jesper-friis", "name": "Jesper Friis", "orcid": "0000-0002-1560-809X" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A crystallography domain ontology based on EMMO and the CIF core dictionary. It is implemented as a formal language. (from https://nfdi4cat.org/services/ontologie-sammlung/)", "download_rdf": "https://raw.githubusercontent.com/emmo-repo/CIF-ontology/main/ontology/cif-core.ttl", "example": "_space_group_symop.operation_xyz", "example_extras": [ "o12" ], "homepage": "https://www.iucr.org/resources/cif", "name": "Crystallographic Information Framework", "preferred_prefix": "emmo.cif", "repository": "https://github.com/emmo-repo/CIF-ontology", "uri_format": "http://emmo.info/emmo/cif-core#$1" }, "emolecules": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Catalog of purchasable reagents and building blocks", "example": "491187", "homepage": "https://reaxys.emolecules.com", "keywords": [ "chemistry", "reagents", "vendor" ], "name": "Reaxys eMolecules", "pattern": "^\\d+$", "preferred_prefix": "emolecules", "uri_format": "https://reaxys.emolecules.com/cgi-bin/more?vid=$1" }, "empiar": { "banana": "EMPIAR", "banana_peel": "-", "contact": { "email": "ardan@ebi.ac.uk", "name": "Ardan Patwardhan", "orcid": "0000-0001-7663-9028" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure", "example": "10595", "homepage": "https://www.ebi.ac.uk/pdbe/emdb", "keywords": [ "bioinformatics", "biology" ], "mappings": { "fairsharing": "FAIRsharing.dff3ef", "miriam": "empiar" }, "name": "Electron Microscopy Public Image Archive", "owners": [ { "name": "European Bioinformatics Institute", "partnered": false, "ror": "02catss52" } ], "pattern": "^\\d+$", "preferred_prefix": "empiar", "publications": [ { "doi": "10.1038/nmeth.3806", "pubmed": "27067018", "title": "EMPIAR: a public archive for raw electron microscopy image data", "year": 2016 } ], "uri_format": "https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1" }, "emsl.project": { "contact": { "email": "montana.smith@pnnl.gov", "github": "mslarae13", "name": "Montana Smith", "orcid": "0000-0002-8683-0050" }, "contributor": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "description": "As a scientific user facility, the Environmental Molecular Sciences Laboratory (EMSL) provides expertise, instrumentation, and resources to 250 projects each year. Current and past projects supported through a variety of EMSL user proposal avenues are publicly searchable on the EMSL website. Project pages provide details including:\n- Research team and institution\n- The EMSL project DOI\n- Link to project data available in EMSLs Data Portal\n- Project type", "example": "60141", "github_request_issue": 835, "homepage": "https://www.emsl.pnnl.gov/projects", "name": "Environmental Molecular Sciences Laboratory Project", "pattern": "^\\d+$", "preferred_prefix": "emsl.project", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.emsl.pnnl.gov/project/$1" }, "ena.embl": { "contact": { "email": "datasubs@ebi.ac.uk", "name": "Guy Cochrane", "orcid": "0000-0001-7954-7057" }, "description": "The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. ENA is made up of a number of distinct databases that includes EMBL-Bank, the Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. 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", "download_owl": "http://aber-owl.net/media/ontologies/EPSO/3/epso.owl", "example": "0000400", "homepage": "http://prism.case.edu/prism/index.php/EpilepsyOntology", "keywords": [ "epilepsy", "neurology", "ontology", "patient care" ], "mappings": { "aberowl": "EPSO", "bioportal": "EPSO", "fairsharing": "FAIRsharing.ttprgy", "ontobee": "EPSO" }, "name": "Epilepsy and Seizure Ontology", "pattern": "^\\d{7}$", "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. 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/eropmoscow:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://erop.inbi.ras.ru/result2.php?PepName=$1" }, "erv": { "description": "Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features.", "example": "THE1B", "homepage": "https://herv.img.cas.cz/", "mappings": { "biocontext": "ERV", "miriam": "erv", "n2t": "erv" }, "name": "Human Endogenous Retrovirus Database", "pattern": "^[A-Za-z0-9\\-\\_]+$", "preferred_prefix": "erv", "uri_format": "https://herv.img.cas.cz/s/$1" }, "esldb": { "description": "eSLDB is a database of protein subcellular localization annotation for eukaryotic organisms. 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/$1" }, "eubopen": { "contact": { "email": "tredup@pharmchem.uni-frankfurt.de", "name": "Claudia Tredup", "orcid": "0000-0001-6518-3344" }, "contributor": { "email": "palayoor.n@northeastern.edu", "github": "nalikapalayoor", "name": "Nalika Palayoor", "orcid": "0009-0008-8406-631X" }, "description": "EUbOPEN is a project focusing on organizing chemogenic library collections, advancing chemical probe discovery, profiling bioactive compounds, and making project data more accessible.", "example": "EUB0000221", "github_request_issue": 1378, "homepage": "https://gateway.eubopen.org", "name": "Enabling and Unlocking Biology in the Open", "pattern": "^EUB\\d{7}$", "preferred_prefix": "eubopen", "publications": [ { "doi": "10.1039/d4md00735b", "pmc": "PMC11605244", "pubmed": "39618964", "title": "Toward target 2035: EUbOPEN - a public-private partnership to enable & unlock biology in the open", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://gateway.eubopen.org/compound/$1" }, "euclinicaltrials": { "description": "The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004.\nIt also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population.", "example": "2008-005144-16", "homepage": "https://www.clinicaltrialsregister.eu/", "mappings": { "biocontext": "EUCLINICALTRIALS", "miriam": "euclinicaltrials", "n2t": "euclinicaltrials" }, "name": "EU Clinical Trials", "pattern": "^\\d{4}\\-\\d{6}\\-\\d{2}$", "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=$1" }, "evm": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "name": "eVOC mouse development stage", "preferred_prefix": "evm", "references": [ "https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-10-r229" ] }, "evr": { "contact": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An open, community-driven registry of conference and event venues.\n\nEVR assigns persistent identifiers (PIDs) to make referencing venues FAIR. This is similar to how ORCID assigns PIDs to researchers and ROR assigns PIDs to research organizations.\n\nThis benefits researchers assembling information about in-person conferences and events by enabling them to refer in an unambiguous way to the venue where it takes place.\n\nThis repository follows the [Open Data, Open Code, Open Infrastructure (O3) principles](https://www.nature.com/articles/s41597-024-03406-w), meaning that the data and code are all in one repository that anyone can contribute to.", "example": "0000001", "github_request_issue": 1363, "homepage": "https://cthoyt.com/evr", "license": "CC0-1.0", "name": "Event Venue Registry", "pattern": "^\\d{7}$", "preferred_prefix": "evr", "repository": "https://github.com/cthoyt/evr", "uri_format": "https://cthoyt.com/evr/$1" }, "exac.gene": { "description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information.", "example": "ENSG00000169174", "homepage": "http://exac.broadinstitute.org/", "mappings": { "biocontext": "EXAC.GENE", "miriam": "exac.gene", "n2t": "exac.gene" }, "name": "ExAC Gene", "pattern": "^ENSG\\d{11}$", "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. 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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. 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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/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_$1", "version": "2025-03-26" }, "fbol": { "comment": "Website down, checked on 2021-10-07", "deprecated": true, "description": "DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms.", "example": "2224", "homepage": "http://www.fungalbarcoding.org/", "mappings": { "biocontext": "FBOL", "miriam": "fbol", "n2t": "fbol", "ncbi": "FBOL" }, "name": "International Fungal Working Group Fungal Barcoding.", "pattern": "^\\d+$", "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?$1" }, "fda.application": { "comment": "The official FDA website doesn't appear to be able to resolve application IDs but these IDs do appear in some PDF documents, e.g., https://www.fda.gov/media/159183/download.", "contributor": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. 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These entities include chemical compounds and natural substances used as flavoring agents, each reviewed by the FEMA Expert Panel for GRAS (Generally Recognized As Safe) status. The identifiers link to safety data and regulatory assessments, including evaluations by the U.S. FDA and, where applicable, the Joint FAO/WHO Expert Committee on Food Additives (JECFA).", "example": "4667", "github_request_issue": 1247, "homepage": "https://www.femaflavor.org", "name": "Flavor and Extract Manufacturers Association", "pattern": "^\\d+$", "preferred_prefix": "fema", "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. 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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": "amalik@ebi.ac.uk", "github": "amalik01", "name": "Adnan Malik", "orcid": "0000-0001-8123-5351" }, "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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It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field.", "example": "FR-FCM-ZYGW", "homepage": "https://flowrepository.org/", "keywords": [ "biology", "cell biology", "life science" ], "mappings": { "fairsharing": "FAIRsharing.veg2d6", "integbio": "nbdc01698", "miriam": "flowrepository", "n2t": "flowrepository", "re3data": "r3d100011280" }, "name": "FlowRepository", "pattern": "^FR\\-FCM\\-\\w{4}$", "preferred_prefix": "flowrepository", "publications": [ { "doi": "10.1002/cyto.a.22106", "pubmed": "22887982", "title": "FlowRepository: a resource of annotated flow cytometry datasets associated with peer-reviewed publications", "year": 2012 }, { "doi": "10.1002/0471142956.cy1018s61", "pubmed": "22752950", "title": "Preparing a Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) compliant manuscript using the International Society for Advancement of Cytometry (ISAC) FCS file repository (FlowRepository.org)", "year": 2012 } ], "uri_format": "https://flowrepository.org/id/$1" }, "flu": { "contact": { "email": "burkesquires@gmail.com", "name": "R. 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(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/$1" }, "fsnp": { "deprecated": true, "description": "The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification.", "example": "rs17852708", "homepage": "http://compbio.cs.queensu.ca/F-SNP/", "keywords": [ "dna", "protein" ], "mappings": { "biocontext": "FSNP", "miriam": "fsnp", "n2t": "fsnp", "prefixcommons": "fsnp" }, "name": "F-SNP", "pattern": "^rs\\d+$", "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=$1" }, "funcbase.fly": { "deprecated": true, "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data.", "example": "10194", "homepage": "http://func.mshri.on.ca/fly", "mappings": { "biocontext": "FUNCBASE.FLY", "miriam": "funcbase.fly", "n2t": "funcbase.fly" }, "name": "FuncBase Fly", "pattern": "^\\d+$", "preferred_prefix": "funcbase.fly", "uri_format": "http://func.mshri.on.ca/fly/genes/list_functional_scores/$1" }, "funcbase.human": { "deprecated": true, "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data.", "example": "119514", "homepage": "http://func.mshri.on.ca/human/", "mappings": { "biocontext": "FUNCBASE.HUMAN", "miriam": "funcbase.human", "n2t": "funcbase.human" }, "name": "FuncBase Human", "pattern": "^\\d+$", "preferred_prefix": "funcbase.human", "uri_format": "http://func.mshri.on.ca/human/genes/list_functional_scores/$1" }, "funcbase.mouse": { "deprecated": true, "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse.", "example": "1351341", "homepage": "http://func.mshri.on.ca/mouse/", "mappings": { "biocontext": "FUNCBASE.MOUSE", "miriam": "funcbase.mouse", "n2t": "funcbase.mouse" }, "name": "FuncBase Mouse", "pattern": "^\\d+$", "preferred_prefix": "funcbase.mouse", "uri_format": "http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1" }, "funcbase.yeast": { "deprecated": true, "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast.", "example": "2701", "homepage": "http://func.mshri.on.ca/yeast", "mappings": { "biocontext": "FUNCBASE.YEAST", "miriam": "funcbase.yeast", "n2t": "funcbase.yeast" }, "name": "FuncBase Yeast", "pattern": "^\\d+$", "preferred_prefix": "funcbase.yeast", "uri_format": "http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1" }, "funderregistry": { "description": "The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world.", "example": "100000001", "example_extras": [ "501100001230" ], "homepage": "https://www.crossref.org/", "mappings": { "miriam": "funderregistry" }, "name": "FunderRegistry", "pattern": "^\\d+$", "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_$1", "version": "2025-03-24" }, "ga4ghdos": { "description": "Assists in resolving data across cloud resources.", "example": "dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d", "homepage": "http://github.com/ga4gh/data-object-service-schemas", "mappings": { "biocontext": "GA4GHDOS", "miriam": "ga4ghdos", "n2t": "ga4ghdos" }, "name": "Data Object Service", "pattern": "^[a-zA-Z0-9\\-:#/\\.]+$", "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#$1" }, "gallont": { "contact": { "email": "adeans@psu.edu", "github": "adeans", "name": "Andy Deans", "orcid": "0000-0002-2119-4663" }, "depends_on": [ "caro", "flopo", "ncbitaxon", "obi", "pato", "po", "poro", "ro" ], "description": "Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls.", "download_json": "https://github.com/adeans/gallont/raw/refs/heads/main/gallont.json", "download_obo": "http://purl.obolibrary.org/obo/gallont.obo", "download_owl": "http://purl.obolibrary.org/obo/gallont.owl", "example": "0000001", "homepage": "https://adeans.github.io/gallont/", "keywords": [ "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "GALLONT", "agroportal": "GALLONT", "bioportal": "GALLONT", "obofoundry": "gallont", "ontobee": "GALLONT" }, "name": "Plant Gall Ontology", "pattern": "^\\d{7}$", "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/$1" }, "gcst": { "description": "The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide.", "example": "GCST000035", "homepage": "https://www.ebi.ac.uk", "mappings": { "miriam": "gcst", "n2t": "gcst" }, "name": "GWAS Catalog", "owners": [ { "name": "European Bioinformatics Institute", "partnered": false, "ror": "02catss52" } ], "pattern": "^GCST\\d{6}\\d*$", "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", "providers": [ { "code": "gemet.multilingual", "description": "An alternate URI that doesn't have the language encoded in it", "homepage": "https://www.eionet.europa.eu/gemet", "name": "GEMET Multilingual", "uri_format": "http://www.eionet.europa.eu/gemet/concept/$1" } ], "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. Nawrocki", "orcid": "0000-0002-2497-3427" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42).", "example": "U49845", "homepage": "https://www.ncbi.nlm.nih.gov/genbank/", "keywords": [ "bioinformatics", "data management", "dna", "epidemiology", "functional genomics", "genomics", "metagenomics", "transcriptomics", "virology" ], "mappings": { "biocontext": "GenBank", "cheminf": "000304", "edam": "2292", "fairsharing": "FAIRsharing.9kahy4", "go": "GenBank", "integbio": "nbdc00276", "prefixcommons": "genbank", "re3data": "r3d100010528", "uniprot": "DB-0028" }, "name": "GenBank", "preferred_prefix": "genbank", "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/genbank:$1" } ], "publications": [ { "doi": "10.1093/nar/gkae1114", "pubmed": "39558184", "title": "GenBank 2025 update", "year": 2024 }, { "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": { "comment": "CTH: this is a provider of the INSDC resources, not a new prefix.", "contact": { "email": "zhaoxuetong@big.ac.cn", "name": "Xuetong Zhao", "orcid": "0000-0002-3019-8615" }, "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", "github_request_issue": 1140, "homepage": "https://ngdc.cncb.ac.cn/genbase/?lang=en", "mappings": { "re3data": "r3d100014353" }, "name": "GenBase", "preferred_prefix": "genbase", "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "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. 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/gendis:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://caps.ncbs.res.in/cgi-bin/mini/databases/gendis/sf.cgi?code=$1" }, "genecards": { "contact": { "email": "marilyn.safran@weizmann.ac.il", "name": "Marilyn Safran", "orcid": "0000-0001-5424-1393" }, "description": "The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene.", "example": "ABL1", "homepage": "http://www.genecards.org/", "keywords": [ "genetics", "genome", "life science", "transcriptomics" ], "mappings": { "biocontext": "GENECARDS", "fairsharing": "FAIRsharing.g7jbvn", "integbio": "nbdc00242", "miriam": "genecards", "n2t": "genecards", "prefixcommons": "genecards", "re3data": "r3d100012015", "uniprot": "DB-0030" }, "name": "GeneCards", "pattern": "^[A-Za-z-0-9_]+(\\@)?$", "preferred_prefix": "genecards", "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/genecards:$1" } ], "publications": [ { "doi": "10.1016/s0168-9525(97)01103-7", "pubmed": "9097728", "title": "GeneCards: integrating information about genes, proteins and diseases", "year": 1997 }, { "doi": "10.1186/s12864-016-2722-2", "pmc": "PMC4928145", "pubmed": "27357693", "title": "VarElect: the phenotype-based variation prioritizer of the GeneCards Suite", "year": 2016 }, { "doi": "10.1002/cpbi.5", "pubmed": "27322403", "title": "The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses", "year": 2016 }, { "doi": "10.1093/database/baw030", "pmc": "PMC4820835", "pubmed": "27048349", "title": "Genic insights from integrated human proteomics in GeneCards", "year": 2016 }, { "doi": "10.1089/omi.2015.0168", "pmc": "PMC4799705", "pubmed": "26983021", "title": "GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data", "year": 2016 }, { "doi": "10.1093/database/bav006", "pmc": "PMC4343183", "pubmed": "25725062", "title": "PathCards: multi-source consolidation of human biological pathways", "year": 2015 }, { "doi": "10.1093/database/baq020", "pmc": "PMC2938269", "pubmed": "20689021", "title": "GeneCards Version 3: the human gene integrator", "year": 2010 }, { "doi": "10.1093/bioinformatics/18.11.1542", "pubmed": "12424129", "title": "GeneCards 2002: towards a complete, object-oriented, human gene compendium", "year": 2002 }, { "doi": "10.1016/S0168-9525(97)01103-7", "title": "GeneCards: integrating information about genes, proteins and diseases." } ], "uri_format": "https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1" }, "genecards.geneannot": { "description": "GeneAnnot provides a revised and improved annotation of Affymetrix probe-sets from HG-U95, HG-U133 and HG-U133 Plus2.0. Probe-sets are related to GeneCards genes, by direct sequence comparison of probes to GenBank, RefSeq and Ensembl mRNA sequences, while assigning sensitivity and specificity scores to each probe-set to gene match.", "example": "GSTA1", "homepage": "http://genecards.weizmann.ac.il/geneannot/", "keywords": [ "gene expression" ], "mappings": { "prefixcommons": "geneannot" }, "name": "GeneAnnot: Microarray Gene Annotation", "preferred_prefix": "genecards.geneannot", "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/geneannot:$1" } ] }, "genecards.geneloc": { "description": "GeneLoc presents an integrated map for each human chromosome, based on data integrated by the GeneLoc algorithm. GeneLoc includes further links to GeneCards, NCBI's Human Genome Sequencing, UniGene, and mapping resources", "example": "17503", "homepage": "http://genecards.weizmann.ac.il/geneloc/", "keywords": [ "genome" ], "mappings": { "prefixcommons": "geneloc" }, "name": "Gene Location", "preferred_prefix": "genecards.geneloc", "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/geneloc:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://genecards.weizmann.ac.il/geneloc-bin/marker_cards.pl?id=$1" }, "genecards.genenote": { "description": "GeneNote is a database of human genes and their expression profiles in healthy tissues. It is based on Weizmann Institute of Science DNA array experiments, which were performed on the Affymetrix HG-U95 set A-E.", "example": "GC06M052656", "homepage": "http://genecards.weizmann.ac.il/genenote/", "keywords": [ "gene expression" ], "mappings": { "prefixcommons": "genenote" }, "name": "Gene Normal Tissue Expression", "preferred_prefix": "genecards.genenote", "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/genenote:$1" } ], "uri_format": "http://bioinfo2.weizmann.ac.il/cgi-bin/genenote/GN_results.pl?keyword_type=2_gc_id&keyword=$1&data_type=norm2&results=yes" }, "genedb": { "deprecated": true, "description": "GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the \"Pathogen Genomics\" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed.", "example": "LinJ.20.0070", "homepage": "https://www.genedb.org/", "keywords": [ "genome", "life science", "sequence" ], "mappings": { "biocontext": "GENEDB", "edam": "1035", "fairsharing": "FAIRsharing.j7esqq", "go": "GeneDB", "integbio": "nbdc00469", "miriam": "genedb", "n2t": "genedb", "ncbi": "GeneDB", "prefixcommons": "genedb", "re3data": "r3d100010626", "wikidata": "P3382" }, "name": "GeneDB", "pattern": "^[\\w\\d\\.-]*$", "preferred_prefix": "genedb", "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/genedb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkh007", "pmc": "PMC308742", "pubmed": "14681429", "title": "GeneDB: a resource for prokaryotic and eukaryotic organisms", "year": 2004 } ], "uri_format": "https://www.genedb.org/gene/$1" }, "genefarm": { "contact": { "email": "sebastien.aubourg@inrae.fr", "name": "sébastien Aubourg", "orcid": "0000-0002-0695-4767" }, "description": "GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products.", "example": "4892", "homepage": "http://urgi.versailles.inra.fr/Genefarm/", "keywords": [ "expression", "genome", "life science", "nucleotide", "sequence" ], "mappings": { "biocontext": "GENEFARM", "fairsharing": "FAIRsharing.2mayq0", "miriam": "genefarm", "n2t": "genefarm", "prefixcommons": "genefarm" }, "name": "GeneFarm", "pattern": "^\\d+$", "preferred_prefix": "genefarm", "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" }, "glottolog": { "appears_in": [ "gsso" ], "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": " Comprehensive reference information for the world's languages, especially the lesser known languages. [from homepage]", "example": "nort3314", "github_request_issue": 1310, "homepage": "https://glottolog.org", "license": "CC-BY-4.0", "name": "Glottolog", "preferred_prefix": "glottolog", "uri_format": "https://glottolog.org/resource/languoid/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. 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/glycomapsdb:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php?mapid=$1" }, "glycomedb": { "contact": { "email": "rr@uga.edu", "github": "ReneRanzinger", "name": "René Ranzinger", "orcid": "0000-0003-3147-448X" }, "description": "GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links.", "example": "G77500AY", "has_canonical": "glytoucan", "homepage": "https://glytoucan.org/", "keywords": [ "life science", "molecules", "small molecules", "structure" ], "mappings": { "biocontext": "GLYCOMEDB", "edam": "2664", "fairsharing": "FAIRsharing.k5k0yh", "integbio": "nbdc00899", "miriam": "glycomedb", "n2t": "glycomedb", "prefixcommons": "glycomedb", "re3data": "r3d100011527" }, "name": "GlycomeDB", "pattern": "^\\w+$", "preferred_prefix": "glycomedb", "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/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=$1" }, "glycopost": { "description": "GlycoPOST is a mass spectrometry data repository for glycomics and glycoproteomics. Users can release their \"raw/processed\" data via this site with a unique identifier number for the paper publication. Submission conditions are in accordance with the Minimum Information Required for a Glycomics Experiment (MIRAGE) guidelines.", "example": "GPST000024", "homepage": "https://glycopost.glycosmos.org", "keywords": [ "glycomics", "life science" ], "mappings": { "fairsharing": "FAIRsharing.2y1KMt", "miriam": "glycopost" }, "name": "GlycoPOST", "pattern": "^GPST[0-9]{6}$", "preferred_prefix": "glycopost", "uri_format": "https://glycopost.glycosmos.org/entry/$1" }, "glycosciencesdb": { "contact": { "email": "thomas@luetteke-online.de", "github": "glycosciences", "name": "Thomas Lütteke", "orcid": "0000-0002-7140-9933" }, "contributor": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "description": "A database to support glycobiology and glycomics research. Its main focus is on 3D structures, including 3D structure models as well as references to PDB entries that feature carbohydrates.", "example": "1", "github_request_issue": 537, "homepage": "http://www.glycosciences.de/database/", "name": "Glycosciences.DB", "pattern": "^\\d+$", "preferred_prefix": "glycosciencesdb", "publications": [ { "doi": "10.1093/nar/gky994", "pmc": "PMC6323918", "pubmed": "30357361", "title": "Glycosciences.DB: an annotated data collection linking glycomics and proteomics data (2018 update)", "year": 2019 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "glycosciences.db" ], "uri_format": "http://www.glycosciences.de/database/start.php?action=explore_linucsid&linucsid=$1" }, "glytoucan": { "contact": { "email": "rr@uga.edu", "github": "ReneRanzinger", "name": "René Ranzinger", "orcid": "0000-0003-3147-448X" }, "description": "GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data.", "example": "G00054MO", "homepage": "https://glytoucan.org", "keywords": [ "glycomics", "structural biology" ], "mappings": { "biocontext": "GLYTOUCAN", "fairsharing": "FAIRsharing.5Pze7l", "integbio": "nbdc02434", "miriam": "glytoucan", "n2t": "glytoucan", "re3data": "r3d100012388", "togoid": "Glytoucan", "uniprot": "DB-0254" }, "name": "GlyTouCan", "pattern": "^G[0-9]{5}[A-Z]{2}$", "preferred_prefix": "glytoucan", "providers": [ { "code": "glygen", "description": "GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data. ", "homepage": "https://www.glygen.org/", "name": "GlyGen", "uri_format": "https://glygen.org/glycan/$1" } ], "publications": [ { "doi": "10.1093/glycob/cwz080", "pubmed": "31616925" }, { "doi": "10.1093/glycob/cwx066", "pmc": "PMC5881658", "pubmed": "28922742", "title": "GlyTouCan: an accessible glycan structure repository", "year": 2017 }, { "doi": "10.1093/nar/gkv1041", "pmc": "PMC4702779", "pubmed": "26476458", "title": "GlyTouCan 1.0--The international glycan structure repository", "year": 2015 } ], "synonyms": [ "glygen" ], "twitter": "glytoucan", "uri_format": "https://glytoucan.org/Structures/Glycans/$1" }, "gmd": { "contact": { "email": "kopka@mpimp-golm.mpg.de", "name": "Joachim Kopka", "orcid": "0000-0001-9675-4883" }, "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena.", "example": "68513255-fc44-4041-bc4b-4fd2fae7541d", "homepage": "http://gmd.mpimp-golm.mpg.de/", "keywords": [ "life science", "metabolomics" ], "mappings": { "biocontext": "GMD", "fairsharing": "FAIRsharing.jykmkw", "miriam": "gmd", "n2t": "gmd", "re3data": "r3d100011046" }, "name": "Golm Metabolome Database", "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", "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/$1" }, "gmelin": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Gmelin database is a large database of organometallic and inorganic compounds updated quarterly. It is based on the German publication Gmelins Handbuch der anorganischen Chemie which was originally published by Leopold Gmelin in 1817; the last print edition, the 8th, appeared in the 1990s.", "example": "1466", "example_extras": [ "606" ], "homepage": "https://link.springer.com/bookseries/562", "mappings": { "edam": "1004", "wikidata": "P1578" }, "name": "Gmelins Handbuch der anorganischen Chemie", "pattern": "^[1-9][0-9]{2,6}$", "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": "2025-01-28" }, "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": [ "DUP_2_5708", "M-8602-T-C" ], "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": "2024-11-03" }, "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", "part_of": "go", "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": "https://geneontology.org/go-cam", "mappings": { "go": "gomodel" }, "name": "Gene Ontology Causal Activity Model", "part_of": "go", "preferred_prefix": "go.model", "providers": [ { "code": "legacy", "description": "This was the old URI for the GO CAM editor", "homepage": "https://model.geneontology.org", "name": "Legacy", "uri_format": "http://noctua.geneontology.org/editor/graph/gomodel:$1" } ], "uri_format": "https://model.geneontology.org/$1" }, "go.ref": { "banana": "GO_REF", "description": "The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of \"GO content\" meetings at which substantial changes in the ontologies are discussed and made.", "example": "0000041", "homepage": "https://geneontology.org/gorefs", "mappings": { "biocontext": "GO_REF", "go": "GO_REF", "miriam": "go_ref", "n2t": "go.ref" }, "name": "Gene Ontology Database references", "namespace_in_lui": true, "part_of": "go", "pattern": "^\\d{7}$", "preferred_prefix": "go.ref", "providers": [ { "code": "legacy", "description": "The README file on GO's github repository has been replaced with a structured YAML file, so this URl is no longer available.", "homepage": "https://github.com/geneontology/go-site/blob/master/metadata/gorefs.yaml", "name": "Legacy", "uri_format": "https://github.com/geneontology/go-site/blob/master/metadata/gorefs/README.md#goref$1" } ], "uri_format": "https://geneontology.org/GO_REF/$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": "https://raw.githubusercontent.com/geneontology/go-site/master/metadata/db-xrefs.yaml", "name": "Gene Ontology Registry", "part_of": "go", "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-$1.md" }, "goa": { "contact": { "email": "r.huntley@ucl.ac.uk", "github": "rachhuntley", "name": "Rachael P. Huntley", "orcid": "0000-0001-6718-3559" }, "description": "The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups.", "example": "P12345", "homepage": "https://www.ebi.ac.uk/GOA/", "keywords": [ "biology", "gene", "life science", "ontology", "protein" ], "mappings": { "biocontext": "GOA", "fairsharing": "FAIRsharing.7zffgc", "integbio": "nbdc00468", "miriam": "goa", "n2t": "goa", "ncbi": "GOA", "prefixcommons": "goa" }, "name": "Gene Ontology Annotation Database", "part_of": "go", "pattern": "^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$", "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=$1" }, "goche": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Represent chemical entities having particular CHEBI roles", "download_owl": "https://raw.githubusercontent.com/geneontology/go-ontology/master/src/ontology/imports/chebi_roles.owl", "example": "25512", "homepage": "https://github.com/geneontology/go-ontology", "keywords": [ "ontology" ], "name": "GO Chemicals", "part_of": "go", "pattern": "^\\d+$", "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/$1" }, "goeco": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A GO annotation is a statement about the function of a particular gene. Each annotation includes an evidence code to indicate how the annotation to a particular term is supported.", "example": "IPI", "homepage": "http://geneontology.org/docs/guide-go-evidence-codes/", "name": "GO Evidence Code", "part_of": "go", "preferred_prefix": "goeco" }, "gold": { "contact": { "email": "tbreddy@lbl.gov", "github": "TBKReddy", "name": "TBK Reddy", "orcid": "0000-0002-0871-5567" }, "description": "The Genomes OnLine Database (GOLD) catalogues genome and metagenome sequencing projects from around the world, along with their associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project.", "example": "Gs0000008", "homepage": "https://gold.jgi.doe.gov/", "keywords": [ "genome", "genomics", "metabolomics", "metagenomics", "ontology and terminology", "phylogenetics" ], "mappings": { "fairsharing": "FAIRsharing.5q1p14", "integbio": "nbdc00483", "miriam": "gold", "prefixcommons": "gold", "re3data": "r3d100010808" }, "name": "Genomes Online Database", "pattern": "^[A-Z][a-z][0-9]+$", "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/gkae1000", "pubmed": "39498478", "title": "Genomes OnLine Database (GOLD) v.10: new features and updates", "year": 2024 }, { "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", "providers": [ { "code": "goldbook.html", "description": "This appears in REX", "homepage": "http://goldbook.iupac.org", "name": "GoldBook direct", "uri_format": "http://goldbook.iupac.org/$1.html" } ], "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", "providers": [ { "code": "alt1", "description": "Alternate URL 1", "homepage": "https://books.google.com", "name": "Alternate URL 1", "uri_format": "https://books.google.com/books/?id=$1" } ], "uri_format": "https://books.google.com/books?id=$1" }, "google.patent": { "contributor_extras": [ { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. 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You can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites.", "example": "PjrpzUIAAAAJ", "homepage": "https://scholar.google.com/", "mappings": { "biolink": "GSID", "wikidata": "P1960" }, "name": "Google Scholar Researcher", "pattern": "^[-_0-9A-Za-z]{12}$", "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. 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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 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}$", "preferred_prefix": "GRO", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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This datatype refers to proteins in Gramene.", "example": "78073", "homepage": "http://www.gramene.org/", "mappings": { "biocontext": "GRAMENE.PROTEIN", "go": "GR_PROTEIN", "miriam": "gramene.protein", "n2t": "gramene.protein" }, "name": "Gramene protein", "pattern": "^\\d+$", "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/$1" }, "greengenes": { "contact": { "email": "GLAndersen@lbl.gov", "name": "Gary L Andersen", "orcid": "0000-0002-1618-9827" }, "deprecated": true, "description": "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.", "example": "100000", "homepage": "http://greengenes.lbl.gov/", "keywords": [ "genetics", "life science", "rna" ], "mappings": { "biocontext": "GREENGENES", "fairsharing": "FAIRsharing.bpxgb6", "integbio": "nbdc01824", "miriam": "greengenes", "n2t": "greengenes", "ncbi": "Greengenes", "prefixcommons": "greengenes", "re3data": "r3d100010549" }, "name": "16S rRNA gene database", "pattern": "^\\d+$", "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. 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/greengenes:$1" } ], "publications": [ { "doi": "10.1128/aem.03006-05", "pmc": "PMC1489311", "pubmed": "16820507", "title": "Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB", "year": 2006 }, { "doi": "10.1128/AEM.03006-05", "title": "Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB." } ], "uri_format": "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1" }, "grid": { "description": "International coverage of the world's leading research organisations, indexing 92% of funding allocated globally.", "example": "grid.225360.0", "homepage": "https://www.grid.ac/", "keywords": [ "data management" ], "mappings": { "biocontext": "GRID", "fairsharing": "FAIRsharing.0pUMYW", "miriam": "grid", "n2t": "grid" }, "name": "Global Research Identifier Database", "pattern": "^grid\\.[0-9]+\\.[a-f0-9]{1,2}$", "preferred_prefix": "grid", "twitter": "grid_ac", "uri_format": "https://www.grid.ac/institutes/$1" }, "grin": { "description": "GRIN provides National Genetic Resources Program (NGRP) personnel and germplasm users continuous access to databases for the maintenance of passport, characterization, evaluation, inventory, and distribution data important for the effective management and utilization of national germplasm collections.", "example": "159787", "homepage": "http://www.ars-grin.gov/", "keywords": [ "life science" ], "mappings": { "fairsharing": "FAIRsharing.3axym7", "prefixcommons": "grin" }, "name": "Germplasm Resources Information Network", "preferred_prefix": "grin", "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/grin:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.ars.usda.gov/research/publications/publications.htm?seq_no_115=$1" }, "grin.taxonomy": { "description": "GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact.", "example": "19333", "homepage": "http://www.ars-grin.gov/", "mappings": { "biocontext": "GRIN.TAXONOMY", "go": "GRIN", "miriam": "grin.taxonomy", "n2t": "grin.taxonomy", "ncbi": "GRIN", "wikidata": "P1421" }, "name": "GRIN URL", "pattern": "^\\d+$", "preferred_prefix": "grin.taxonomy", "uri_format": "https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomydetail.aspx?id=$1" }, "gro": { "contact": { "email": "vlee@ebi.ac.uk", "name": "Vivian Lee" }, "deprecated": true, "description": "The Gene Regulation Ontology (GRO) is a conceptual model for the domain of gene regulation. 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The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank.", "example": "10142", "homepage": "http://bioinformatics.ramapo.edu/GRSDB2/", "keywords": [ "dna", "rna" ], "mappings": { "biocontext": "GRSDB", "miriam": "grsdb", "n2t": "grsdb", "prefixcommons": "grsdb" }, "name": "G-Rich Sequences Database", "pattern": "^\\d+$", "preferred_prefix": "grsdb", "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/grsdb:$1" } ], "uri_format": "http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1" }, "gsfa": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The \"Codex General Standard for Food Additives\" (GSFA, Codex STAN 192-1995) sets forth the conditions under which permitted food additives may be used in all foods, whether or not they have previously been standardized by Codex. The Preamble of the GSFA contains additional information for interpreting the data. Users are encouraged to consult the Preamble when using this database.", "example": "174", "homepage": "http://www.fao.org/gsfaonline", "name": "General Standard for Food Additives Online Database", "pattern": "^\\d+$", "preferred_prefix": "gsfa", "synonyms": [ "FAO/WHO_standards" ], "uri_format": "http://www.fao.org/gsfaonline/additives/details.html?id=$1" }, "gsso": { "appears_in": [ "ontoavida", "scdo" ], "banana": "GSSO", "contact": { "email": "kronkcj@mail.uc.edu", "github": "Superraptor", "name": "Clair Kronk", "orcid": "0000-0001-8397-8810" }, "description": "The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment. A large focus of the ontology is its consideration of LGBTQIA+ terminology.", "download_json": "http://purl.obolibrary.org/obo/gsso.json", "download_obo": "http://purl.obolibrary.org/obo/gsso.obo", "download_owl": "http://purl.obolibrary.org/obo/gsso.owl", "example": "002368", "homepage": "https://gsso.research.cchmc.org/", "keywords": [ "obo", "ontology" ], "license": "Apache 2.0 License", "mappings": { "aberowl": "GSSO", "bioportal": "GSSO", "miriam": "gsso", "obofoundry": "gsso", "ols": "gsso", "ontobee": "GSSO" }, "name": "Gender, Sex, and Sexual Orientation Ontology", "namespace_in_lui": true, "pattern": "^\\d{6}$", "preferred_prefix": "GSSO", "rdf_uri_format": "http://purl.obolibrary.org/obo/GSSO_$1", "repository": "https://github.com/Superraptor/GSSO", "uri_format": "http://purl.obolibrary.org/obo/GSSO_$1", "version": "2.0.5" }, "gtdb": { "contact": { "email": "donovan.parks@gmail.com", "github": "donovan-h-parks", "name": "Donovan Parks", "orcid": "0000-0001-6662-9010" }, "contributor": { "email": "aireland@lbl.gov", "github": "ialarmedalien", "name": "AJ Ireland", "orcid": "0000-0003-1982-9065" }, "description": "The Genome Taxonomy Database (GTDB) is an initiative to establish a standardized microbial taxonomy based on genome phylogeny.", "example": "g__Prochlorococcus_A", "github_request_issue": 1242, "homepage": "https://gtdb.ecogenomic.org", "license": "CC-BY-SA-4.0", "mappings": { "pathguide": "190" }, "name": "Genome Taxonomy Database", "pattern": "^[cdfgops]__\\w+\\S+$", "preferred_prefix": "gtdb", "publications": [ { "doi": "10.1093/nar/gkab776", "pmc": "PMC8728215", "pubmed": "34520557", "title": "GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy", "year": 2021 }, { "doi": "10.1038/s41564-021-00918-8", "pubmed": "34155373", "title": "A standardized archaeal taxonomy for the Genome Taxonomy Database", "year": 2021 }, { "doi": "10.1038/s41587-020-0501-8", "pubmed": "32341564", "title": "A complete domain-to-species taxonomy for Bacteria and Archaea", "year": 2020 }, { "doi": "10.1038/nbt.4229", "pubmed": "30148503", "title": "A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life", "year": 2018 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://gtdb.ecogenomic.org/tree?r=$1" }, "gtex": { "description": "The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation.", "example": "BRIP1", "homepage": "https://www.gtexportal.org", "mappings": { "biocontext": "GTEX", "biolink": "GTEx", "miriam": "gtex", "n2t": "gtex" }, "name": "Genotype-Tissue Expression", "pattern": "^\\w.+$", "preferred_prefix": "gtex", "uri_format": "https://www.gtexportal.org/home/gene/$1" }, "gtr": { "appears_in": [ "mondo" ], "comment": "Identifiers appearing in MONDO don't match any of the resources apparent endpoints", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Genetic Testing Registry (GTR®) provides a central location for voluntary submission of genetic test information by providers. The scope includes the test's purpose, methodology, validity, evidence of the test's usefulness, and laboratory contacts and credentials. The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease", "example": "AN0097748", "homepage": "https://www.ncbi.nlm.nih.gov/gtr/", "name": "Genetic Testing Registry", "preferred_prefix": "gtr", "synonyms": [ "medgen.gtr" ], "uri_format": "https://www.ncbi.nlm.nih.gov/gtr/conditions/$1" }, "gudmap": { "contact": { "email": "simon.harding@ed.ac.uk", "github": "simondharding", "name": "Simon Douglas Harding", "orcid": "0000-0002-9262-8318" }, "description": "The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract.", "example": "Q-2958", "homepage": "http://www.gudmap.org/", "keywords": [ "cell biology", "developmental biology", "genomics", "molecular biology" ], "mappings": { "biocontext": "GUDMAP", "fairsharing": "FAIRsharing.910c39", "miriam": "gudmap", "n2t": "gudmap", "re3data": "r3d100012193" }, "name": "Genitourinary Development Molecular Anatomy Project", "pattern": "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$", "preferred_prefix": "gudmap", "publications": [ { "doi": "10.1242/dev.063594", "pmc": "PMC3188593", "pubmed": "21652655", "title": "The GUDMAP database--an online resource for genitourinary research", "year": 2011 }, { "doi": "10.1681/asn.2007101078", "pubmed": "18287559", "title": "GUDMAP: the genitourinary developmental molecular anatomy project", "year": 2008 }, { "doi": "10.1681/ASN.2007101078", "title": "GUDMAP: the genitourinary developmental molecular anatomy project." } ], "twitter": "GUDMAP", "uri_format": "https://gudmap.org/id/$1" }, "gwascentral.marker": { "description": "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker.", "example": "HGVM15354", "homepage": "https://www.gwascentral.org/markers", "mappings": { "biocontext": "GWASCENTRAL.MARKER", "miriam": "gwascentral.marker", "n2t": "gwascentral.marker" }, "name": "GWAS Central Marker", "pattern": "^HGVM\\d+$", "preferred_prefix": "gwascentral.marker", "uri_format": "https://www.gwascentral.org/marker/$1" }, "gwascentral.phenotype": { "description": "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Phenotype.", "example": "HGVPM623", "homepage": "https://www.gwascentral.org/phenotypes", "mappings": { "biocontext": "GWASCENTRAL.PHENOTYPE", "miriam": "gwascentral.phenotype", "n2t": "gwascentral.phenotype" }, "name": "GWAS Central Phenotype", "pattern": "^HGVPM\\d+$", "preferred_prefix": "gwascentral.phenotype", "uri_format": "https://www.gwascentral.org/phenotype/$1" }, "gwascentral.study": { "deprecated": true, "description": "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study.", "example": "HGVST1828", "homepage": "https://www.gwascentral.org/studies", "keywords": [ "gene", "genome" ], "mappings": { "biocontext": "GWASCENTRAL.STUDY", "miriam": "gwascentral.study", "n2t": "gwascentral.study", "prefixcommons": "hgvbase" }, "name": "GWAS Central Study", "pattern": "^HGVST\\d+$", "preferred_prefix": "gwascentral.study", "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/hgvbase:$1" } ], "uri_format": "https://www.gwascentral.org/study/$1" }, "gxa.expt": { "description": "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments.", "example": "E-MTAB-2037", "homepage": "https://www.ebi.ac.uk/gxa/", "mappings": { "biocontext": "GXA.EXPT", "miriam": "gxa.expt", "n2t": "gxa.expt" }, "name": "GXA Expt", "owners": [ { "name": "European Bioinformatics Institute", "partnered": false, "ror": "02catss52" } ], "pattern": "^[AEP]-\\w{4}-\\d+$", "preferred_prefix": "gxa.expt", "providers": [ { "code": "omicsdi", "description": "GXA Expt through OmicsDI", "homepage": "https://www.omicsdi.org/", "name": "GXA Expt through OmicsDI", "uri_format": "https://www.omicsdi.org/dataset/atlas-experiments/$1" } ], "uri_format": "https://www.ebi.ac.uk/gxa/experiments/$1" }, "gxa.gene": { "description": "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes.", "example": "AT4G01080", "homepage": "https://www.ebi.ac.uk/gxa/", "mappings": { "biocontext": "GXA.GENE", "miriam": "gxa.gene", "n2t": "gxa.gene" }, "name": "GXA Gene", "owners": [ { "name": "European Bioinformatics Institute", "partnered": false, "ror": "02catss52" } ], "pattern": "^\\w+$", "preferred_prefix": "gxa.gene", "uri_format": "https://www.ebi.ac.uk/gxa/genes/$1" }, "habronattus": { "contact": { "email": "peteremidford@yahoo.com", "name": "Peter Midford", "orcid": "0000-0001-6512-3296" }, "deprecated": true, "homepage": "http://www.mesquiteproject.org/ontology/Habronattus/index.html", "keywords": [ "obo", "ontology" ], "mappings": { "biocontext": "HABRONATTUS", "obofoundry": "habronattus" }, "name": "Habronattus courtship", "preferred_prefix": "HABRONATTUS", "rdf_uri_format": "http://purl.obolibrary.org/obo/HABRONATTUS_$1", "uri_format": "http://purl.obolibrary.org/obo/HABRONATTUS_$1" }, "hagr.genage": { "contact": { "email": "jp@senescence.info", "name": "Joao Pedro de Magalhaes", "orcid": "0000-0002-6363-2465" }, "description": "GenAge is a database of human and model organism genes related to longevity and aging, maintained by the Human Ageing Genomics Resources (HAGR) group.", "example": "0001", "homepage": "http://genomics.senescence.info/genes/", "keywords": [ "aging", "genes", "longevity" ], "mappings": { "prefixcommons": "genage" }, "name": "The Ageing Gene Database", "preferred_prefix": "hagr.genage", "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/genage:$1" } ], "publications": [ { "doi": "10.1093/nar/gks1155", "pmc": "PMC3531213", "pubmed": "23193293", "title": "Human Ageing Genomic Resources: integrated databases and tools for the biology and genetics of ageing", "year": 2012 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://genomics.senescence.info/genes/details.php?id=$1" }, "hagr.gendr": { "contact": { "email": "jp@senescence.info", "name": "Joao Pedro de Magalhaes", "orcid": "0000-0002-6363-2465" }, "description": "GenDR is a database of genes associated with dietary restriction (DR). GenDR includes two datasets: 1) genes inferred from experiments in model organisms in which genetic manipulations cancel out or disrupt the life-extending effects of DR; 2) genes robustly altered due to DR, derived from a meta-analysis of microarray DR studies in mammals", "example": "2", "homepage": "http://genomics.senescence.info/diet/", "keywords": [ "aging", "dietary restriction", "genes", "longevity" ], "mappings": { "prefixcommons": "gendr" }, "name": "The Dietary Restriction Gene Database", "preferred_prefix": "hagr.gendr", "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/gendr:$1" } ], "publications": [ { "doi": "10.1371/journal.pgen.1002834", "pmc": "PMC3415404", "pubmed": "22912585", "title": "Dissecting the gene network of dietary restriction to identify evolutionarily conserved pathways and new functional genes", "year": 2012 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://genomics.senescence.info/diet/details.php?id=$1" }, "hamap": { "contact": { "email": "alan.bridge@isb-sib.ch", "name": "Alan Bridge", "orcid": "0000-0003-2148-9135" }, "description": "HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries.", "example": "MF_01400", "homepage": "https://hamap.expasy.org/", "keywords": [ "life science", "protein" ], "mappings": { "biocontext": "HAMAP", "edam": "2766", "fairsharing": "FAIRsharing.63m4ss", "go": "HAMAP", "miriam": "hamap", "n2t": "hamap", "prefixcommons": "hamap", "uniprot": "DB-0041" }, "name": "High-quality Automated and Manual Annotation of microbial Proteomes", "pattern": "^MF_\\d+$", "preferred_prefix": "hamap", "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/hamap:$1" } ], "publications": [ { "doi": "10.1093/nar/gku1002", "pmc": "PMC4383873", "pubmed": "25348399", "title": "HAMAP in 2015: updates to the protein family classification and annotation system", "year": 2014 }, { "doi": "10.1093/nar/gks1157", "pmc": "PMC3531088", "pubmed": "23193261", "title": "HAMAP in 2013, new developments in the protein family classification and annotation system", "year": 2012 } ], "uri_format": "https://hamap.expasy.org/unirule/$1" }, "hancestro": { "contact": { "email": "dwelter.ontologist@gmail.com", "github": "daniwelter", "name": "Danielle Welter", "orcid": "0000-0003-1058-2668" }, "description": "Human ancestry ontology for the NHGRI GWAS Catalog", "download_owl": "http://purl.obolibrary.org/obo/hancestro.owl", "example": "0290", "homepage": "https://ebispot.github.io/hancestro/", "keywords": [ "demographics", "genome-wide association study", "human genetics", "obo", "ontology", "population genetics" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "HANCESTRO", "biolink": "HANCESTRO", "bioportal": "HANCESTRO", "fairsharing": "FAIRsharing.rja8qp", "obofoundry": "hancestro", "ols": "hancestro", "ontobee": "HANCESTRO" }, "name": "Human Ancestry Ontology", "owners": [ { "name": "European Bioinformatics Institute", "partnered": false, "ror": "02catss52" } ], "pattern": "^\\d{4}$", "preferred_prefix": "HANCESTRO", "providers": [ { "code": "legacy", "description": "Legacy URI", "homepage": "http://www.ebi.ac.uk/ancestro", "name": "Legacy", "uri_format": "http://www.ebi.ac.uk/ancestro/ancestro_$1" } ], "publications": [ { "doi": "10.1186/s13059-018-1396-2", "pmc": "PMC5815218", "pubmed": "29448949", "title": "A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog", "year": 2018 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/HANCESTRO_$1", "repository": "https://github.com/EBISPOT/ancestro", "uri_format": "http://purl.obolibrary.org/obo/HANCESTRO_$1", "version": "2025-02-24" }, "hao": { "contact": { "email": "diapriid@gmail.com", "github": "mjy", "name": "Matt Yoder", "orcid": "0000-0002-5640-5491" }, "description": "A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)", "download_obo": "http://purl.obolibrary.org/obo/hao.obo", "download_owl": "http://purl.obolibrary.org/obo/hao.owl", "example": "0000187", "homepage": "http://hymao.org", "keywords": [ "anatomy", "image", "life science", "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "HAO", "biocontext": "HAO", "bioportal": "HAO", "fairsharing": "FAIRsharing.kj3m5n", "obofoundry": "hao", "ols": "hao", "ontobee": "HAO" }, "name": "Hymenoptera Anatomy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "HAO", "publications": [ { "doi": "10.1371/journal.pone.0015991", "pmc": "PMC3012123", "pubmed": "21209921", "title": "A gross anatomy ontology for hymenoptera", "year": 2010 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/HAO_$1", "repository": "https://github.com/hymao/hao", "uri_format": "http://purl.obolibrary.org/obo/HAO_$1", "version": "2023-06-01" }, "hao.ref": { "contact": { "email": "diapriid@gmail.com", "github": "mjy", "name": "Matt Yoder", "orcid": "0000-0002-5640-5491" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Literature references in the Hymenoptera Anatomy Ontology Portal", "example": "98127", "github_request_issue": 1322, "homepage": "http://hymao.org", "name": "Hymenoptera Anatomy Reference", "pattern": "^\\d+$", "preferred_prefix": "hao.ref", "uri_format": "http://api.hymao.org/api/ref/$1" }, "hathitrust": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Hathitrust is a partnership of academic and research institutions, offering a collection of millions of titles digitized from libraries around the world.", "example": "008893080", "github_request_issue": 510, "homepage": "https://www.hathitrust.org", "name": "Hathi Trust Digital Library", "pattern": "^\\d+$", "preferred_prefix": "hathitrust", "uri_format": "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", "providers": [ { "code": "biopragmatics", "description": "A static site generated for the HBA resource", "homepage": "https://biopragmatics.github.io/providers", "name": "Biopragmatics Browser", "uri_format": "https://biopragmatics.github.io/providers/hba/$1" } ], "uri_format": "https://purl.brain-bican.org/ontology/hbao/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 Thalassemias", "preferred_prefix": "hbvar", "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/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/$1" }, "hcvdb": { "description": "the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses.", "example": "M58335", "homepage": "https://euhcvdb.lyon.inserm.fr", "keywords": [ "gene" ], "mappings": { "biocontext": "HCVDB", "miriam": "hcvdb", "n2t": "hcvdb", "prefixcommons": "hcv" }, "name": "Hepatitis C Virus Database Project", "pattern": "^M\\d{5}$", "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.lyon.inserm.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1" }, "hdl": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Welcome to the web site of the Handle.Net Registry (HNR), run by Corporation for National Research Initiatives (CNRI). CNRI is a Multi-Primary Administrator (MPA) of the Global Handle Registry (GHR), authorized by the DONA Foundation to allot prefixes to users of the Handle System. The DONA Foundation is a non-profit organization based in Geneva that has taken over responsibility for the evolution of CNRI's Digital Object (DO) Architecture including outreach around the world. One of the Foundation's responsibilities is to administer and maintain the overall operation of the GHR, a task that was previously performed by CNRI. (from website)", "example": "2381/12775", "example_extras": [ "391/00-0000-0000-0009-3C7E-F" ], "homepage": "https://www.handle.net/", "keywords": [ "centrally registered identifier", "omics", "subject agnostic" ], "mappings": { "fairsharing": "FAIRsharing.0b7e54" }, "name": "Handle", "pattern": "^\\d+/.+$", "preferred_prefix": "hdl", "synonyms": [ "handle" ], "uri_format": "http://hdl.handle.net/$1" }, "hdr": { "deprecated": true, "description": "The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders.", "example": "63", "homepage": "http://research.nhgri.nih.gov/apps/homeodomain/web/", "keywords": [ "genome" ], "mappings": { "biocontext": "HDR", "miriam": "hdr", "n2t": "hdr", "pathguide": "307", "prefixcommons": "hdr" }, "name": "Homeodomain Research", "pattern": "^\\d+$", "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_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=$1" }, "hgnc": { "contact": { "email": "elspeth@genenames.org", "name": "Elspeth Bruford", "orcid": "0000-0002-8380-5247" }, "description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database.", "download_owl": "http://aber-owl.net/media/ontologies/HGNC/2/hgnc.owl", "example": "16793", "homepage": "http://www.genenames.org", "keywords": [ "classification", "gene", "gene name", "life science", "non-coding rna", "ontology", "protein", "pseudogene" ], "license": "CC0-1.0", "logo": "https://www.genenames.org/img/hgnc/logo/hgnc-logo-dark-bckgrnd-large.svg", "mappings": { "aberowl": "HGNC", "bartoc": "20688", "biocontext": "HGNC", "bioportal": "HGNC", "cellosaurus": "HGNC", "edam": "2298", "fairsharing": "FAIRsharing.amcv1e", "go": "HGNC", "hl7": "2.16.840.1.113883.6.281", "miriam": "hgnc", "n2t": "hgnc", "ncbi": "HGNC", "prefixcommons": "hgnc", "togoid": "Hgnc", "uniprot": "DB-0042", "wikidata": "P354" }, "name": "HUGO Gene Nomenclature Committee", "pattern": "^\\d{1,5}$", "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", "publications": [ { "doi": "10.15252/msb.202211325", "pmc": "PMC10167483", "pubmed": "36938926", "title": "Automated assembly of molecular mechanisms at scale from text mining and curated databases", "year": 2023 }, { "doi": "10.15252/msb.20177651", "pmc": "PMC5731347", "pubmed": "29175850", "title": "From word models to executable models of signaling networks using automated assembly", "year": 2017 } ], "uri_format": "https://db.indra.bio/statements/from_agents?&format=html&agent0=$1@HGNC" } ], "publications": [ { "doi": "10.15252/msb.202211325", "pmc": "PMC10167483", "pubmed": "36938926", "title": "Automated assembly of molecular mechanisms at scale from text mining and curated databases", "year": 2023 }, { "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 }, { "doi": "10.15252/msb.20177651", "pmc": "PMC5731347", "pubmed": "29175850", "title": "From word models to executable models of signaling networks using automated assembly", "year": 2017 } ], "uri_format": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1" }, "hgnc.genefamily": { "description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families.", "example": "2029", "has_canonical": "hgnc.genegroup", "homepage": "http://www.genenames.org", "license": "CC0-1.0", "mappings": { "biocontext": "HGNC.GENEFAMILY", "miriam": "hgnc.genefamily", "n2t": "hgnc.genefamily" }, "name": "HGNC gene family", "pattern": "^\\d+$", "preferred_prefix": "hgnc.genefamily", "synonyms": [ "GFAM", "HGNC_GROUP", "hgnc.family" ], "uri_format": "https://www.genenames.org/cgi-bin/genefamilies/set/$1" }, "hgnc.genegroup": { "description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families.", "example": "141", "homepage": "https://www.genenames.org", "license": "CC0-1.0", "mappings": { "miriam": "hgnc.genegroup" }, "name": "HGNC Gene Group", "pattern": "^\\d+$", "preferred_prefix": "hgnc.genegroup", "uri_format": "https://www.genenames.org/data/genegroup/#!/group/$1" }, "hgnc.symbol": { "description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol.", "example": "DAPK1", "homepage": "https://www.genenames.org/", "license": "CC0-1.0", "mappings": { "biocontext": "HGNC.SYMBOL", "miriam": "hgnc.symbol", "n2t": "hgnc.symbol", "togoid": "HgncSymbol", "wikidata": "P353" }, "name": "HGNC gene symbol", "pattern": "^[A-Za-z-0-9_]+(\\@)?$", "preferred_prefix": "hgnc.symbol", "providers": [ { "code": "cbgda", "description": "A database of key host genes involved in the pathogenesis of different diseases identified through genome-wide CRISPR screens", "homepage": "http://cbgda.zhounan.org/main", "name": "CRISPR Based Gene-Disease Associations", "publications": [ { "doi": "10.1093/database/baae077", "pmc": "PMC11363955", "pubmed": "39213392", "title": "CBGDA: a manually curated resource for gene-disease associations based on genome-wide CRISPR", "year": 2024 } ], "uri_format": "http://cbgda.zhounan.org/geneinfo?gene=$1" }, { "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": "g2p", "description": "A resource for linking genetic screening outputs to protein sequences and structures", "homepage": "https://g2p.broadinstitute.org/", "name": "Genomics 2 Proteins Portal", "publications": [ { "doi": "10.1038/s41592-024-02409-0", "pmc": "PMC11466821", "pubmed": "39294369", "title": "Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures", "year": 2024 } ], "uri_format": "https://g2p.broadinstitute.org/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" } ], "publications": [ { "doi": "10.1038/s41592-024-02409-0", "pmc": "PMC11466821", "pubmed": "39294369", "title": "Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures", "year": 2024 }, { "doi": "10.1093/database/baae077", "pmc": "PMC11363955", "pubmed": "39213392", "title": "CBGDA: a manually curated resource for gene-disease associations based on genome-wide CRISPR", "year": 2024 } ], "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": [ "GRCh38(chr11):g.112088970del", "NC_000011.10(NM_001276503.2):c.169+998del", "NC_000011.10:g.112088970del", "NG_012337.3(NM_003002.4):c.274G>T", "NG_012337.3(NM_003002.4):r.(274g>u)" ], "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=$1" }, "hinv.locus": { "deprecated": true, "description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view.", "example": "HIX0004394", "homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp", "mappings": { "biocontext": "HINV.LOCUS", "miriam": "hinv.locus", "n2t": "hinv.locus" }, "name": "H-InvDb Locus", "pattern": "^HIX\\d{7}(\\.\\d+)?$", "preferred_prefix": "hinv.locus", "uri_format": "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1" }, "hinv.protein": { "deprecated": true, "description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view.", "example": "HIP000030660", "homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp", "mappings": { "biocontext": "HINV.PROTEIN", "miriam": "hinv.protein", "n2t": "hinv.protein" }, "name": "H-InvDb Protein", "pattern": "^HIP\\d{9}(\\.\\d+)?$", "preferred_prefix": "hinv.protein", "uri_format": "http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1" }, "hinv.transcript": { "deprecated": true, "description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view.", "example": "HIT000195363", "homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp", "mappings": { "biocontext": "HINV.TRANSCRIPT", "miriam": "hinv.transcript", "n2t": "hinv.transcript" }, "name": "H-InvDb Transcript", "pattern": "^HIT\\d{9}(\\.\\d+)?$", "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/$1" }, "hogenom": { "contact": { "email": "perriere@biomserv.univ-lyon1.fr", "name": "Guy Perrière", "orcid": "0000-0002-6850-6265" }, "description": "HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier.", "example": "HOMO_3.PE998", "homepage": "http://hogenom.univ-lyon1.fr/", "keywords": [ "classification", "life science", "phylogenetics", "phylogeny", "sequence" ], "mappings": { "biocontext": "HOGENOM", "fairsharing": "FAIRsharing.qe8tz8", "integbio": "nbdc01858", "miriam": "hogenom", "n2t": "hogenom", "prefixcommons": "hogenom", "uniprot": "DB-0044" }, "name": "Database of Complete Genome Homologous Genes Families", "pattern": "^[\\w\\.]+$", "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://hogenom.univ-lyon1.fr/query_sequence?Go=Submit+Query&seq=$1" }, "hoip": { "comment": "The ontology file was deleted in https://github.com/yuki-yamagata/hoip/commit/73fcfa114d71a76a984a9ce1166e50d7ebafe158, making it impossible to link to the ontology afterwards.", "contact": { "email": "yuki.yamagata@riken.jp", "github": "yuki-yamagata", "name": "Yuki Yamagata", "orcid": "0000-0002-9673-1283" }, "contributor": { "email": "j.harry.caufield@gmail.com", "github": "caufieldjh", "name": "Harry Caufield", "orcid": "0000-0001-5705-7831" }, "description": "An ontology of processes triggered by homeostatic imbalance, with a focus on COVID-19 infectious processes.", "download_owl": "https://github.com/yuki-yamagata/hoip/blob/c70ae6d4868ca951d075cec409e863fa4abe19b2/hoip_0308.owl", "example": "0040379", "github_request_issue": 668, "homepage": "https://knowledge.brc.riken.jp/bioresource/ontology/HOIP", "keywords": [ "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "HOIP", "bioportal": "HOIP" }, "name": "Homeostasis imbalance process ontology", "pattern": "^\\d{7}$", "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_$1" }, "holofood.animal": { "contact": { "email": "tgilbert@sund.ku.dk", "name": "Tom Gilbert", "orcid": "0000-0002-5805-7195" }, "contributor": { "email": "palayoor.n@northeastern.edu", "github": "nalikapalayoor", "name": "Nalika Palayoor", "orcid": "0009-0008-8406-631X" }, "description": "The HoloFood Data Portal centralizes access to datasets from the HoloFood project, which explores host microbiota interactions in salmon and chicken production. It links phenotypic data with microbiome samples and derived genomic resources and therefore simplifies data integration, supporting researchers in multiomics and microbiome studies. The identifiers in the animal semantic space correspond to animals that samples in the database are obtained from.", "example": "SAMEA112904733", "github_request_issue": 1400, "homepage": "https://www.holofooddata.org", "name": "HoloFood animal", "pattern": "^SAMEA\\d{9}$", "preferred_prefix": "holofood.animal", "publications": [ { "doi": "10.1093/database/baae112", "pmc": "PMC11724189", "pubmed": "39797569", "title": "HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production", "year": 2025 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://www.holofooddata.org/animal/$1" }, "holofood.sample": { "contact": { "email": "tgilbert@sund.ku.dk", "name": "Tom Gilbert", "orcid": "0000-0002-5805-7195" }, "contributor": { "email": "palayoor.n@northeastern.edu", "github": "nalikapalayoor", "name": "Nalika Palayoor", "orcid": "0009-0008-8406-631X" }, "description": "The HoloFood Data Portal centralizes access to datasets from the HoloFood project, which explores host microbiota interactions in salmon and chicken production. It links phenotypic data with microbiome samples and derived genomic resources and therefore simplifies data integration, supporting researchers in multiomics and microbiome studies. The identifiers in the samples semantic space represent samples derived from animals in HoloFood trials.", "example": "SAMEA10104908", "github_request_issue": 1400, "homepage": "https://www.holofooddata.org", "name": "HoloFood sample", "pattern": "^SAMEA\\d{8}$", "preferred_prefix": "holofood.sample", "publications": [ { "doi": "10.1093/database/baae112", "pmc": "PMC11724189", "pubmed": "39797569", "title": "HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production", "year": 2025 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://www.holofooddata.org/sample/$1" }, "hom": { "contact": { "email": "bgee@sib.swiss", "github": "fbastian", "name": "Frederic Bastian", "orcid": "0000-0002-9415-5104" }, "description": "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.", "download_owl": "http://purl.obolibrary.org/obo/hom.owl", "example": "0000049", "homepage": "https://github.com/BgeeDB/homology-ontology", "keywords": [ "anatomy", "homologous", "life cycle stage", "life science", "molecular entity", "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "HOM", "biocontext": "HOM", "bioportal": "HOM", "fairsharing": "FAIRsharing.efv7gw", "obofoundry": "hom", "ols": "hom", "ontobee": "HOM" }, "name": "Homology Ontology", "pattern": "^\\d{7}$", "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_$1", "version": "2015-01-07" }, "homd.seq": { "contact": { "email": "tchen@forsyth.org", "github": "tsute", "name": "Tsute Chen", "orcid": "0000-0001-6689-317X" }, "description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information.", "example": "SEQF10030.1", "homepage": "http://www.homd.org/", "keywords": [ "genome", "microbial" ], "mappings": { "biocontext": "HOMD.SEQ", "miriam": "homd.seq", "n2t": "homd.seq", "prefixcommons": "homd.seq" }, "name": "HOMD Sequence Metainformation", "pattern": "^SEQF\\d+(.\\d+)?$", "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": "https://www.homd.org/genome/genome_description?gid=$1" }, "homd.taxon": { "contact": { "email": "tchen@forsyth.org", "github": "tsute", "name": "Tsute Chen", "orcid": "0000-0001-6689-317X" }, "description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information.", "example": "811", "homepage": "http://www.homd.org/", "keywords": [ "microbial", "taxonomy" ], "mappings": { "biocontext": "HOMD.TAXON", "miriam": "homd.taxon", "n2t": "homd.taxon", "ncbi": "HOMD", "prefixcommons": "homd.taxon" }, "name": "Human Oral Microbiome Database", "pattern": "^\\d+$", "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://bio2rdf.org", "name": "Bio2RDF", "uri_format": "https://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" }, "homosaurus": { "appears_in": [ "gsso" ], "contact": { "email": "adolphok@vcu.edu", "name": "Keahi Kaʻiwalani Adolpho", "orcid": "0000-0003-1769-112X" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An international LGBTQ+ linked data vocabulary", "example": "queerNewspapers", "github_request_issue": 1310, "homepage": "http://homosaurus.org", "license": "CC BY NC-ND 4.0", "name": "Homosaurus", "preferred_prefix": "homosaurus", "providers": [ { "code": "homosaurus.v2", "description": "Homosaurus API v2", "homepage": "https://homosaurus.org", "name": "Homosaurus API v2", "uri_format": "http://homosaurus.org/v2/$1" }, { "code": "homosaurus.v3", "description": "Homosaurus API v3", "homepage": "https://homosaurus.org", "name": "Homosaurus API v3", "uri_format": "http://homosaurus.org/v3/$1" } ], "repository": "https://github.com/DigitalTransgenderArchive/homosaurus_site", "uri_format": "http://homosaurus.org/terms/$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" }, "deprecated": true, "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=$1&db=HOVERGEN" }, "hp": { "appears_in": [ "chiro", "maxo", "scdo" ], "banana": "HP", "contact": { "email": "dr.sebastian.koehler@gmail.com", "github": "drseb", "name": "Sebastian Koehler", "orcid": "0000-0002-5316-1399" }, "description": "The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM.", "download_json": "http://purl.obolibrary.org/obo/hp.json", "download_obo": "http://purl.obolibrary.org/obo/hp.obo", "download_owl": "http://purl.obolibrary.org/obo/hp.owl", "example": "0011140", "homepage": "http://www.human-phenotype-ontology.org/", "keywords": [ "biomedical science", "disease phenotype", "disorder", "genetics", "obo", "omics", "ontology", "pathology", "phenomics", "preclinical studies" ], "license": "hpo", "logo": "https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/logo/HPO-logo-black_small.png", "mappings": { "aberowl": "HPO", "bartoc": "1937", "biocontext": "HPO", "bioportal": "HPO", "fairsharing": "FAIRsharing.kbtt7f", "hl7": "2.16.840.1.113883.6.339", "integbio": "nbdc02559", "miriam": "hp", "n2t": "hp", "obofoundry": "hp", "ols": "hp", "ontobee": "HP", "wikidata": "P3841" }, "mastodon": "hpo@masto.ai", "name": "Human Phenotype Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "HP", "publications": [ { "doi": "10.1093/nar/gkad1005", "pubmed": "37953324", "title": "The Human Phenotype Ontology in 2024: phenotypes around the world", "year": 2024 }, { "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_$1", "version": "2025-01-16" }, "hpa": { "contact": { "email": "mathias.uhlen@scilifelab.se", "name": "Mathias Uhlen", "orcid": "0000-0002-4858-8056" }, "description": "The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers.", "example": "ENSG00000026508", "homepage": "http://www.proteinatlas.org/", "keywords": [ "biomedical science", "protein", "proteomics", "structure", "systems biology", "transcriptomics" ], "mappings": { "biocontext": "HPA", "fairsharing": "FAIRsharing.j0t0pe", "go": "HPA", "miriam": "hpa", "n2t": "hpa", "prefixcommons": "hpa", "re3data": "r3d100010931", "uniprot": "DB-0046" }, "name": "Human Protein Atlas tissue profile information", "pattern": "^ENSG\\d{11}$", "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=$1" }, "hprd": { "contact": { "email": "pandey@jhmi.edu", "name": "Akhilesh Pandey", "orcid": "0000-0001-9943-6127" }, "deprecated": true, "description": "The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.", "example": "00001", "homepage": "http://www.hprd.org/", "keywords": [ "protein", "structure" ], "mappings": { "biocontext": "HPRD", "fairsharing": "FAIRsharing.y2qws7", "integbio": "nbdc00103", "miriam": "hprd", "n2t": "hprd", "pathguide": "14", "prefixcommons": "hprd", "re3data": "r3d100010978" }, "name": "Human Protein Reference Database", "pattern": "^\\d+$", "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_$1", "version": "2025-01-23" }, "hsdb": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas.", "example": "5621", "homepage": "https://pubchem.ncbi.nlm.nih.gov/source/hsdb", "mappings": { "integbio": "nbdc00930", "wikidata": "P2062" }, "name": "Hazardous Substances Data Bank", "pattern": "^\\d+$", "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_$1", "version": "2021-12-13" }, "hssp": { "contact": { "email": "chris@sanderlab.org", "name": "Chris Sander", "orcid": "0000-0001-6059-6270" }, "description": "HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein.", "example": "102l", "homepage": "http://swift.cmbi.kun.nl/swift/hssp/", "keywords": [ "clustering", "protein", "sequence" ], "mappings": { "biocontext": "HSSP", "miriam": "hssp", "n2t": "hssp", "ncbi": "HSSP", "prefixcommons": "hssp" }, "name": "Database of homology-derived secondary structure of proteins", "pattern": "^\\w{4}$", "preferred_prefix": "hssp", "providers": [ { "code": "CURATOR_REVIEW", "description": "HSSP at CMBI", "homepage": "ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/", "name": "HSSP at CMBI", "uri_format": "ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/$1.hssp.bz2" }, { "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/hssp:$1" } ], "publications": [ { "doi": "10.1093/nar/24.1.201", "pmc": "PMC145595", "pubmed": "8594579", "title": "The HSSP database of protein structure-sequence alignments", "year": 1996 }, { "pmc": "PMC308328", "pubmed": "7937066", "title": "The HSSP database of protein structure-sequence alignments", "year": 1994 } ], "uri_format": "ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$1.hssp.bz2" }, "htn": { "contact": { "email": "aellenhicks@gmail.com", "github": "aellenhicks", "name": "Amanda Hicks", "orcid": "0000-0002-1795-5570" }, "description": "An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines", "download_owl": "http://purl.obolibrary.org/obo/htn.owl", "example": "00000014", "homepage": "https://github.com/aellenhicks/htn_owl", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "HTN", "bioportal": "HTN", "obofoundry": "htn", "ols": "htn", "ontobee": "HTN" }, "name": "Hypertension Ontology", "pattern": "^\\d{8}$", "preferred_prefix": "HTN", "rdf_uri_format": "http://purl.obolibrary.org/obo/HTN_$1", "repository": "https://github.com/aellenhicks/htn_owl", "uri_format": "http://purl.obolibrary.org/obo/HTN_$1" }, "huge": { "contact": { "email": "ohara@kazusa.or.jp", "name": "Osamu Ohara", "orcid": "0000-0002-3328-9571" }, "description": "The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.", "example": "KIAA0001", "homepage": "http://www.kazusa.or.jp/huge/", "keywords": [ "computational biology", "dna", "life science", "protein", "structure" ], "mappings": { "biocontext": "HUGE", "fairsharing": "FAIRsharing.zx2ztd", "integbio": "nbdc00104", "miriam": "huge", "n2t": "huge", "prefixcommons": "huge", "uniprot": "DB-0049" }, "name": "Human Unidentified Gene-Encoded", "pattern": "^KIAA\\d{4}$", "preferred_prefix": "huge", "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/huge:$1" } ], "publications": [ { "doi": "10.1093/nar/gkh035", "pmc": "PMC308769", "pubmed": "14681467", "title": "HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE", "year": 2004 } ], "uri_format": "https://www.kazusa.or.jp/huge/gfpage/$1" }, "humap": { "contact": { "email": "ksdrew@uic.edu", "github": "ksdrew", "name": "Kevin Drew", "orcid": "0000-0002-1260-4413" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The hu.MAP integrates several large scale protein interaction datasets to obtain a comprehensive view of protein complexes.", "example": "huMAP3_04143.1", "github_request_issue": 1249, "homepage": "https://humap3.proteincomplexes.org", "license": "CC0-1.0", "name": "Human Protein Complex Map", "preferred_prefix": "humap", "publications": [ { "doi": "10.15252/msb.202010016", "pmc": "PMC8111494", "pubmed": "33973408", "title": "hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies", "year": 2021 }, { "doi": "10.15252/msb.20167490", "pmc": "PMC5488662", "pubmed": "28596423", "title": "Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes", "year": 2017 } ], "synonyms": [ "humap3" ], "uri_format": "https://humap3.proteincomplexes.org/displayComplexes?complex_key=$1" }, "iao": { "appears_in": [ "agro", "clyh", "duo", "ecocore", "ecto", "fovt", "labo", "maxo", "mcro", "pco", "psdo", "xpo" ], "contact": { "email": "zhengj2007@gmail.com", "github": "zhengj2007", "name": "Jie Zheng", "orcid": "0000-0002-2999-0103" }, "description": "An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch.", "download_obo": "http://purl.obolibrary.org/obo/iao.obo", "download_owl": "http://purl.obolibrary.org/obo/iao.owl", "example": "0000030", "homepage": "https://github.com/information-artifact-ontology/IAO/", "keywords": [ "assay", "biomedical science", "data identity and mapping", "data management", "drug report", "experimental measurement", "knowledge and information systems", "obo", "ontology", "protocol", "reagent", "study design", "subject agnostic" ], "license": "CC-BY-4.0", "logo": "https://avatars0.githubusercontent.com/u/13591168?v=3&s=200", "mappings": { "aberowl": "IAO", "biocontext": "IAO", "bioportal": "IAO", "fairsharing": "FAIRsharing.gq1xtx", "go": "IAO", "miriam": "iao", "n2t": "iao", "obofoundry": "iao", "ols": "iao", "ontobee": "IAO" }, "name": "Information Artifact Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "IAO", "providers": [ { "code": "legacy", "description": "A URI from the semanticweb.og", "homepage": "http://www.semanticweb.org", "name": "Legacy URI", "uri_format": "http://www.semanticweb.org/ontologies/2011/9/Ontology1317751904226.owl#IAO_$1" } ], "publications": [ { "doi": "10.3233/978-1-61499-101-4-68", "pubmed": "22874154", "title": "An information artifact ontology perspective on data collections and associated representational artifacts", "year": 2012 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/IAO_$1", "repository": "https://github.com/information-artifact-ontology/IAO", "uri_format": "http://purl.obolibrary.org/obo/IAO_$1", "version": "2022-11-07" }, "icd10": { "contact": { "email": "info@who.int", "name": "World Health Organization" }, "contributor_extras": [ { "github": "joeflack4", "name": "Joe Flack", "orcid": "0000-0002-2906-7319" }, { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" }, { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } ], "description": "The 10th revision of the International Classification of Diseases (ICD) issued by the World Health Organization (WHO). ICD is formally named 'The International Statistical Classification of Diseases and Related Health Problems'. It contains codes for diseases, signs and symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or diseases.\n\nNote that the WHO version of ICD-10 is distinct from the ICD-10-CM (Clinical Modification) issued by the U.S. National Center for Health Statistics for use in the United States.", "example": "C34", "example_decoys": [ "G00X", "C34.90", "C4A.8", "C91.Z", "C91.Z0" ], "example_extras": [ "A01.1", "G00", "R25", "R25-R29", "R25.3", "V20", "XVIII" ], "homepage": "https://icd.who.int/browse10", "keywords": [ "biomedical science", "classification", "diagnosis", "disease", "epidemiology", "global health", "health science", "ontology", "taxonomy" ], "license": "https://cdn.who.int/media/docs/default-source/publishing-policies/copyright/who-faq-licensing-icd-10.pdf", "mappings": { "aberowl": "ICD10", "bartoc": "447", "biocontext": "ICD", "biolink": "ICD10", "bioportal": "ICD10", "edam": "2611", "fairsharing": "FAIRsharing.nj16g", "hl7": "2.16.840.1.113883.6.3", "miriam": "icd", "n2t": "icd", "prefixcommons": "icd", "wikidata": "P494" }, "name": "International Classification of Diseases, 10th Revision", "pattern": "^(([XVI]+)|([A-Z][0-9]+((-[A-Z][0-9]+)|(\\.[0-9]))?))$", "preferred_prefix": "icd10", "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/icd:$1" }, { "code": "icd10_2008", "description": "The 2008 revision of ICD-10", "homepage": "https://icd.who.int/browse10/2008/en#", "name": "ICD-10 Version 2008", "uri_format": "https://icd.who.int/browse10/2008/en#/$1" }, { "code": "icd10_2010", "description": "The 2010 revision of ICD-10", "homepage": "https://icd.who.int/browse10/2010/en#", "name": "ICD-10 Version 2010", "uri_format": "https://icd.who.int/browse10/2010/en#/$1" }, { "code": "icd10_2014", "description": "The 2014 revision of ICD-10", "homepage": "https://icd.who.int/browse10/2014/en#", "name": "ICD-10 Version 2014", "uri_format": "https://icd.who.int/browse10/2014/en#/$1" }, { "code": "icd10_2015", "description": "The 2015 revision of ICD-10", "homepage": "https://icd.who.int/browse10/2015/en#", "name": "ICD-10 Version 2015", "uri_format": "https://icd.who.int/browse10/2015/en#/$1" }, { "code": "icd10_2016", "description": "The 2016 revision of ICD-10", "homepage": "https://icd.who.int/browse10/2016/en#", "name": "ICD-10 Version 2016", "uri_format": "https://icd.who.int/browse10/2016/en#/$1" }, { "code": "icdcodelookup", "description": "This site is dedicated exclusively to helping you look up ICD-10 codes, quickly access the codes you use most, and become more comfortable with the new code set in general.", "homepage": "https://icdcodelookup.com/icd-10/codes", "name": "ICD Code Lookup", "uri_format": "https://icdcodelookup.com/icd-10/codes/$1" } ], "synonyms": [ "ICD", "ICD-10", "ICD10", "ICD10WHO" ], "uri_format": "https://icd.who.int/browse10/2019/en#/$1" }, "icd10cm": { "contact": { "email": "pbrooks@hcfa.gov", "name": "Patricia Brooks" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "ICD-10-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States issued by the National Center for Health Statistics (NCHS) and Centers for Medicare & Medicaid Services (CMS).", "example": "F45.21", "example_decoys": [ "C000", "c00", "C00-D499", "C00-99", "C34.90000" ], "example_extras": [ "C00-D49", "C34", "C34.90", "C4A.8", "C91.Z", "C91.Z0", "T37.0X1A", "U49" ], "homepage": "https://www.icd10data.com/ICD10CM", "keywords": [ "biomedical science", "diagnosis", "disease", "electronic health record", "health science", "medicine", "morbidity", "ontology" ], "mappings": { "aberowl": "ICD10CM", "bioportal": "ICD10CM", "fairsharing": "FAIRsharing.hpvbxb", "hl7": "2.16.840.1.113883.6.90", "wikidata": "P4229" }, "name": "International Classification of Diseases, 10th Revision, Clinical Modification", "pattern": "^([A-Z][0-9][0-9AB]((-[A-Z][0-9][0-9AB])|(\\.[0-9A-KXZ]([0-9A-EXYZ]([0-9A-HX][0-59A-HJKMNP-S]?)?)?)?))$", "preferred_prefix": "icd10cm", "providers": [ { "code": "bioportal.purl", "description": "PURL from BioPortal", "homepage": "http://purl.bioontology.org/ontology/ICD10CM", "name": "BioPortal PURL", "uri_format": "http://purl.bioontology.org/ontology/ICD10CM/$1" } ], "synonyms": [ "ICD10CM" ], "uri_format": "https://icd.codes/icd10cm/$1" }, "icd10pcs": { "contact": { "email": "patricia.brooks2@cms.hhs.gov", "name": "Pat Brooks" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "ICD-10-PCS is being developed as the successor to Volume 3 of the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM). For more information about ICD-9-CM, see the ICD-9-CM source synopsis.\n\nICD-10-PCS will be the official system of assigning codes to procedures associated with hospital utilization in the United States. ICD-10-PCS codes will support data collection, payment and electronic health records.", "example": "01N50ZZ", "homepage": "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ICD10PCS", "keywords": [ "biomedical science", "classification", "diagnosis", "disease", "electronic health record", "epidemiology", "health science", "hospital", "morbidity", "ontology" ], "mappings": { "aberowl": "ICD10PCS", "bioportal": "ICD10PCS", "fairsharing": "FAIRsharing.85k1jm", "hl7": "2.16.840.1.113883.6.4", "wikidata": "P1690" }, "name": "International Classification of Diseases, 10th Revision, Procedure Coding System", "preferred_prefix": "icd10pcs", "uri_format": "https://www.findacode.com/code.php?set=ICD10PCS&c=$1" }, "icd11": { "comment": "Clinical codes from an ICD-11 linearization (a structured subset of the ICD-11 Foundation tailored for specific use cases, such as morbidity or mortality coding), such as RA00.0, have their own namespace (icd11.code).", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" } ], "description": "The ICD-11 Foundation is the comprehensive base layer of the International Classification of Diseases, encompassing all diagnostic concepts, definitions, and semantic relationships, designed for flexibility and adaptability across various use cases, including research, ontology development, and detailed health data analysis.", "example": "402558626", "homepage": "https://icd.who.int/", "keywords": [ "biomedical science", "diagnosis", "disease", "electronic health record", "epidemiology", "global health", "health science", "morbidity" ], "license": "CC-BY-ND-3.0-IGO", "mappings": { "biolink": "icd11.foundation", "fairsharing": "FAIRsharing.97805c", "hl7": "2.16.840.1.113883.6.347", "integbio": "nbdc02556", "wikidata": "P7807" }, "name": "International Classification of Diseases, 11th Revision (Foundation Component)", "pattern": "^[1-9]\\d*$", "preferred_prefix": "icd11", "providers": [ { "code": "api", "description": "This goes to an API endpoint. For more information, see https://icd.who.int/icdapi", "homepage": "https://icd.who.int", "name": "ICD 11 API Endpoint", "uri_format": "http://id.who.int/icd/entity/$1" }, { "code": "foundation", "description": "This goes to the Foundation interface to ICD11", "homepage": "https://icd.who.int/browse/2024-01/foundation", "name": "ICD 11 Foundation", "uri_format": "https://icd.who.int/browse/2024-01/foundation/en#$1" }, { "code": "mms", "description": "This goes to the Mortality and Morbidity Statistics interface to ICD11", "homepage": "https://icd.who.int/browse/2024-01/mms", "name": "ICD 11 Mortality and Morbidity Statistics", "uri_format": "https://icd.who.int/browse/2024-01/mms/en#$1" } ], "rdf_uri_format": "http://id.who.int/icd/entity/$1", "references": [ "https://icd.who.int/docs/icd-api/license/" ], "synonyms": [ "ICD-11", "ICD11", "icd11.foundation" ], "uri_format": "https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/$1" }, "icd11.code": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ICD-11 code is a standardized alphanumeric identifier used to classify and document diseases, conditions, and health-related issues for global healthcare and statistical purposes.", "example": "NA06.8D", "example_extras": [ "CA71.2", "FB82.00", "XM34M9" ], "github_request_issue": 1349, "homepage": "https://icd.who.int/en", "license": "http://www.who.int/about/licensing/copyright_form/en", "name": "ICD 11 Codes", "pattern": "^[0-9A-Z]+(\\.[0-9A-Z]+)?$", "preferred_prefix": "icd11.code", "references": [ "https://github.com/biopragmatics/bioregistry/issues/1344" ] }, "icd9": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The International Classification of Diseases (ICD) is designed to promote international comparability in the collection, processing, classification, and presentation of mortality statistics.", "example": "277.9", "homepage": "https://www.cdc.gov/nchs/icd/icd9.htm", "mappings": { "biolink": "ICD9", "hl7": "2.16.840.1.113883.6.42", "wikidata": "P493" }, "name": "International Classification of Diseases, 9th Revision", "pattern": "^(\\d\\d\\d|V\\d\\d|E[8-9]\\d\\d)(\\.\\d{1,2})?$", "preferred_prefix": "icd9", "synonyms": [ "ICD9", "ICD9_2005", "MTHICD9_2006" ], "uri_format": "http://www.icd9data.com/getICD9Code.ashx?icd9=$1" }, "icd9cm": { "contact": { "email": "pbrooks@hcfa.gov", "name": "Patricia Brooks" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States.", "example": "784", "homepage": "https://www.cdc.gov/nchs/icd/icd9cm.htm", "keywords": [ "biomedical science", "diagnosis", "disease", "epidemiology", "health science", "medicine", "morbidity", "ontology", "preclinical studies" ], "mappings": { "aberowl": "ICD9CM", "bioportal": "ICD9CM", "fairsharing": "FAIRsharing.10zsxb", "hl7": "2.16.840.1.113883.6.2", "wikidata": "P1692" }, "name": "International Classification of Diseases, 9th Revision, Clinical Modification", "pattern": "^([\\dA-Z]\\d{2}(\\.\\d{1,3}|))|(\\d{2}(\\.\\d{1,2}|))$", "preferred_prefix": "icd9cm", "synonyms": [ "IC9CM", "ICD9CM", "ICD9CM_2005", "ICD9CM_2006", "ICDCM_2005" ], "uri_format": "http://icd9cm.chrisendres.com/index.php?action=search&srchtext=$1" }, "icdc": { "contact": { "email": "annika.jahnke-bornemann@uni-hamburg.de", "name": "Annika Jahnke-Bornemann", "orcid": "0000-0001-7815-151X" }, "description": "The Integrated Canine Data Commons is one of several repositories within the NCI Cancer Research Data Commons (CRDC), a cloud-based data science infrastructure that provides secure access to a large, comprehensive, and expanding collection of cancer research data. The ICDC was established to further research on human cancers by enabling comparative analysis with canine cancer.", "example": "000009", "homepage": "https://caninecommons.cancer.gov/#/", "keywords": [ "atmospheric science", "earth science", "meteorology", "oceanography", "remote sensing", "social science" ], "mappings": { "fairsharing": "FAIRsharing.d95034", "miriam": "icdc", "re3data": "r3d100010405" }, "name": "Integrated Canine Data Commons", "pattern": "^\\d{6}$", "preferred_prefix": "icdc", "twitter": "ICDC_Hamburg", "uri_format": "https://caninecommons.cancer.gov/#/study/$1" }, "icdo": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The International Classification of Diseases for Oncology (ICD-O) is a domain-specific extension of the International Statistical Classification of Diseases and Related Health Problems for tumor diseases", "example": "9861/3", "homepage": "https://www.who.int/classifications/icd/adaptations/oncology/en/", "mappings": { "bartoc": "445", "hl7": "2.16.840.1.113883.6.43", "prefixcommons": "icdo", "wikidata": "P563" }, "name": "International Classification of Diseases for Oncology", "pattern": "^[8-9]\\d{3}(/[0-3])?$", "preferred_prefix": "icdo", "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/icdo:$1" } ], "synonyms": [ "ICD-O", "ICDO" ], "uri_format": "http://codes.iarc.fr/search.php?cx=009987501641899931167%3A2_7lsevqpdm&cof=FORID%3A9&ie=UTF-8&ie=ISO-8859-1&oe=ISO-8859-1&sa=&q=$1" }, "iceberg.cime": { "contact": { "email": "hyou@sjtu.edu.cn", "name": "Hong-Yu Ou", "orcid": "0000-0001-9439-1660" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "ICEs have also been reported capable to mobilize other genetic elements, such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles for the spread of antiobiotic resistances and virulence factors. However, unlike ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack the machinery of other conjugative elements.", "example": "6", "homepage": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_CIME.php?type=alpha&alpha=100", "keywords": [ "biology", "genomics" ], "name": "ICEberg cis-integrative and mobilizable element", "part_of": "iceberg", "pattern": "^\\d+$", "preferred_prefix": "iceberg.cime", "publications": [ { "doi": "10.1093/nar/gky1123", "pmc": "PMC6323972", "pubmed": "30407568", "title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements", "year": 2019 }, { "doi": "10.1093/nar/gkr846", "pmc": "PMC3244999", "pubmed": "22009673", "title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria", "year": 2011 } ], "uri_format": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_CIME.php?cime_id=$1_CIME" }, "iceberg.element": { "description": "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements.", "example": "100", "homepage": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=alpha&alpha=100", "mappings": { "biocontext": "ICEBERG.ELEMENT", "miriam": "iceberg.element", "n2t": "iceberg.element" }, "name": "ICEberg integrative and conjugative element", "part_of": "iceberg", "pattern": "^\\d+$", "preferred_prefix": "iceberg.element", "publications": [ { "doi": "10.1093/nar/gky1123", "pmc": "PMC6323972", "pubmed": "30407568", "title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements", "year": 2019 }, { "doi": "10.1093/nar/gkr846", "pmc": "PMC3244999", "pubmed": "22009673", "title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria", "year": 2011 } ], "synonyms": [ "iceberg.ice" ], "uri_format": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=$1" }, "iceberg.family": { "contact": { "email": "hyou@sjtu.edu.cn", "name": "Hong-Yu Ou", "orcid": "0000-0001-9439-1660" }, "description": "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families.", "example": "1", "homepage": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_fam.php", "mappings": { "biocontext": "ICEBERG.FAMILY", "miriam": "iceberg.family", "n2t": "iceberg.family" }, "name": "ICEberg family", "part_of": "iceberg", "pattern": "^\\d+$", "preferred_prefix": "iceberg.family", "publications": [ { "doi": "10.1093/nar/gky1123", "pmc": "PMC6323972", "pubmed": "30407568", "title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements", "year": 2019 }, { "doi": "10.1093/nar/gkr846", "pmc": "PMC3244999", "pubmed": "22009673", "title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria", "year": 2011 } ], "uri_format": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=fam&fam_id=$1" }, "iceberg.ime": { "contact": { "email": "hyou@sjtu.edu.cn", "name": "Hong-Yu Ou", "orcid": "0000-0001-9439-1660" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "ICEs have also been reported capable to mobilize other genetic elements, such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles for the spread of antiobiotic resistances and virulence factors. However, unlike ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack the machinery of other conjugative elements.", "example": "1", "homepage": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_IME.php?type=alpha&alpha=100", "keywords": [ "biology", "genomics" ], "name": "ICEberg integrative and mobilizable element", "part_of": "iceberg", "pattern": "^\\d+$", "preferred_prefix": "iceberg.ime", "publications": [ { "doi": "10.1093/nar/gky1123", "pmc": "PMC6323972", "pubmed": "30407568", "title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements", "year": 2019 }, { "doi": "10.1093/nar/gkr846", "pmc": "PMC3244999", "pubmed": "22009673", "title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria", "year": 2011 } ], "uri_format": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_IME.php?ime_id=$1_IME" }, "icechem": { "description": "The Integrated Chemical Environment (ICE) provides high-quality curated data and appropriate tools to support development and evaluation of new, revised, and alternative methods. ICE provides free online access to curated in vivo and in vitro test data, in silico toxicity predictions and chemical property data, reference chemical lists, and computational tools for chemical characterization and predicting toxicity.\nICE supports the following: (i) Data integration: brings together available data, including data on formulations; (ii) Results exploration: enables dynamic, graphical exploration with publication-quality graphics; (iii) Data analysis: allows characterization of data using online workflows, and (iv) FAIR data access: data are findable, accessible, interoperable, and reusable.", "example": "DTXSID7032004", "homepage": "https://ice.ntp.niehs.nih.gov", "mappings": { "miriam": "ice.chem" }, "name": "Integrated Chemical Environment - Chemical data", "pattern": "^\\d{2,7}-\\d{2}-\\d|DTXSID\\d{7,9}|[A-Z]{14}-[A-Z]{8}[SN][A-Z]-[A-Z]$", "preferred_prefix": "icechem", "uri_format": "https://ice.ntp.niehs.nih.gov/api/v1/search?chemid=$1" }, "iceo": { "comment": "ICEO is not consistent about its identfiers like ICEO:0000595:1 and ICEO:0000595_1", "contact": { "email": "liumeng94@sjtu.edu.cn", "github": "Lemon-Liu", "name": "Meng LIU", "orcid": "0000-0003-3781-6962" }, "description": "A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning.", "download_owl": "http://purl.obolibrary.org/obo/iceo.owl", "example": "0000712_1", "example_extras": [ "0000712" ], "homepage": "https://github.com/ontoice/ICEO", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "ICEO", "bioportal": "ICEO", "obofoundry": "iceo", "ols": "iceo", "ontobee": "ICEO" }, "name": "Integrative and Conjugative Element Ontology", "pattern": "^\\d{7}(_\\d)?$", "preferred_prefix": "ICEO", "publications": [ { "doi": "10.1038/s41597-021-01112-5", "pmc": "PMC8776819", "pubmed": "35058462", "title": "ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements", "year": 2022 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/ICEO_$1", "repository": "https://github.com/ontoice/ICEO", "uri_format": "http://purl.obolibrary.org/obo/ICEO_$1", "version": "2.1" }, "icepo": { "contact": { "email": "pascale.gaudet@isb-sib.ch", "github": "pgaudet", "name": "Pascale Gaudet", "orcid": "0000-0003-1813-6857" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Ion Channel Electrophysiology Ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools. ", "download_obo": "https://download.nextprot.org/pub/current_release/controlled_vocabularies/icepo.obo", "example": "0000002", "homepage": "https://download.nextprot.org/pub/current_release/controlled_vocabularies/", "keywords": [ "ontology" ], "name": "Ion Channel Electrophysiology Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "icepo", "publications": [ { "pmc": "PMC4823818", "title": "ICEPO: the ion channel electrophysiology ontology" } ], "twitter": "neXtProt_news", "uri_format": "https://biopragmatics.github.io/providers/icepo/$1" }, "icf": { "comment": "This might be possible to roll directly into ICD11", "contact": { "email": "info@who.int", "name": "The World Health Organization" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The International Classification of Functioning, Disability and Health, known more commonly as ICF, is a classification of health and health-related domains. As the functioning and disability of an individual occurs in a context, ICF also includes a list of environmental factors. ICF is the WHO framework for measuring health and disability at both individual and population levels.", "download_owl": "http://aber-owl.net/media/ontologies/ICF/3/icf.owl", "example": "326705068", "homepage": "https://icd.who.int/dev11/l-icf/en", "keywords": [ "biomedical science", "electronic health record", "health science", "medicine", "ontology", "primary health care" ], "mappings": { "aberowl": "ICF", "bioportal": "ICF", "fairsharing": "FAIRsharing.7rngj0", "hl7": "2.16.840.1.113883.6.254" }, "name": "International Classification of Functioning, Disability and Health", "pattern": "^\\d+$", "preferred_prefix": "icf", "uri_format": "https://icd.who.int/dev11/l-icf/en#/http://id.who.int/icd/entity/$1" }, "iclc": { "description": "Cell line collections (Providers)", "example": "ATL98012", "homepage": "http://www.iclc.it", "mappings": { "cellosaurus": "ICLC" }, "name": "Interlab Cell Line Collection", "pattern": "^\\w{3}\\d+$", "preferred_prefix": "iclc", "uri_format": "http://www.iclc.it/details/det_list.php?line_id=$1" }, "icldb": { "contact": { "email": "surjeet.arya@uky.edu", "name": "Surjeet Kumar Arya", "orcid": "0000-0002-2212-4771" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "We have developed an online database describing the known cell lines from Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera that originated from crop pest insects. Cell line information has been primarily obtained from previous compilations of insect cell lines. (from homepage)", "example": "64ba", "homepage": "https://entomology.ca.uky.edu/aginsectcellsdatabase", "mappings": { "cellosaurus": "ICLDB" }, "name": "Insect Cell Line Database", "preferred_prefix": "icldb", "uri_format": "https://entomology.ca.uky.edu/content/$1" }, "ico": { "appears_in": [ "scdo" ], "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", "name": "Yongqun Oliver He", "orcid": "0000-0001-9189-9661" }, "description": "The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field.", "download_owl": "http://purl.obolibrary.org/obo/ico.owl", "example": "0000066", "homepage": "https://github.com/ICO-ontology/ICO", "keywords": [ "biomedical science", "clinical studies", "health science", "medicine", "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "ICO", "biocontext": "ICO", "bioportal": "ICO", "fairsharing": "FAIRsharing.b9znd5", "obofoundry": "ico", "ols": "ico", "ontobee": "ICO" }, "name": "Informed Consent Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "ICO", "rdf_uri_format": "http://purl.obolibrary.org/obo/ICO_$1", "repository": "https://github.com/ICO-ontology/ICO", "uri_format": "http://purl.obolibrary.org/obo/ICO_$1", "version": "2025-03-15" }, "ideal": { "contact": { "email": "sfukuchi@maebashi-it.ac.jp", "github": "sfukuchi", "name": "Satoshi Fukuchi", "orcid": "0000-0002-5705-3061" }, "description": "IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments.", "example": "IID00001", "homepage": "https://www.ideal-db.org", "keywords": [ "biology" ], "mappings": { "biocontext": "IDEAL", "fairsharing": "FAIRsharing.h3y42f", "integbio": "nbdc01456", "miriam": "ideal", "n2t": "ideal", "pathguide": "701", "uniprot": "DB-0251" }, "name": "Intrinsically Disordered proteins with Extensive Annotations and Literature", "pattern": "^IID\\d+$", "preferred_prefix": "ideal", "publications": [ { "doi": "10.1093/nar/gkt1010", "pmc": "PMC3965115", "pubmed": "24178034", "title": "IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners", "year": 2013 } ], "uri_format": "http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=$1" }, "ido": { "appears_in": [ "scdo" ], "contact": { "email": "Lindsay.Cowell@utsouthwestern.edu", "github": "lgcowell", "name": "Lindsay Cowell", "orcid": "0000-0003-1617-8244" }, "contributor_extras": [ { "email": "github@yohannparis.com", "github": "YohannParis", "name": "Yohann Paris", "orcid": "0009-0006-6049-1392" } ], "description": "Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases.", "download_owl": "http://purl.obolibrary.org/obo/ido.owl", "example": "0000504", "homepage": "http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology", "keywords": [ "biomedical science", "classification", "disease", "disease process modeling", "molecular infection biology", "obo", "ontology", "preclinical studies" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "IDO", "biocontext": "IDO", "bioportal": "IDO", "fairsharing": "FAIRsharing.aae3v6", "miriam": "ido", "n2t": "ido", "obofoundry": "ido", "ols": "ido", "ontobee": "IDO" }, "name": "Infectious Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "IDO", "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/IDO_$1" } ], "publications": [ { "doi": "10.1186/s13326-021-00245-1", "pmc": "PMC8286442", "pubmed": "34275487", "title": "The Infectious Disease Ontology in the age of COVID-19", "year": 2021 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/IDO_$1", "repository": "https://github.com/infectious-disease-ontology/infectious-disease-ontology", "uri_format": "http://purl.obolibrary.org/obo/IDO_$1", "version": "2017-11-03" }, "idocovid19": { "contact": { "email": "johnbeverley2021@u.northwestern.edu", "github": "johnbeve", "name": "John Beverly", "orcid": "0000-0002-1118-1738" }, "description": "The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease.", "download_owl": "https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-covid-19/master/ontology/ido%20covid-19", "example": "0001191", "homepage": "https://github.com/infectious-disease-ontology-extensions/ido-covid-19", "keywords": [ "ontology" ], "mappings": { "aberowl": "IDO-COVID-19", "bioportal": "IDO-COVID-19", "ols": "idocovid19" }, "name": "The COVID-19 Infectious Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "idocovid19", "providers": [ { "code": "obo1", "description": "This variation uses incorrect usage of dashes instead of underscores", "homepage": "http://purl.obolibrary.org", "name": "Incorrect OBO PURL variation 1", "uri_format": "http://purl.obolibrary.org/obo/IDO-COVID-19_$1" } ], "repository": "https://github.com/infectious-disease-ontology-extensions/ido-covid-19", "uri_format": "http://purl.obolibrary.org/obo/COVIDO_$1", "version": "2020-21-07" }, "idoden": { "contact": { "email": "elvira@imbb.forth.gr", "name": "Elvira Mitraka", "orcid": "0000-0003-0719-3485" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology for dengue fever.", "download_owl": "http://aber-owl.net/media/ontologies/IDODEN/6/idoden.owl", "example": "0003463", "homepage": "https://bioportal.bioontology.org/ontologies/IDODEN", "keywords": [ "medicine", "ontology" ], "mappings": { "aberowl": "IDODEN", "bioportal": "IDODEN", "fairsharing": "FAIRsharing.askzq4" }, "name": "Dengue Fever Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "idoden", "references": [ "https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0003479" ], "uri_format": "http://purl.bioontology.org/ontology/IDODEN_$1" }, "idog": { "contact": { "email": "baoym@big.ac.cn", "name": "Yiming Bao", "orcid": "0000-0002-9922-9723" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Provides the worldwide dog research community a variety of data services including access to genes, genomes, SNPs, breed/disease Traits, gene expression experiments, dog-guman homology, and literatur. In addition, iDog provides online tools for performing genomic data visualization and analyses.", "example": "4", "homepage": "https://ngdc.cncb.ac.cn/idog/", "license": "CC-BY-4.0", "mappings": { "integbio": "nbdc02480", "re3data": "r3d100012176" }, "name": "Integrated Resource for Domestic Dog", "pattern": "^\\d+$", "preferred_prefix": "idog", "publications": [ { "doi": "10.1093/nar/gky1041", "pmc": "PMC6323916", "pubmed": "30371881", "title": "iDog: an integrated resource for domestic dogs and wild canids", "year": 2019 } ], "references": [ "https://github.com/biopragmatics/bioregistry/pull/725" ], "uri_format": "https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action?breedId=$1" }, "idomal": { "appears_in": [ "scdo" ], "contact": { "email": "topalis@imbb.forth.gr", "name": "Pantelis Topalis", "orcid": "0000-0002-1635-4810" }, "deprecated": true, "description": "An application ontology to cover all aspects of malaria as well as the intervention attempts to control it.", "download_obo": "http://purl.obolibrary.org/obo/idomal.obo", "download_owl": "http://purl.obolibrary.org/obo/idomal.owl", "example": "0002350", "example_extras": [ "50000015" ], "homepage": "https://www.vectorbase.org/ontology-browser", "keywords": [ "biomedical science", "disease", "intervention design", "life science", "malaria", "molecular infection biology", "obo", "ontology", "pathogen" ], "license": "CC0-1.0", "mappings": { "aberowl": "IDOMAL", "biocontext": "IDOMAL", "bioportal": "IDOMAL", "fairsharing": "FAIRsharing.2q8c28", "obofoundry": "idomal", "ols": "idomal", "ontobee": "IDOMAL" }, "name": "Malaria Ontology", "pattern": "^(5?)\\d{7}$", "preferred_prefix": "IDOMAL", "publications": [ { "doi": "10.1186/2041-1480-4-16", "pmc": "PMC3848731", "pubmed": "24034841", "title": "IDOMAL: the malaria ontology revisited", "year": 2013 }, { "doi": "10.1186/1475-2875-9-230", "pmc": "PMC2925367", "pubmed": "20698959", "title": "IDOMAL: an ontology for malaria", "year": 2010 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/IDOMAL_$1", "repository": "https://github.com/VEuPathDB-ontology/IDOMAL", "twitter": "VectorBase", "uri_format": "http://purl.obolibrary.org/obo/IDOMAL_$1", "version": "2015-03-16" }, "idoo": { "description": "Identifiers.org Ontology", "example": "DataCollection", "homepage": "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology", "mappings": { "miriam": "idoo", "n2t": "idoo" }, "name": "Identifiers.org Ontology", "pattern": "^[0-9a-zA-Z]+$", "preferred_prefix": "idoo", "uri_format": "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1" }, "idot": { "description": "Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets.", "example": "luiPattern", "homepage": "http://biomodels.net/vocab/idot.rdf", "mappings": { "biocontext": "idot", "miriam": "idot", "n2t": "idot" }, "name": "Identifiers.org Terms", "pattern": "^[A-Za-z]+$", "preferred_prefix": "idot", "uri_format": "https://biomodels.net/vocab/idot.rdf#$1" }, "idpo": { "contact": { "email": "f.quaglia@ibiom.cnr.it", "github": "federicaquaglia", "name": "Federica Quaglia", "orcid": "0000-0002-0341-4888" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "IDPO is used to describe structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state. GO is used to describe functional aspects of an IDP/IDR.", "example": "00056", "homepage": "https://www.disprot.org/ontology", "keywords": [ "protein analysis", "protein structure", "proteins", "proteomics", "structural biochemistry", "structural bioinformatics", "structural biology" ], "mappings": { "fairsharing": "FAIRsharing.bc973b" }, "name": "Intrinsically Disordered Proteins Ontology", "pattern": "^\\d{5}$", "preferred_prefix": "idpo", "publications": [ { "doi": "10.1093/nar/gkad928", "pubmed": "37904585", "title": "DisProt in 2024: improving function annotation of intrinsically disordered proteins", "year": 2024 }, { "doi": "10.1093/database/baae009", "title": "Best practices for the manual curation of intrinsically disordered proteins in DisProt", "year": 2024 } ], "uri_format": "https://www.disprot.org/idpo/IDPO:$1" }, "idr": { "contact": { "email": "j.a.moore@dundee.ac.uk", "name": "Josh Moore", "orcid": "0000-0003-4028-811X" }, "description": "Image Data Resource (IDR) is an online, public data repository that seeks to store, integrate and serve image datasets from published scientific studies. We have collected and are continuing to receive existing and newly created “reference image\" datasets that are valuable resources for a broad community of users, either because they will be frequently accessed and cited or because they can serve as a basis for re-analysis and the development of new computational tools.", "example": "0001", "homepage": "https://idr.openmicroscopy.org", "keywords": [ "biomedical science", "botany", "life science" ], "mappings": { "fairsharing": "FAIRsharing.6wf1zw", "miriam": "idr", "re3data": "r3d100012435" }, "name": "Image Data Resource", "pattern": "^[0-9]{4}$", "preferred_prefix": "idr", "publications": [ { "doi": "10.1038/nmeth.4326", "pmc": "PMC5536224", "pubmed": "28775673", "title": "The Image Data Resource: A Bioimage Data Integration and Publication Platform", "year": 2017 } ], "twitter": "openmicroscopy", "uri_format": "https://idr.openmicroscopy.org/search/?query=Name:idr$1" }, "iedb.assay": { "contact": { "email": "rvita@liai.org", "github": "rvita", "name": "Randi Vita", "orcid": "0000-0001-8957-7612" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "Identifiers for specific experimental assays that serve as evidence for immune-related studies.", "example": "1691753", "github_request_issue": 1204, "homepage": "https://www.iedb.org/", "keywords": [ "bioinformatics", "immunology", "life science" ], "mappings": { "fairsharing": "FAIRsharing.c886cd", "integbio": "nbdc00924", "re3data": "r3d100012702" }, "name": "Immune Epitope Database Assays", "part_of": "iedb", "pattern": "^\\d+$", "preferred_prefix": "iedb.assay", "publications": [ { "doi": "10.1093/nar/gku938", "pmc": "PMC4384014", "pubmed": "25300482", "title": "The immune epitope database (IEDB) 3.0", "year": 2014 }, { "doi": "10.1111/j.1365-2567.2012.03611.x", "pmc": "PMC3461392", "pubmed": "22681406", "title": "The immune epitope database: a historical retrospective of the first decade", "year": 2012 }, { "doi": "10.1093/nar/gkp1004", "pmc": "PMC2808938", "pubmed": "19906713", "title": "The immune epitope database 2.0", "year": 2009 }, { "pubmed": "16312048", "title": "The immune epitope database and analysis resource: from vision to blueprint", "year": 2004 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. 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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/tied:$1" } ], "publications": [ { "doi": "10.1093/nar/gku938", "pmc": "PMC4384014", "pubmed": "25300482", "title": "The immune epitope database (IEDB) 3.0", "year": 2014 }, { "doi": "10.1111/j.1365-2567.2012.03611.x", "pmc": "PMC3461392", "pubmed": "22681406", "title": "The immune epitope database: a historical retrospective of the first decade", "year": 2012 }, { "doi": "10.1093/nar/gkp1004", "pmc": "PMC2808938", "pubmed": "19906713", "title": "The immune epitope database 2.0", "year": 2009 }, { "pubmed": "16312048", "title": "The immune epitope database and analysis resource: from vision to blueprint", "year": 2004 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. 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IGSNs are obtained from IGSN e.V. Agents.", "example": "AU124", "homepage": "https://ev.igsn.org/home", "keywords": [ "archaeology", "biological sample", "centrally registered identifier", "data management", "earth science", "environmental science", "geochemistry", "geology", "hydrogeology", "omics", "physical samples" ], "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaVVDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--4d19e53906f86cdaca6a9752fde1dd82276b7f22/igsn-original.jpg?disposition=inline", "mappings": { "fairsharing": "FAIRsharing.c7f365", "miriam": "igsn", "n2t": "igsn" }, "name": "International Generic Sample Number", "pattern": "^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$", "preferred_prefix": "igsn", "publications": [ { "doi": "10.5334/dsj-2023-005", "title": "Scaling Identifiers and their Metadata to Gigascale: An Architecture to Tackle the Challenges of Volume and Variety", "year": 2023 }, { "doi": "10.5334/dsj-2021-033", "title": "Towards Globally Unique Identification of Physical Samples: Governance and Technical Implementation of the IGSN Global Sample Number", "year": 2021 }, { "doi": "10.5334/dsj-2017-002", "title": "Utilizing the International Geo Sample Number Concept in Continental Scientific Drilling During ICDP Expedition COSC-1", "year": 2017 }, { "doi": "10.5281/zenodo.5118289", "title": "IGSN 2040 Summary Report: Defining the Future of the IGSN as a Global Persistent Identifier for Material Samples", "year": 2021 }, { "doi": "10.1007/978-3-030-85040-1_162", "title": "International Generic Sample Number", "year": 2023 } ], "repository": "https://igsn.github.io/", "uri_format": "http://igsn.org/$1" }, "igsr": { "contact": { "email": "flicek@ebi.ac.uk", "name": "Paul Flicek", "orcid": "0000-0002-3897-7955" }, "description": "The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set. The 1000 Genomes Project ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data. As the project ended, the Data Coordination Centre at EMBL-EBI has received continued funding from the Wellcome Trust to maintain and expand the resource. IGSR was set up to do this and has the following aims: ensure the future access to and usability of the 1000 Genomes reference data; incorporate additional published genomic data on the 1000 Genomes samples; and expand the data collection to include new populations not represented in the 1000 Genomes Project.", "example": "NA06985", "homepage": "https://www.internationalgenome.org/", "keywords": [ "comparative genomics", "genomics" ], "mappings": { "cellosaurus": "IGSR", "fairsharing": "FAIRsharing.4Vs9VM", "re3data": "r3d100010180" }, "name": "International Genome Sample Resource", "preferred_prefix": "igsr", "publications": [ { "doi": "10.1093/nar/gkz836", "pmc": "PMC6943028", "pubmed": "31584097", "title": "The International Genome Sample Resource (IGSR) collection of open human genomic variation resources", "year": 2020 }, { "doi": "10.1038/nature15393", "pmc": "PMC4750478", "pubmed": "26432245", "title": "A global reference for human genetic variation", "year": 2015 } ], "twitter": "1000genomes", "uri_format": "https://www.internationalgenome.org/data-portal/sample/$1" }, "ihw": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The International Histocompatibility Working Group provides a comprehensive inventory of HLA reference genes to support worldwide research in immunogenetics. We also offer selected cell lines and DNA from our substantial DNA Bank of more than 1,000 cell lines from selected families, as well as individuals with diverse ethnicity and immunologic characteristics.", "example": "IHW09326", "homepage": "https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html", "mappings": { "cellosaurus": "IHW" }, "name": "International Histocompatibility Workshop cell lines", "pattern": "^IHW\\d+$", "preferred_prefix": "ihw" }, "illumina.probe": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Illumina probe identifiers for microarrays, such as those in Illumina HumanRef-6 v2.0 expression beadchip.", "example": "ILMN_129894", "homepage": "https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-6790/A-GEOD-6790.adf.txt", "keywords": [ "transcriptomics" ], "name": "Illumina Probe Identifier", "pattern": "^ILMN_\\d+$", "preferred_prefix": "illumina.probe", "references": [ "https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-9184/A-GEOD-9184_comments.txt" ] }, "imanis": { "description": "Cell line collections (Providers)", "example": "CL070", "homepage": "https://www.imanislife.com/collections/cell-lines/", "mappings": { "cellosaurus": "Imanis" }, "name": "Imanis Life Sciences cell line products", "preferred_prefix": "imanis", "uri_format": "https://www.imanislife.com/?s=$1" }, "imdrf": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The International Medical Device Regulators Forum (IMDRF) is a forum of voluntary medical device regulators from around the world who have come together to build on the strong foundational work of the Global Harmonization Task Force on Medical Devices (GHTF), and to accelerate international medical device regulatory harmonization and convergence.", "homepage": "http://www.imdrf.org/", "name": "International Medical Device Regulators Forum", "no_own_terms": true, "preferred_prefix": "imdrf", "references": [ "https://www.fda.gov/medical-devices/mandatory-reporting-requirements-manufacturers-importers-and-device-user-facilities/mdr-adverse-event-codes" ] }, "imex": { "banana": "IM", "banana_peel": "-", "contact": { "email": "orchard@ebi.ac.uk", "github": "sandraorchard", "name": "Sandra Orchard", "orcid": "0000-0002-8878-3972" }, "description": "The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources.", "example": "19210-3", "example_extras": [ "19210" ], "homepage": "https://www.imexconsortium.org/", "keywords": [ "interaction", "molecule" ], "mappings": { "biocontext": "IMEX", "miriam": "imex", "n2t": "imex", "pathguide": "422", "prefixcommons": "imex", "re3data": "r3d100010669" }, "name": "International Molecular Exchange", "owners": [ { "name": "European Bioinformatics Institute", "partnered": false, "ror": "02catss52" } ], "pattern": "^\\d+(-\\d+)?$", "preferred_prefix": "imex", "providers": [ { "code": "CURATOR_REVIEW", "description": "IMEx Consortium though Intact", "homepage": "https://www.ebi.ac.uk/intact/", "name": "IMEx Consortium though Intact", "uri_format": "https://imexcentral.org/icentral/imex/rec/$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/imex:$1" }, { "code": "intact.search", "description": "Search page on IntAct", "homepage": "https://www.ebi.ac.uk/intact", "name": "IntAct Search", "uri_format": "https://www.ebi.ac.uk/intact/search?query=IM-$1" } ], "publications": [ { "doi": "10.1002/pmic.200700286", "pubmed": "17893861", "title": "Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition", "year": 2007 } ], "uri_format": "https://www.ebi.ac.uk/intact/imex/main.xhtml?query=IM-$1" }, "img.gene": { "contact": { "email": "nckyrpides@lbl.gov", "name": "Nikos C. Kyrpides", "orcid": "0000-0002-6131-0462" }, "description": "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information.", "example": "638309541", "homepage": "http://img.jgi.doe.gov/", "keywords": [ "gene", "genome" ], "mappings": { "biocontext": "IMG.GENE", "miriam": "img.gene", "n2t": "img.gene", "prefixcommons": "img.gene" }, "name": "Integrated Microbial Genomes Gene", "pattern": "^\\d+$", "preferred_prefix": "img.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. 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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/img.taxon:$1" } ], "publications": [ { "doi": "10.1093/nar/gkm846", "pmc": "PMC2238897", "pubmed": "17933782", "title": "The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions", "year": 2007 } ], "uri_format": "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1" }, "imgt.hla": { "contact": { "email": "steven.marsh@ucl.ac.uk", "name": "Steven G. E. Marsh", "orcid": "0000-0003-2855-4120" }, "description": "IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature.", "example": "A*01:01:01:01", "homepage": "https://www.ebi.ac.uk/imgt/hla/allele.html", "keywords": [ "biomedical science", "dna", "immunogenetics", "immunology", "protein", "rna" ], "mappings": { "biocontext": "IMGT.HLA", "cellosaurus": "IPD-IMGT/HLA", "edam": "2773", "fairsharing": "FAIRsharing.e28v7g", "go": "IMGT_HLA", "integbio": "nbdc00106", "miriam": "imgt.hla", "n2t": "imgt.hla", "ncbi": "IMGT/HLA", "prefixcommons": "imgthla", "re3data": "r3d100010804" }, "name": "IMGT/HLA human major histocompatibility complex sequence database", "owners": [ { "name": "European Bioinformatics Institute", "partnered": false, "ror": "02catss52" } ], "pattern": "^[A-Z0-9*:]+$", "preferred_prefix": "imgt.hla", "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/imgt.ligm:$1" } ], "publications": [ { "doi": "10.1093/nar/gkj088", "pmc": "PMC1347451", "pubmed": "16381979", "title": "IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell receptor nucleotide sequences", "year": 2006 } ], "uri_format": "http://www.imgt.org/ligmdb/view?id=$1" }, "imgt.primerdb": { "description": "The IMGT/PRIMER-DB database provides standardized information on oligonucleotides or primers of the immunoglobulins (IG) and T cell receptors (TR).", "example": "IPP900099", "homepage": "http://imgt.org/IMGTPrimerDB/", "keywords": [ "dna" ], "mappings": { "prefixcommons": "imgt.primerdb", "re3data": "r3d100012535" }, "name": "IMGT/PRIMER-DB", "preferred_prefix": "imgt.primerdb", "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/imgt.primerdb:$1" } ], "uri_format": "http://imgt.org/IMGTPrimerDB/Check_PrDB.pl?numacc0=$1&origin=view&source=PrList" }, "imotdb": { "comment": "This resource doesn't exist on the web anymore", "deprecated": true, "description": "The interacting motif database or iMOTdb , lists interacting motifs thatare identified for all structural entries in the PDB. The conserved patterns or finger prints are identified for individual structural entries and also grouped together for reporting the common motifs shared among all superfamily members.", "example": "53784", "homepage": "http://caps.ncbs.res.in/imotdb/", "keywords": [ "interaction", "protein" ], "mappings": { "pathguide": "207", "prefixcommons": "imotdb" }, "name": "Database of Spatially Interacting Motifs in Proteins", "preferred_prefix": "imotdb", "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/imotdb:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi?sfcode=$1" }, "imr": { "contact": { "email": "curator@inoh.org", "name": "INOH curators" }, "deprecated": true, "description": "MoleculeRole Ontology is an ontology for proteins/chemicals. It is used to annotate protein family names, generic/concrete protein names and chemical names in the INOH pathway data.", "example": "0000001", "homepage": "http://www.inoh.org", "keywords": [ "obo", "ontology", "protein", "small molecule" ], "mappings": { "biocontext": "IMR", "obofoundry": "imr", "prefixcommons": "imr" }, "name": "Molecule role (INOH Protein name/family name ontology)", "pattern": "^\\d{7}$", "preferred_prefix": "IMR", "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/imr:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/IMR_$1", "uri_format": "http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IMR&id=$1" }, "imsr.apb": { "description": "The NHMRC Australian PhenomeBank (APB) is a non-profit repository of mouse strains used in Medical Research. The database allows you to search for murine strains, housed or archived in Australia, carrying mutations in particular genes, strains with transgenic alterations and for mice with particular phenotypes. 1876 publicly available strains, 922 genes, 439 transgenes The APB has two roles: Provide and maintain a central database of genetically modified mice held in Australia either live or as cryopreserved material; Establish and maintain a mouse strain archive. Strains are archived as cryopreserved sperm or embryos. [from RRID]", "example": "7345", "homepage": "https://pb.apf.edu.au/phenbank/homePage.html", "keywords": [ "allele", "alteration", "chromosome", "database", "embryo", "gene", "live mouse", "murine", "mutation", "phenotype", "sperm", "strain", "transgene", "transgenic" ], "mappings": { "rrid": "IMSR_APB" }, "name": "NHMRC Australian PhenomeBank", "pattern": "^\\d+$", "preferred_prefix": "imsr.apb", "uri_format": "https://pb.apf.edu.au/phenbank/strain.html?id=$1" }, "imsr_em": { "contact": { "email": "d.smedley@qmul.ac.uk", "name": "Damian Smedley", "orcid": "0000-0002-5836-9850" }, "description": "Non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. Users may browse by strain, gene, phenotype, or human disease. Its primary objective is to establish and manage a unified repository for maintaining medically relevant mouse mutants and making them available to the scientific community. Therefore, EMMA archives mutant strains and distributes them to requesting researchers. EMMA also hosts courses in cryopreservation, to promote the use and dissemination of frozen embryos and spermatozoa. Dissemination of knowledge is further fostered by a dedicated resource database. Anybody who wants their mutant mouse strains cryopreserved may deposit strains with EMMA. However depositors must be aware that these strains become freely available to other researchers after being deposited.With more than 8400 mutant mouse strains and asmall but increasing number of rat mutant strains available, EMMA is the primary mouse repository in Europe and the third largest non-profit repository worldwide. [from RRID]", "example": "11478", "homepage": "https://www.infrafrontier.eu/emma/", "keywords": [ "mouse", "mutant mouse repository", "mutant mouse strain", "mutant strain" ], "mappings": { "rrid": "IMSR_EM" }, "name": "European Mouse Mutant Archive", "pattern": "^\\d+$", "preferred_prefix": "imsr_em", "publications": [ { "pubmed": "19783817" }, { "pubmed": "17709347" } ], "uri_format": "https://www.infrafrontier.eu/emma/strain-search/straindetails/?q=$1" }, "imsr_tac": { "description": "Supplier of mice for research purposes. [from RRID]", "example": "1178", "homepage": "https://www.taconic.com/", "keywords": [ "gene", "genetic engineering", "knockout", "mice", "model", "mouse", "repository", "research", "strain", "subject", "supply", "transgenic" ], "mappings": { "rrid": "IMSR_TAC" }, "name": "Taconic Biosciences", "preferred_prefix": "imsr_tac", "uri_format": "https://scicrunch.org/resolver/RRID:IMSR_TAC_$1" }, "inaturalist.observation": { "contributor": { "github": "oolonek", "name": "Pierre-Marie Allard", "orcid": "0000-0003-3389-2191" }, "description": "The identifier for an observation in iNaturalist", "example": "36010371", "github_request_issue": 517, "homepage": "https://www.inaturalist.org/observations", "mappings": { "wikidata": "P5683" }, "name": "iNaturalist Observation", "pattern": "^[1-9]\\d*$", "preferred_prefix": "inaturalist.observation", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.inaturalist.org/observations/$1" }, "inaturalist.place": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Identifier for a place in iNaturalist", "example": "7207", "homepage": "https://www.inaturalist.org/places", "mappings": { "wikidata": "P7471" }, "name": "iNaturalist Place", "pattern": "^[1-9]\\d*$", "preferred_prefix": "inaturalist.place", "uri_format": "https://www.inaturalist.org/places/$1" }, "inaturalist.taxon": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Identifier for a species in iNaturalist", "example": "21723", "homepage": "https://www.inaturalist.org/taxa", "mappings": { "wikidata": "P3151" }, "name": "iNaturalist Taxonomy", "pattern": "^[1-9]\\d{0,6}$", "preferred_prefix": "inaturalist.taxon", "uri_format": "https://www.inaturalist.org/taxa/$1" }, "inaturalist.user": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Identifier for a user in iNaturalist", "example": "1426686", "homepage": "https://www.inaturalist.org/users", "keywords": [ "person" ], "name": "iNaturalist User", "pattern": "^[1-9]\\d*$", "preferred_prefix": "inaturalist.user", "uri_format": "https://www.inaturalist.org/users/$1" }, "inchi": { "contact": { "email": "jmg11@cam.ac.uk", "name": "Stephen R. Heller", "orcid": "0000-0002-5538-8482" }, "description": "The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources. It is derived solely from a structural representation of that substance, such that a single compound always yields the same identifier.", "example": "InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3", "homepage": "http://www.chemspider.com/", "keywords": [ "centrally registered identifier", "chemical descriptor", "chemical entity", "chemical structure", "cheminformatics", "chemistry", "knowledge and information systems", "molecular entity", "molecular structure" ], "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBcUVFIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--250afbf70b1e3f9c188231ff2fb50477040a71f5/inchi-wheel.png?disposition=inline", "mappings": { "biocontext": "INCHI", "fairsharing": "FAIRsharing.ddk9t9", "miriam": "inchi", "n2t": "inchi", "wikidata": "P234" }, "name": "InChI", "pattern": "^InChI\\=1S?\\/[A-Za-z0-9\\.]+(\\+[0-9]+)?(\\/[cnpqbtmsih][A-Za-z0-9\\-\\+\\(\\)\\,\\/\\?\\;\\.]+)*$", "preferred_prefix": "inchi", "providers": [ { "code": "CURATOR_REVIEW", "description": "InChI through NIST", "homepage": "http://webbook.nist.gov/chemistry", "name": "InChI through NIST", "uri_format": "http://webbook.nist.gov/cgi/cbook.cgi?$1" }, { "code": "ebi", "description": "InChI through ChEBI", "homepage": "https://www.ebi.ac.uk/chebi/", "name": "InChI through ChEBI", "uri_format": "https://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString=$1" }, { "code": "um", "description": "InChI through RDF Open Molecules", "homepage": "http://rdf.openmolecules.net/", "name": "InChI through RDF Open Molecules", "uri_format": "http://rdf.openmolecules.net/?$1" } ], "publications": [ { "doi": "10.1186/s13321-021-00517-z", "pmc": "PMC8147039", "pubmed": "34030732", "title": "InChI version 1.06: now more than 99.99% reliable", "year": 2021 }, { "doi": "10.1186/s13321-015-0068-4", "pmc": "PMC4486400", "pubmed": "26136848", "title": "InChI, the IUPAC International Chemical Identifier", "year": 2015 }, { "doi": "10.1007/s10822-015-9854-3", "pubmed": "26081259", "title": "Many InChIs and quite some feat", "year": 2015 }, { "doi": "10.1186/s13321-024-00847-8", "title": "InChI isotopologue and isotopomer specifications", "year": 2024 } ], "repository": "https://github.com/IUPAC-InChI/InChI", "twitter": "inchi_trust", "uri_format": "http://www.chemspider.com/$1" }, "inchikey": { "description": "The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI.", "example": "RYYVLZVUVIJVGH-UHFFFAOYSA-N", "homepage": "http://www.chemspider.com/", "mappings": { "biocontext": "INCHIKEY", "miriam": "inchikey", "n2t": "inchikey", "togoid": "InchiKey", "wikidata": "P235" }, "name": "InChIKey", "pattern": "^[A-Z]{14}\\-[A-Z]{10}(\\-[A-Z])?$", "preferred_prefix": "inchikey", "providers": [ { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", "homepage": "https://scholia.toolforge.org/", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/inchikey/$1" } ], "uri_format": "https://www.chemspider.com/search?params=$1" }, "informall": { "appears_in": [ "doid" ], "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The InformAll database was developed to provide a credible source of information on allergenic food materials of both plant and animal origin.", "example": "410", "github_request_issue": 1311, "homepage": "http://research.bmh.manchester.ac.uk/informAll/", "name": "InformAll Allergenic Food Database", "pattern": "^\\d+$", "preferred_prefix": "informall", "uri_format": "http://research.bmh.manchester.ac.uk/informall/allergenic-food/?FoodId=$1" }, "inhand": { "comment": "This nomenclature is available via email. Truly a disgrace.", "contact": { "email": "harkemaj@msu.edu", "name": "Jack R Harkema", "orcid": "0000-0003-4682-0824" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The standard reference for nomenclature and diagnostic criteria in toxicologic pathology.", "homepage": "https://www.goreni.org/gr3_nomenclature.php", "keywords": [ "biomedical science", "disease", "toxicity" ], "mappings": { "fairsharing": "FAIRsharing.9gqfpm" }, "name": "The International Harmonization of Nomenclature and Diagnostic criteria", "preferred_prefix": "inhand", "proprietary": true, "publications": [ { "doi": "10.1177/0192623309353423", "pubmed": "20032296", "title": "Proliferative and nonproliferative lesions of the rat and mouse respiratory tract", "year": 2009 } ] }, "inn": { "comment": "can not find a place to resolve to", "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.", "example": "fluticasone", "homepage": "https://www.who.int/teams/health-product-and-policy-standards/inn", "mappings": { "wikidata": "P2275" }, "name": "International Nonproprietary Names", "preferred_prefix": "inn", "synonyms": [ "INN_ID" ], "uri_format": "https://mednet-communities.net/inn/db/ViewINN.aspx?i=$1" }, "innatedb": { "contact": { "email": "david.lynn@flinders.edu.au", "name": "David Lynn", "orcid": "0000-0003-4664-1404" }, "description": "InnateDB has been developed to facilitate systems level investigations of the mammalian (human, mouse and bovine) innate immune response. Its goal is to provide a manually-curated knowledgebase of the genes, proteins, and particularly, the interactions and signaling responses involved in mammalian innate immunity. InnateDB incorporates information of the whole human, mouse and bovine interactomes by integrating interaction and pathway information from several of the major publicly available databases but aims to capture an improved coverage of the innate immunity interactome through manual curation.", "example": "20021", "homepage": "http://www.innatedb.ca/", "keywords": [ "gene", "immunology", "interaction", "life science", "pathway", "protein" ], "mappings": { "fairsharing": "FAIRsharing.rb2drw", "integbio": "nbdc01870", "pathguide": "264", "prefixcommons": "innatedb", "re3data": "r3d100010676" }, "name": "A Knowledge Resource for Innate Immunity Interactions and Pathways", "preferred_prefix": "innatedb", "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/innatedb:$1" } ], "publications": [ { "doi": "10.1093/nar/gks1147", "pmc": "PMC3531080", "pubmed": "23180781", "title": "InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation", "year": 2012 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "twitter": "innatedb", "uri_format": "http://www.innatedb.ca/getGeneCard.do?id=$1" }, "ino": { "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", "name": "Yongqun Oliver He", "orcid": "0000-0001-9189-9661" }, "description": "he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles.", "download_owl": "http://purl.obolibrary.org/obo/ino.owl", "example": "0000003", "homepage": "https://github.com/INO-ontology/ino", "keywords": [ "life science", "molecular interaction", "network model", "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "INO", "biolink": "INO", "bioportal": "INO", "fairsharing": "FAIRsharing.mm72as", "obofoundry": "ino", "ols": "ino", "ontobee": "INO" }, "name": "Interaction Network Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "INO", "publications": [ { "doi": "10.1186/s13040-016-0118-0", "pmc": "PMC5168857", "pubmed": "28031747", "title": "The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature", "year": 2016 }, { "doi": "10.1186/2041-1480-6-2", "pmc": "PMC4362819", "pubmed": "25785184", "title": "Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions", "year": 2015 }, { "doi": "10.1186/2041-1480-2-s2-s8", "pmc": "PMC3102897", "pubmed": "21624163", "title": "Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology", "year": 2011 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/INO_$1", "repository": "https://github.com/INO-ontology/ino", "uri_format": "http://purl.obolibrary.org/obo/INO_$1", "version": "1.1.13" }, "insdc": { "description": "The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences.", "example": "X58356", "homepage": "https://www.ncbi.nlm.nih.gov/Genbank/", "keywords": [ "dna" ], "mappings": { "biocontext": "INSDC", "integbio": "nbdc02567", "miriam": "insdc", "n2t": "insdc", "prefixcommons": "insdc", "togoid": "Insdc" }, "name": "Nucleotide Sequence Database", "pattern": "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4,6}\\d{8,10}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$", "preferred_prefix": "insdc", "providers": [ { "code": "CURATOR_REVIEW", "description": "INSDC through DDBJ", "homepage": "http://www.ddbj.nig.ac.jp/", "name": "INSDC through DDBJ", "uri_format": "https://getentry.ddbj.nig.ac.jp/getentry?database=ddbj&accession_number=$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/insdc:$1" }, { "code": "ebi", "description": "INSDC through European Nucleotide Archive (ENA)", "homepage": "https://www.ebi.ac.uk/ena/", "name": "INSDC through European Nucleotide Archive (ENA)", "uri_format": "https://www.ebi.ac.uk/ena/data/view/$1" }, { "code": "ncbi", "description": "INSDC through Nucleotide database at NCBI", "homepage": "https://www.ncbi.nlm.nih.gov/nuccore/", "name": "INSDC through Nucleotide database at NCBI", "uri_format": "https://www.ncbi.nlm.nih.gov/nuccore/$1" } ], "publications": [ { "doi": "10.1093/nar/gkae1058", "pubmed": "39535044", "title": "The international nucleotide sequence database collaboration (INSDC): enhancing global participation", "year": 2024 }, { "doi": "10.1093/nar/18.6.1517", "pmc": "PMC330520", "pubmed": "2326192", "title": "Recent changes in the GenBank On-line Service", "year": 1990 }, { "doi": "10.1093/nar/gkl986", "pmc": "PMC1781245", "pubmed": "17202161", "title": "GenBank", "year": 2007 }, { "doi": "10.1093/nar/gkl913", "pmc": "PMC1897316", "pubmed": "17148479", "title": "EMBL Nucleotide Sequence Database in 2006", "year": 2006 }, { "doi": "10.1126/science.298.5597.1333b", "pubmed": "12436968", "title": "Nucleotide sequence database policies", "year": 2002 } ], "uri_format": "https://www.ncbi.nlm.nih.gov/nuccore/$1" }, "insdc.cds": { "description": "The coding sequence or protein identifiers as maintained in INSDC.", "example": "AAA35559", "has_canonical": "ncbiprotein", "homepage": "http://getentry.ddbj.nig.ac.jp", "mappings": { "biocontext": "INSDC.CDS", "miriam": "insdc.cds", "n2t": "insdc.cds" }, "name": "INSDC CDS", "pattern": "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4}\\d{8}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$", "preferred_prefix": "insdc.cds", "providers": [ { "code": "CURATOR_REVIEW", "description": "INSDC CDS through ENA", "homepage": "https://www.ebi.ac.uk/ena", "name": "INSDC CDS through ENA", "uri_format": "https://www.ebi.ac.uk/ena/data/view/$1" }, { "code": "CURATOR_REVIEW", "description": "INSDC CDS through NCBI", "homepage": "https://www.ncbi.nlm.nih.gov/protein/", "name": "INSDC CDS through NCBI", "uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1" } ], "uri_format": "http://getentry.ddbj.nig.ac.jp/getentry/dad/$1" }, "insdc.gca": { "description": "The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage.", "example": "GCA_000155495.1", "has_canonical": "ncbi.assembly", "homepage": "https://www.ebi.ac.uk/ena/browse/genome-assembly-database", "mappings": { "biocontext": "INSDC.GCA", "miriam": "insdc.gca", "n2t": "insdc.gca" }, "name": "Genome assembly database - INSDC accessions", "pattern": "^GCA_[0-9]{9}(\\.[0-9]+)?$", "preferred_prefix": "insdc.gca", "providers": [ { "code": "ncbi", "description": "Genome assembly database NCBI", "homepage": "https://www.ncbi.nlm.nih.gov/datasets/genome/", "name": "Genome assembly database NCBI", "uri_format": "https://www.ncbi.nlm.nih.gov/datasets/genome/$1" } ], "uri_format": "https://www.ebi.ac.uk/ena/data/view/$1" }, "insdc.gcf": { "description": "The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database RefSeq accessions does not extend to viroids and bacteriophage.", "example": "GCF_000001405", "has_canonical": "ncbi.assembly", "homepage": "https://www.ncbi.nlm.nih.gov/", "mappings": { "miriam": "refseq.gcf" }, "name": "Genome assembly database - RefSeq accessions", "pattern": "^GCF_[0-9]{9}(\\.[0-9]+)?$", "preferred_prefix": "insdc.gcf", "synonyms": [ "insdc.gcf" ], "uri_format": "https://www.ncbi.nlm.nih.gov/datasets/genome/$1" }, "insdc.run": { "comment": "https://www.insdc.org/ is the authoritative source for INSDC. However, confusingly, they don't mention runs in this table. I think we should ask them to include. ENA is a partner and they have documentation [here](https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html). Runs | (E\\|D\\|S)RR[0-9]{6,} | ERR123456 -- | -- | --", "contributor": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "description": "An experimental run, served thrugh the ENA", "example": "ERR436051", "github_request_issue": 131, "homepage": "https://www.insdc.org/", "name": "International Nucleotide Sequence Database Collaboration (INSDC) Run", "pattern": "^(E|D|S)RR[0-9]{6,}$", "preferred_prefix": "insdc.run", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.ebi.ac.uk/ena/browser/view/$1" }, "insdc.sra": { "contact": { "email": "Hugh.Shanahan@rhul.ac.uk", "github": "hughshanahan", "name": "Hugh P Shanahan", "orcid": "0000-0003-1374-6015" }, "description": "The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.", "example": "SRX000007", "homepage": "https://www.ncbi.nlm.nih.gov/sra", "keywords": [ "biology", "epidemiology", "genomics", "virology" ], "mappings": { "biocontext": "INSDC.SRA", "fairsharing": "FAIRsharing.g7t2hv", "miriam": "insdc.sra", "n2t": "insdc.sra", "re3data": "r3d100010775" }, "name": "Sequence Read Archive", "pattern": "^[SED]R[APRSXZ]\\d+$", "preferred_prefix": "insdc.sra", "providers": [ { "code": "ddbj", "description": "DDBJ Sequence Read Archive (DRA)", "homepage": "https://www.ddbj.nig.ac.jp/dra/index-e.html", "name": "DDBJ Sequence Read Archive (DRA)", "uri_format": "https://ddbj.nig.ac.jp/resource/sra-experiment/$1" }, { "code": "ebi", "description": "European Nucleotide Archive (ENA)", "homepage": "https://www.ebi.ac.uk/ena", "name": "European Nucleotide Archive (ENA)", "uri_format": "https://www.ebi.ac.uk/ena/data/view/$1" } ], "publications": [ { "doi": "10.1186/s13742-015-0064-7", "pmc": "PMC4425880", "pubmed": "25960871", "title": "Investigation into the annotation of protocol sequencing steps in the sequence read archive", "year": 2015 }, { "doi": "10.1093/nar/gkr854", "pmc": "PMC3245110", "pubmed": "22009675", "title": "The Sequence Read Archive: explosive growth of sequencing data", "year": 2011 }, { "doi": "10.1093/nar/gkm1000", "pmc": "PMC2238880", "pubmed": "18045790", "title": "Database resources of the National Center for Biotechnology Information", "year": 2007 } ], "uri_format": "https://www.ncbi.nlm.nih.gov/sra/$1" }, "intact": { "contact": { "email": "kalpanap@ebi.ac.uk", "github": "Kalpanapanneerselvam", "name": "Kalpana Panneerselvam", "orcid": "0000-0003-2534-198X" }, "contributor_extras": [ { "email": "sbalu@ebi.ac.uk", "github": "CP-SB", "name": "Sucharitha Balu", "orcid": "0000-0001-7456-0594" } ], "description": "IntAct provides a freely available, open source database system and analysis tools for protein interaction data.", "example": "EBI-2307691", "homepage": "https://www.ebi.ac.uk/intact/", "keywords": [ "biology", "interaction", "protein" ], "license": "CC-BY-4.0", "mappings": { "biocontext": "INTACT", "fairsharing": "FAIRsharing.d05nwx", "go": "IntAct", "integbio": "nbdc00507", "miriam": "intact", "n2t": "intact", "pathguide": "111", "prefixcommons": "intact", "re3data": "r3d100010671", "togoid": "Intact", "uniprot": "DB-0051" }, "name": "IntAct protein interaction database", "owners": [ { "name": "European Bioinformatics Institute", "partnered": false, "ror": "02catss52" } ], "pattern": "^EBI\\-[0-9]+$", "preferred_prefix": "intact", "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/intact:$1" } ], "publications": [ { "doi": "10.1002/cpz1.70018", "pubmed": "39401100", "title": "IntAct Database for Accessing IMEx's Contextual Metadata of Molecular Interactions", "year": 2024 }, { "doi": "10.1093/nar/gkt1115", "pmc": "PMC3965093", "pubmed": "24234451", "title": "The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases", "year": 2013 }, { "doi": "10.1038/nmeth.1637", "pmc": "PMC3246345", "pubmed": "21716279", "title": "PSICQUIC and PSISCORE: accessing and scoring molecular interactions", "year": 2011 }, { "doi": "10.1093/nar/gkp878", "pmc": "PMC2808934", "pubmed": "19850723", "title": "The IntAct molecular interaction database in 2010", "year": 2009 }, { "doi": "10.1186/1741-7007-5-44", "pmc": "PMC2189715", "pubmed": "17925023", "title": "Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions", "year": 2007 }, { "doi": "10.1093/nar/gkh052", "pmc": "PMC308786", "pubmed": "14681455", "title": "IntAct: an open source molecular interaction database", "year": 2004 } ], "twitter": "intact_project", "uri_format": "https://www.ebi.ac.uk/intact/interaction/$1" }, "intact.molecule": { "description": "IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules.", "example": "EBI-366083", "homepage": "https://www.ebi.ac.uk/intact/", "mappings": { "biocontext": "INTACT.MOLECULE", "miriam": "intact.molecule", "n2t": "intact.molecule" }, "name": "IntAct Molecule", "pattern": "^EBI\\-[0-9]+$", "preferred_prefix": "intact.molecule", "publications": [ { "doi": "10.1002/cpz1.70018", "pubmed": "39401100", "title": "IntAct Database for Accessing IMEx's Contextual Metadata of Molecular Interactions", "year": 2024 } ], "uri_format": "https://www.ebi.ac.uk/intact/search?query=$1" }, "integbio": { "contact": { "email": "kwsm@dbcls.rois.ac.jp", "github": "skwsm", "name": "Shuichi Kawashima", "orcid": "0000-0001-7883-3756" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Integbio Database Catalog provides whereabouts information (URL), database description, biological species and other attributes (metadata) of Japanese and international life science databases to make it easier for users to find databases they need. This catalog has been developed as a part of the integration of life science databases promoted by four ministries in Japan: the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), The Ministry of Health, Labor, and Welfare (MHLW), the Ministry of Agriculture, Forestry, and Fisheries (MAFF), and the Ministry of Economy, Trade, and Industry of Japan (METI). (from https://integbio.jp/dbcatalog/en/about)", "example": "nbdc01071", "homepage": "https://integbio.jp/en/", "license": "CC0-1.0", "logo": "https://integbio.jp/templates/integbio/images/logo/logo.png", "name": "Integbio", "pattern": "^nbdc\\d+$", "preferred_prefix": "integbio", "uri_format": "https://catalog.integbio.jp/dbcatalog/en/record/$1" }, "interfil": { "description": "The Intermediate Filament Database functions as a continuously updated review of the intermediate filament field and it is hoped that users will contribute to the development and expansion of the database on a regular basis. Contributions may include novel variants, new patients with previously discovered sequence and allelic variants.", "example": "NM_006262", "homepage": "http://www.interfil.org", "keywords": [ "genome" ], "mappings": { "prefixcommons": "interfil" }, "name": "Human Intermediate Filament Database", "preferred_prefix": "interfil", "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/interfil:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.interfil.org/details.php?id=$1" }, "interlex": { "contact": { "email": "mmartone@ucsd.edu", "github": "memartone", "name": "Maryann Elizabeth Martone", "orcid": "0000-0002-8406-3871" }, "description": "InterLex is a dynamic lexicon, initially built on the foundation of NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed to help improve the way that biomedical scientists communicate about their data, so that information systems can find data more easily and provide more powerful means of integrating data across distributed resources and datasets. InterLex allows for the association of data fields and data values to common data elements and terminologies enabling the crowdsourcing of data-terminology mappings within and across communities. InterLex provides a stable layer on top of the many other existing terminologies, lexicons, ontologies, and common data element collections and provides a set of inter-lexical and inter-data-lexical mappings. ", "example": "0101963", "homepage": "https://www.fdilab.org", "keywords": [ "anatomy", "biomedical science", "brain", "imaging", "neurobiology" ], "mappings": { "fairsharing": "FAIRsharing.67sssf", "miriam": "ilx", "wikidata": "P696" }, "name": "InterLex", "pattern": "^[0-9]+$", "preferred_prefix": "interlex", "publications": [ { "doi": "10.3389/fninf.2013.00018", "pmc": "PMC3757470", "pubmed": "24009581", "title": "NeuroLex.org: an online framework for neuroscience knowledge", "year": 2013 } ], "references": [ "https://github.com/AllenInstitute/nomenclature" ], "synonyms": [ "ILX" ], "uri_format": "https://scicrunch.org/scicrunch/interlex/view/ilx_$1" }, "interpro": { "contact": { "email": "agb@ebi.ac.uk", "name": "Alex Bateman", "orcid": "0000-0002-6982-4660" }, "description": "InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.", "example": "IPR016380", "homepage": "http://www.ebi.ac.uk/interpro/index.html", "keywords": [ "bioinformatics", "biology", "domain", "obo", "ontology", "protein" ], "license": "CC0-1.0", "mappings": { "biocontext": "IPR", "biolink": "interpro", "edam": "1133", "fairsharing": "FAIRsharing.pda11d", "go": "InterPro", "integbio": "nbdc00108", "miriam": "interpro", "n2t": "interpro", "ncbi": "InterPro", "obofoundry": "ipr", "prefixcommons": "interpro", "re3data": "r3d100010798", "togoid": "Interpro", "uniprot": "DB-0052", "wikidata": "P2926" }, "name": "InterPro", "pattern": "^IPR\\d{6}$", "preferred_prefix": "interpro", "providers": [ { "code": "CURATOR_REVIEW", "description": "Bio2RDF", "homepage": "http://bio2rdf.org/", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/interpro:$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/interpro:$1" } ], "publications": [ { "doi": "10.1093/nar/gkae1082", "pubmed": "39565202", "title": "InterPro: the protein sequence classification resource in 2025", "year": 2024 }, { "doi": "10.1093/nar/gkac993", "pmc": "PMC9825450", "pubmed": "36350672", "title": "InterPro in 2022", "year": 2023 }, { "doi": "10.1093/nar/gkaa977", "pmc": "PMC7778928", "pubmed": "33156333", "title": "The InterPro protein families and domains database: 20 years on", "year": 2021 }, { "doi": "10.1093/nar/gky1100", "pmc": "PMC6323941", "pubmed": "30398656", "title": "InterPro in 2019: improving coverage, classification and access to protein sequence annotations", "year": 2019 }, { "doi": "10.1093/nar/gki106", "pmc": "PMC540060", "pubmed": "15608177", "title": "InterPro, progress and status in 2005", "year": 2005 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/IPR_$1", "repository": "https://proteinswebteam.github.io/interpro-blog/", "synonyms": [ "IP", "IPR", "InterPro" ], "twitter": "InterProDB", "uri_format": "https://www.ebi.ac.uk/interpro/entry/InterPro/$1" }, "iobc": { "contact": { "email": "kushida@biosciencedbc.jp", "github": "kushidatatsuya", "name": "Tatsuya Kushida", "orcid": "0000-0002-0784-4113" }, "description": "Interlinking Ontology for Biological Concepts (IOBC) contains approximately 80,000 biological concepts such as biological phenomena, diseases, molecular functions, gene products, chemicals, and medical cares, and approximately 20,000 related concepts such as earth science and environmental science. The concepts are structured by thirty-five relations such as has function, has role, has quality, and precedes. Each concept has both of English and Japanese labels. For further information including the developmental method, see papers in the PUBLICATIONS PAGE. The license for this ontology is specified in the Creative Commons Attribution-NonCommercial 4.0 International. If you use data from this ontology, please be sure attribute this ontology as follows: \"Interlinking Ontology for Biological Concepts © National Bioscience Database Center licensed under CC Attribution-NonCommercial 4.0 International\".", "download_owl": "http://aber-owl.net/media/ontologies/IOBC/25/iobc.owl", "example": "200906038218908385", "example_extras": [ "AC21", "AC21_cat", "OWLClass_00000000000000000321" ], "homepage": "https://github.com/kushidat/IOBC", "keywords": [ "ontology" ], "license": "CC-BY-NC-4.0", "mappings": { "aberowl": "IOBC", "bioportal": "IOBC" }, "name": "Interlinking Ontology for Biological Concepts", "preferred_prefix": "iobc", "publications": [ { "doi": "10.1007/s00354-019-00074-y", "title": "Interconnection of Biological Knowledge Using NikkajiRDF and Interlinking Ontology for Biological Concepts", "year": 2019 } ], "repository": "https://github.com/kushidat/IOBC", "uri_format": "http://purl.jp/bio/4/id/$1" }, "ipi": { "deprecated": true, "description": "IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI maintaisn a database of cross references between the primary data sources, it provides minimally redundant but complete sets of proteins for featured species, and it maintains stable and unique identifiers.", "example": "IPI00000001", "homepage": "http://www.ebi.ac.uk/IPI", "keywords": [ "protein" ], "mappings": { "biocontext": "IPI", "integbio": "nbdc00911", "prefixcommons": "ipi" }, "name": "International Protein Index", "preferred_prefix": "ipi", "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/ipi:$1" } ], "publications": [ { "doi": "10.1002/pmic.200300721", "pubmed": "15221759", "title": "The International Protein Index: an integrated database for proteomics experiments", "year": 2004 } ], "uri_format": "http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$1&format=default" }, "irct": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Iranian Registry of Clinical Trials. This is a Primary Registry in the WHO Registry Network set up with the help from the Ministry of Health and Medical Education (MOHME) and hosted by Iran University of Medical Sciences (IUMS). (from homepage)\nNote that the website uses a different identifier then the one reported in this semantic space.", "example": "IRCT20080904001199N7", "homepage": "https://en.irct.ir/", "name": "Iranian Registry of Clinical Trials", "pattern": "^IRCT\\d+N\\d+$", "preferred_prefix": "irct", "references": [ "https://en.irct.ir/trial/65035" ] }, "ird.segment": { "contact": { "email": "richard.scheuermann@nih.gov", "github": "scheuerm", "name": "Richard H. Scheuermann", "orcid": "0000-0003-1355-892X" }, "description": "Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s).", "example": "CY077097", "homepage": "http://www.fludb.org/", "keywords": [ "gene", "protein" ], "mappings": { "biocontext": "IRD.SEGMENT", "miriam": "ird.segment", "n2t": "ird.segment", "prefixcommons": "ird.segment" }, "name": "IRD Segment Sequence", "pattern": "^\\w+(\\_)?\\d+(\\.\\d+)?$", "preferred_prefix": "ird.segment", "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/ird.segment:$1" } ], "publications": [ { "doi": "10.1093/nar/gkm905", "pmc": "PMC2238987", "pubmed": "17965094", "title": "BioHealthBase: informatics support in the elucidation of influenza virus host pathogen interactions and virulence", "year": 2007 } ], "uri_format": "http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1" }, "irefweb": { "contact": { "email": "shoshana@sickkids.ca", "name": "Shoshana J. Wodak", "orcid": "0000-0002-0701-6545" }, "deprecated": true, "description": "iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived.", "example": "617102", "homepage": "http://wodaklab.org/iRefWeb/", "keywords": [ "interaction", "life science", "protein" ], "mappings": { "biocontext": "IREFWEB", "fairsharing": "FAIRsharing.t31wcb", "miriam": "irefweb", "n2t": "irefweb", "pathguide": "300", "prefixcommons": "irefweb", "re3data": "r3d100012725" }, "name": "iRefWeb", "pattern": "^\\d+$", "preferred_prefix": "irefweb", "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/irefweb:$1" } ], "publications": [ { "doi": "10.1093/database/baq023", "pmc": "PMC2963317", "pubmed": "20940177", "title": "iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence", "year": 2010 } ], "twitter": "wodaklab", "uri_format": "http://wodaklab.org/iRefWeb/interaction/show/$1" }, "iresite": { "contact": { "email": "martin.pospisek@natur.cuni.cz", "name": "Martin Pospíšek", "orcid": "0000-0002-9490-8911" }, "description": "The IRESite database presents information about experimentally studied IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract the eukaryotic ribosomal translation initiation complex and thus promote translation initiation independently of the presence of the commonly utilized 5'-terminal 7mG cap structure.", "example": "322", "homepage": "http://www.iresite.org", "keywords": [ "life science", "regulation", "rna" ], "mappings": { "fairsharing": "FAIRsharing.kd39j4", "integbio": "nbdc01752", "prefixcommons": "iresite" }, "name": "Database of experimentally verified IRES structures", "preferred_prefix": "iresite", "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/iresite:$1" } ], "publications": [ { "doi": "10.1093/nar/gkp981", "pmc": "PMC2808886", "pubmed": "19917642", "title": "IRESite--a tool for the examination of viral and cellular internal ribosome entry sites", "year": 2009 }, { "doi": "10.1093/nar/gkj081", "pmc": "PMC1347444", "pubmed": "16381829", "title": "IRESite: the database of experimentally verified IRES structures (www.iresite.org)", "year": 2006 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.iresite.org/IRESite_web.php?page=view&entry_id=$1" }, "iro": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "example": "0000008", "name": "Insect Resistance Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "iro", "uri_format": "https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:$1" }, "isbn": { "description": "The International Standard Book Number (ISBN) is for identifying printed books.", "example": "9789211613865", "example_extras": [ "978-92-1-161386-5" ], "homepage": "http://isbndb.com/", "keywords": [ "bibliography" ], "mappings": { "biocontext": "ISBN-13", "biolink": "isbn", "edam": "2634", "go": "ISBN", "miriam": "isbn", "n2t": "isbn", "prefixcommons": "isbn" }, "name": "International Standard Book Number", "pattern": "^(ISBN)?(-13|-10)?[:]?[ ]?(\\d{2,3}[ -]?)?\\d{1,5}[ -]?\\d{1,7}[ -]?\\d{1,6}[ -]?(\\d|X)$", "preferred_prefix": "isbn", "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/isbn:$1" }, { "code": "google.isbn", "description": "Google Books provider for ISBN numbers", "homepage": "https://books.google.com", "name": "Google Books", "uri_format": "https://books.google.com/books?isbn=$1" }, { "code": "worldcat", "description": "ISBN database at WorldCat", "homepage": "http://www.worldcat.org/", "name": "ISBN database at WorldCat", "uri_format": "http://www.worldcat.org/isbn/$1" } ], "synonyms": [ "ISBN-10", "ISBN-13" ], "uri_format": "https://isbnsearch.org/isbn/$1" }, "ised": { "description": "ISED catalogues the influenza sequence and epitope information obtained in countries worldwide and currently hosts a total of 49368 influenza A and 4761 influenza B virus sequence data including pandemic A/H1N1 2009 virus sequences collected in 42 countries, and a total of 545 amantadine-resistant influenza virus sequences collected in Korea.", "example": "AY209920", "homepage": "http://influenza.korea.ac.kr", "keywords": [ "protein" ], "mappings": { "prefixcommons": "ised" }, "name": "Influenza Sequence and Epitope Database", "preferred_prefix": "ised", "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/ised:$1" } ] }, "isfinder": { "contact": { "email": "patricia.siguier@univ-tlse3.fr", "name": "Patricia Siguier", "orcid": "0000-0003-1620-6495" }, "deprecated": true, "description": "ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available.", "example": "ISA1083-2", "homepage": "http://www-is.biotoul.fr/i", "keywords": [ "gene", "life science", "sequence" ], "mappings": { "biocontext": "ISFINDER", "fairsharing": "FAIRsharing.xhpc3h", "integbio": "nbdc00510", "miriam": "isfinder", "n2t": "isfinder", "ncbi": "ISFinder", "prefixcommons": "isfinder" }, "name": "Insertion sequence elements database", "pattern": "^IS\\w+(\\-\\d)?$", "preferred_prefix": "isfinder", "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/isfinder:$1" } ], "publications": [ { "doi": "10.1093/nar/gkj014", "pmc": "PMC1347377", "pubmed": "16381877", "title": "ISfinder: the reference centre for bacterial insertion sequences", "year": 2006 } ], "uri_format": "https://www-is.biotoul.fr/scripts/ficheIS.php?name=$1" }, "isni": { "description": "ISNI is the ISO certified global standard number for identifying the millions of contributors to creative works and those active in their distribution, including researchers, inventors, writers, artists, visual creators, performers, producers, publishers, aggregators, and more. It is part of a family of international standard identifiers that includes identifiers of works, recordings, products and right holders in all repertoires, e.g. DOI, ISAN, ISBN, ISRC, ISSN, ISTC, and ISWC.\n\nThe mission of the ISNI International Authority (ISNI-IA) is to assign to the public name(s) of a researcher, inventor, writer, artist, performer, publisher, etc. a persistent unique identifying number in order to resolve the problem of name ambiguity in search and discovery; and diffuse each assigned ISNI across all repertoires in the global supply chain so that every published work can be unambiguously attributed to its creator wherever that work is described.", "example": "000000012281955X", "homepage": "http://www.isni.org", "mappings": { "bartoc": "20464", "biolink": "isni", "miriam": "isni", "n2t": "isni", "wikidata": "P213" }, "name": "International Standard Name Identifier", "pattern": "^[0-9]{15}[0-9X]{1}$", "preferred_prefix": "isni", "providers": [ { "code": "isni.short", "description": "Unqualified ISNI URI", "homepage": "http://www.isni.org", "name": "ISNI short", "uri_format": "http://www.isni.org/$1" } ], "uri_format": "http://www.isni.org/isni/$1" }, "iso.3166": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An identifier for a country in numeric format per ISO 3166-1", "example": "554", "homepage": "https://www.iso.org/iso-3166-country-codes.html", "mappings": { "wikidata": "P299" }, "name": "ISO 3166-1 Country Code", "pattern": "^\\d+$", "preferred_prefix": "iso.3166", "uri_format": "https://data.who.int/countries/$1" }, "iso15926": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The primary purpose of ISO 15926 is to provide a foundation ontology to support the integration and sharing of data related to the lifecycle of a process plant in such a way that it is consistent, unambiguous, and minimizing the number of ways something could be expressed. Further purpose of ISO 15926-14 is to meet needs for OWL 2 ontologies that are based on ISO 15926-2, that enable efficient reasoning and that capture lifecycle information. A specific purpose is to demonstrate lifecycle modelling through a representation of the lifecycle model of ISO/IEC 81346-1. Another specific purpose is to exemplify how this standard can be used to develop industrial ontologies through various real-world use cases from industry. (from https://nfdi4cat.org/services/ontologie-sammlung/)", "download_rdf": "https://github.com/uwasystemhealth/modular_ontologies/raw/master/LIS-14.ttl", "example": "activityBoundOf", "homepage": "https://15926.org/home/", "name": "ISO 15926-14", "preferred_prefix": "iso15926", "uri_format": "http://standards.iso.org/iso/15926/part14/$1" }, "isrctn": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The ISRCTN registry is a primary clinical trial registry recognised by WHO and ICMJE that accepts all clinical research studies (whether proposed, ongoing or completed), providing content validation and curation and the unique identification number necessary for publication. All study records in the database are freely accessible and searchable. (from homepage)", "example": "ISRCTN10175490", "homepage": "https://www.isrctn.com/", "name": "International Traditional Medicine Clinical Trial Registry", "pattern": "^ISRCTN\\d+$", "preferred_prefix": "isrctn", "providers": [ { "code": "doi", "description": "DOI resolution of ISRCTN", "homepage": "https://doi.org/10.1186", "name": "DOI", "uri_format": "https://doi.org/10.1186/$1" } ], "uri_format": "https://www.isrctn.com/$1" }, "issn": { "description": "The International Standard Serial Number (ISSN) is a unique eight-digit number used to identify a print or electronic periodical publication, rather than individual articles or books.", "example": "0745-4570", "homepage": "https://portal.issn.org", "mappings": { "biocontext": "ISSN", "biolink": "issn", "go": "ISSN", "miriam": "issn", "n2t": "issn" }, "name": "International Standard Serial Number", "pattern": "^\\d{4}-\\d{3}[\\dX]$", "preferred_prefix": "issn", "providers": [ { "code": "CURATOR_REVIEW", "description": "ISSN at Library of Congress", "homepage": "http://catalog.loc.gov/webvoy.htm", "name": "ISSN at Library of Congress", "uri_format": "https://catalog.loc.gov/vwebv/search?searchCode=STNO&searchArg=$1&searchType=1&recCount=25" } ], "uri_format": "https://portal.issn.org/resource/ISSN/$1" }, "istransbase": { "contact": { "email": "oriental-cds@163.com", "name": "Dongsheng Cao" }, "contributor": { "email": "shah.tanay2@northeastern.edu", "github": "tanayshah2", "name": "Tanay Shah", "orcid": "0009-0001-1912-5132" }, "description": "ISTransbase is a highly reliable and accessible database that focuses on inhibitors and substrates of drug transporters, offering a wealth of vital information encompassing experimental methods, transport parameters, and references.", "example": "IST028", "github_request_issue": 1145, "homepage": "https://istransbase.scbdd.com/", "name": "ISTransbase", "preferred_prefix": "istransbase", "publications": [ { "doi": "10.1093/database/baae053", "pmc": "PMC11214160", "pubmed": "38943608", "title": "ISTransbase: an online database for inhibitor and substrate of drug transporters", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://istransbase.scbdd.com/database/trans/$1" }, "itis": { "contact": { "email": "itiswebmaster@itis.gov", "name": "Gerald Guala", "orcid": "0000-0002-4972-3782" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Information system with taxonomic data on plants, animals, fungi, and microbes of North America and the world.", "example": "589462", "homepage": "https://www.itis.gov/", "keywords": [ "biodiversity", "life science", "taxonomy" ], "license": "CC0-1.0", "mappings": { "bartoc": "17791", "fairsharing": "FAIRsharing.t19hpa", "integbio": "nbdc00916", "re3data": "r3d100011213", "wikidata": "P815" }, "name": "Integrated Taxonomic Information System", "pattern": "^\\d+$", "preferred_prefix": "itis", "uri_format": "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=$1" }, "itmctr": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The International Traditional Medicine Clinical Trial Registry (ITMCTR) is a non-profit online register of clinical trials being conducted in the field of traditional medicine. It isoperated by the China Academy of Chinese Medical Sciences and The China Center For Evidence Based Traditional Chinese Medicine. It is recognized as a Primary Registry of WHO, and contributes data to the WHO ICTRP. (from website)", "example": "ITMCTR2023000002", "homepage": "http://itmctr.ccebtcm.org.cn", "logo": "http://itmctr.ccebtcm.org.cn/Content/images/ny_logo.png", "name": "International Traditional Medicine Clinical Trial Registry", "pattern": "^ITMCTR\\d+$", "preferred_prefix": "itmctr" }, "ito": { "banana": "ITO", "banana_peel": "_", "contact": { "email": "matthias.samwald@meduniwien.ac.at", "name": "Matthias Samwald", "orcid": "0000-0002-4855-2571" }, "description": "The Intelligence Task Ontology (ITO) provides a comprehensive map of machine intelligence tasks, as well as broader human intelligence or hybrid human/machine intelligence tasks.", "download_owl": "http://aber-owl.net/media/ontologies/ITO/17/ito.owl", "example": "01625", "homepage": "https://openbiolink.github.io/ITOExplorer/", "keywords": [ "artificial intelligence", "machine learning", "natural language processing", "ontology" ], "mappings": { "aberowl": "ITO", "bioportal": "ITO", "fairsharing": "FAIRsharing.89e853", "miriam": "ito" }, "name": "Intelligence Task Ontology", "pattern": "^\\d+$", "preferred_prefix": "ito", "publications": [ { "doi": "10.1038/s41597-022-01435-x", "pmc": "PMC9205953", "pubmed": "35715466", "title": "A curated, ontology-based, large-scale knowledge graph of artificial intelligence tasks and benchmarks", "year": 2022 }, { "doi": "10.5281/zenodo.5561989", "title": "Intelligence Task Ontology and Knowledge Graph (ITO)", "year": 2022 }, { "doi": "10.48550/arxiv.2110.01434", "title": "A curated, ontology-based, large-scale knowledge graph of artificial intelligence tasks and benchmarks", "year": 2021 } ], "repository": "https://github.com/OpenBioLink/ITO", "uri_format": "https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https://identifiers.org/ito:ITO_$1" }, "iuphar.family": { "description": "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references families of receptors or subunits.", "example": "78", "homepage": "http://www.guidetopharmacology.org/", "keywords": [ "protein" ], "license": "CC-BY-SA-4.0", "mappings": { "biocontext": "IUPHAR.FAMILY", "miriam": "iuphar.family", "n2t": "iuphar.family", "prefixcommons": "iuphar.family" }, "name": "IUPHAR family", "pattern": "^\\d+$", "preferred_prefix": "iuphar.family", "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/iuphar.family:$1" } ], "synonyms": [ "IUPHARfam" ], "uri_format": "http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$1" }, "iuphar.ligand": { "description": "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands.", "example": "1755", "homepage": "http://www.guidetopharmacology.org/GRAC/LigandListForward?database=all", "license": "CC-BY-SA-4.0", "mappings": { "biocontext": "IUPHAR.LIGAND", "biolink": "GTOPDB", "miriam": "iuphar.ligand", "n2t": "iuphar.ligand", "togoid": "IupharLigand", "wikidata": "P595" }, "name": "Guide to Pharmacology Ligand", "pattern": "^\\d+$", "preferred_prefix": "iuphar.ligand", "synonyms": [ "IUPHAR_LIGAND", "IUPHAR_LIGAND_ID" ], "uri_format": "http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1" }, "iuphar.receptor": { "contact": { "email": "simon.harding@igmm.ed.ac.uk", "github": "simondharding", "name": "Simon D Harding", "orcid": "0000-0002-9262-8318" }, "description": "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits.", "example": "101", "homepage": "http://www.guidetopharmacology.org/targets.jsp", "license": "CC-BY-SA-4.0", "mappings": { "biocontext": "IUPHAR.RECEPTOR", "go": "IUPHAR_RECEPTOR", "miriam": "iuphar.receptor", "n2t": "iuphar.receptor", "uniprot": "DB-0182", "wikidata": "P5458" }, "name": "Guide to Pharmacology Target", "pattern": "^\\d+$", "preferred_prefix": "iuphar.receptor", "publications": [ { "doi": "10.1093/nar/gkab1010", "pmc": "PMC8689838", "pubmed": "34718737", "title": "The IUPHAR/BPS guide to PHARMACOLOGY in 2022: curating pharmacology for COVID-19, malaria and antibacterials", "year": 2022 }, { "doi": "10.1111/j.1476-5381.2012.02141.x", "pmc": "PMC3575771", "pubmed": "23003568", "title": "GuideToPharmacology.org--an update", "year": 2012 } ], "synonyms": [ "IUPHAR_GPCR", "IUPHARobj" ], "uri_format": "http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1" }, "ivdb": { "description": "IVDB hosts complete genome sequences of influenza A virus generated by BGI and curates all other published influenza virus sequences after expert annotations. IVDB provides a series of tools and viewers for analyzing the viral genomes, genes, genetic polymorphisms and phylogenetic relationships comparatively.", "example": "E13035", "homepage": "http://influenza.psych.ac.cn/", "keywords": [ "dna", "gene", "genome" ], "mappings": { "prefixcommons": "ivdb" }, "name": "Influenza Virus Database", "preferred_prefix": "ivdb", "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/ivdb:$1" } ], "uri_format": "http://influenza.psych.ac.cn/search/detail.jsp?segment.gb_id=$1" }, "jax": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Information about the C57BL/6J. 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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/jcm:$1" } ], "uri_format": "http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1" }, "jcrb": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Cell line collections (Providers)", "example": "JCRB1355", "homepage": "https://cellbank.nibiohn.go.jp", "mappings": { "cellosaurus": "JCRB" }, "name": "JRBC Cell Bank", "pattern": "^JCRB\\d+$", "preferred_prefix": "jcrb", "uri_format": "https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO=$1" }, "jcsd": { "contributor_extras": [ { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" } ], "description": "The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST).", "example": "J55.713G", "homepage": "http://jglobal.jst.go.jp/en/", "keywords": [ "drug" ], "mappings": { "biocontext": "JCSD", "miriam": "jcsd", "n2t": "jcsd", "prefixcommons": "nikkaji" }, "name": "Japan Chemical Substance Dictionary", "pattern": "^J\\d{1,3}(\\.\\d{3})?(\\.\\d{1,3})?[A-Za-z]$", "preferred_prefix": "jcsd", "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/nikkaji:$1" }, { "code": "stirdf", "description": "Appears in iobc", "homepage": "http://stirdf.jst.go.jp", "name": "Unknown", "uri_format": "http://stirdf.jst.go.jp/cde/nikkaji/$1" } ], "synonyms": [ "Nikkaji number", "nikkaji" ], "uri_format": "http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$1" }, "jecfa": { "contact": { "email": "kpetersen@who.int", "name": "Kim Petersen" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "JECFA provides identifiers for flavors, food additives, contaminants, toxicants, and veterinary drugs. Each entry includes chemical details, acceptable or tolerable intake limits, and links to related reports and monographs.", "example": "2116", "github_request_issue": 1247, "homepage": "https://apps.who.int/food-additives-contaminants-jecfa-database", "mappings": { "wikidata": "P9557" }, "name": "Joint FAO/WHO Expert Committee on Food Additives", "pattern": "^\\d+$", "preferred_prefix": "jecfa", "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" } }, "jgi.proposal": { "contact": { "email": "sewilson@lbl.gov", "name": "Steven E. Wilson", "orcid": "0000-0002-8489-208X" }, "contributor": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "contributor_extras": [ { "email": "aclum@lbl.gov", "github": "aclum", "name": "Alicia Clum", "orcid": "0000-0002-5004-3362" } ], "description": "Identifiers for proposals/projects at the Joint Genome Institute", "example": "502930", "github_request_issue": 853, "homepage": "https://genome.jgi.doe.gov/portal/", "name": "Joint Genome Institute Proposals", "pattern": "^\\d+$", "preferred_prefix": "jgi.proposal", "publications": [ { "doi": "10.1128/msystems.00804-20", "pmc": "PMC8269246", "pubmed": "34006627", "title": "DOE JGI Metagenome Workflow", "year": 2021 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://genome.jgi.doe.gov/portal/lookup?keyName=proposalId&groupOnly=1&app=Info&keyValue=$1" }, "jrct": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This system submits an implementation plan to the Minister of Health, Labor and Welfare for clinical research conducted at medical institutions, etc. based on the provisions of the 'Clinical Research Act' and the 'Act on Ensuring Safety of Regenerative Medicine, etc.' It is a system for performing notification procedures such as In addition, based on the clinical research practice standards stipulated in the same law, we disclose information that the World Health Organization (WHO) requires to be disclosed, information that ensures the transparency of the research process, and information that contributes to the selection of participation in clinical research by the public. (translated from website)", "example": "jRCTs041220087", "homepage": "https://jrct.niph.go.jp", "name": "Japan Registry of Clinical Trials", "pattern": "^jRCT\\w?\\d+$", "preferred_prefix": "jrct", "providers": [ { "code": "", "description": "", "homepage": "", "name": "", "uri_format": "https://jrct.niph.go.jp/latest-detail/$1" } ], "uri_format": "https://jrct.niph.go.jp/en-latest-detail/$1" }, "jstor": { "description": "JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration.", "example": "3075966", "homepage": "http://www.jstor.org/", "mappings": { "biocontext": "JSTOR", "go": "JSTOR", "miriam": "jstor", "n2t": "jstor" }, "name": "Digital archive of scholarly articles", "pattern": "^\\d+$", "preferred_prefix": "jstor", "uri_format": "http://www.jstor.org/stable/$1" }, "jws": { "contact": { "email": "brettolivier@gmail.com", "github": "bgoli", "name": "Brett G. Olivier", "orcid": "0000-0002-5293-5321" }, "description": "JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser.", "example": "achcar11", "homepage": "http://jjj.biochem.sun.ac.za/models/", "keywords": [ "model", "pathway" ], "mappings": { "biocontext": "JWS", "miriam": "jws", "n2t": "jws", "prefixcommons": "jws" }, "name": "JWS Online", "pattern": "^\\w+$", "preferred_prefix": "jws", "providers": [ { "code": "CURATOR_REVIEW", "description": "JWS Online Model Repository at Manchester", "homepage": "http://jjj.mib.ac.uk/models", "name": "JWS Online Model Repository at Manchester", "uri_format": "http://jjj.mib.ac.uk/models/$1" }, { "code": "CURATOR_REVIEW", "description": "JWS Online Model Repository at Amsterdam", "homepage": "http://jjj.bio.vu.nl/models/", "name": "JWS Online Model Repository at Amsterdam", "uri_format": "http://jjj.bio.vu.nl/models/$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/jws:$1" } ], "publications": [ { "doi": "10.1093/bioinformatics/bth200", "pubmed": "15072998", "title": "Web-based kinetic modelling using JWS Online", "year": 2004 } ], "uri_format": "https://jjj.bio.vu.nl/models/$1" }, "kaggle": { "description": "Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions.", "example": "nasa/kepler-exoplanet-search-results", "homepage": "https://kaggle.com", "mappings": { "miriam": "kaggle", "n2t": "kaggle", "re3data": "r3d100012705" }, "name": "Kaggle", "pattern": "^[0-9a-zA-Z\\-]+\\/[0-9a-zA-Z\\-]+$", "preferred_prefix": "kaggle", "uri_format": "https://www.kaggle.com/$1" }, "kaken": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "identifier for researchers in Japan used in goverment-based research funding (from 1980s)", "example": "00011461", "homepage": "https://nrid.nii.ac.jp/ja/search/?kw=", "keywords": [ "person", "researcher" ], "mappings": { "wikidata": "P9776" }, "name": "e-Rad researcher number", "pattern": "^\\d{8}$", "preferred_prefix": "kaken", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1171" ], "uri_format": "https://nrid.nii.ac.jp/ja/nrid/10000$1" }, "kclb": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Cell line collections (Providers)", "example": "10020.2", "homepage": "https://cellbank.snu.ac.kr/english", "mappings": { "cellosaurus": "KCLB" }, "name": "Korean Cell Line Bank", "preferred_prefix": "kclb", "uri_format": "https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ=$1" }, "kcris": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Clinical Research Information Service (CRIS) is a non-profit online registration system for clinical trials (researches) to be conducted in Korea. It has been established at the Korea Disease Control and Prevention Agency (KDCA) with support from the Ministry of Health and Welfare (MOHW). It joined the WHO International Clinical Trials Registry Platform (ICTRP) as 11th member of Primary Registry. (from about page)\nNote that the web page that resolves this trial does not correspond to the semantic space", "example": "KCT0008394", "homepage": "https://cris.nih.go.kr", "name": "Korean Clinical Research Information Service", "pattern": "^KCT\\d+$", "preferred_prefix": "kcris", "references": [ "https://cris.nih.go.kr/cris/search/detailSearchEn.do?seq=23973" ] }, "kegg": { "comment": "KEGG prefix has been split into several others", "deprecated": true, "description": "Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.", "example": "hsa00190", "homepage": "http://www.kegg.jp/", "mappings": { "biocontext": "KEGG", "biolink": "KEGG", "cheminf": "000409", "go": "KEGG", "integbio": "nbdc00530", "miriam": "kegg", "n2t": "kegg", "pathguide": "16", "uniprot": "DB-0053" }, "name": "Kyoto Encyclopedia of Genes and Genomes", "pattern": "^([CHDEGTMKR]\\d+)|(\\w+:[\\w\\d\\.-]*)|([a-z]{3,5})|(\\w{2,4}\\d{5})$", "preferred_prefix": "kegg", "publications": [ { "doi": "10.1093/nar/gkw1092", "pmc": "PMC5210567", "pubmed": "27899662", "title": "KEGG: new perspectives on genomes, pathways, diseases and drugs", "year": 2016 } ], "synonyms": [ "KEGG" ], "uri_format": "http://www.kegg.jp/entry/$1" }, "kegg.brite": { "description": "KEGG BRITE is a collection of hierarchical classifications (see new hierarchies and last updates) representing our knowledge on various aspects of biological systems. In contrast to KEGG PATHWAY, which is limited to molecular interactions and reactions, KEGG BRITE incorporates many different types of relationships.", "example": "ko00071", "homepage": "http://www.genome.jp/kegg/brite.html", "keywords": [ "classification", "ontology", "pathway" ], "mappings": { "biolink": "KEGG.BRITE", "integbio": "nbdc00115", "prefixcommons": "kegg.brite" }, "name": "KEGG BRITE", "part_of": "kegg", "preferred_prefix": "kegg.brite", "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/kegg.brite:$1" } ], "uri_format": "http://www.genome.jp/kegg-bin/get_htext?-p+/kegg/brite/br+br$1" }, "kegg.compound": { "contact": { "email": "kanehisa@kuicr.kyoto-u.ac.jp", "name": "Minoru Kanehisa", "orcid": "0000-0001-6123-540X" }, "description": "KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life.", "example": "C12345", "homepage": "https://www.genome.jp/kegg/ligand.html", "keywords": [ "small molecule" ], "mappings": { "biocontext": "KEGG.COMPOUND", "edam": "2605", "integbio": "nbdc00814", "miriam": "kegg.compound", "n2t": "kegg.compound", "prefixcommons": "kegg.compound", "wikidata": "P665" }, "name": "KEGG Compound", "part_of": "kegg", "pattern": "^C\\d+$", "preferred_prefix": "kegg.compound", "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/kegg.compound:$1" } ], "publications": [ { "doi": "10.1002/0471250953.bi0112s38", "pubmed": "22700311", "title": "Using the KEGG database resource", "year": 2012 } ], "synonyms": [ "KEGG COMPOUND", "KEGG.COMPOUND" ], "uri_format": "https://www.kegg.jp/entry/$1" }, "kegg.dgroup": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": " KEGG DGROUP contains structurally and functionally related groups of D number entries in KEGG DRUG. There are five types of drug groups.\n\n Chemical - grouped as identical chemical structures with minor variations of salts, hydration states, etc.\n Structure - grouped as similar chemical structures having the same skeleton, etc.\n Target - grouped by drug targets\n Class - drug classes often representing similar mechanisms of action\n Metabolism - grouped by substrates, inhibitors and inducers of drug metabolizing enzymes and transporters\n\nChemical groups are often used for identifying essentially the same active ingredients of drugs in different countries.", "example": "DG00301", "homepage": "http://www.genome.jp/kegg/reaction/", "mappings": { "biolink": "KEGG.DGROUP" }, "name": "KEGG Drug Group", "part_of": "kegg", "pattern": "^DG\\d+$", "preferred_prefix": "kegg.dgroup", "references": [ "https://github.com/prefixcommons/prefixes/pull/4" ], "synonyms": [ "KEGG_DGROUP", "KEGG_DRUG_GROUP" ] }, "kegg.disease": { "description": "The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. Diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system.", "example": "H00076", "homepage": "http://www.genome.jp/kegg/disease/", "keywords": [ "classification" ], "mappings": { "biocontext": "KEGG.DISEASE", "integbio": "nbdc00813", "miriam": "kegg.disease", "n2t": "kegg.disease", "prefixcommons": "kegg.disease" }, "name": "KEGG Disease", "part_of": "kegg", "pattern": "^H\\d+$", "preferred_prefix": "kegg.disease", "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/kegg.disease:$1" } ], "uri_format": "http://www.kegg.jp/entry/$1" }, "kegg.drug": { "contact": { "email": "kanehisa@kuicr.kyoto-u.ac.jp", "name": "Minoru Kanehisa", "orcid": "0000-0001-6123-540X" }, "description": "KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules.", "example": "D00123", "homepage": "https://www.genome.jp/kegg/drug/", "keywords": [ "small molecule" ], "mappings": { "biocontext": "KEGG.DRUG", "edam": "2609", "integbio": "nbdc00812", "miriam": "kegg.drug", "n2t": "kegg.drug", "prefixcommons": "kegg.drug", "wikidata": "P665" }, "name": "KEGG Drug", "part_of": "kegg", "pattern": "^D\\d+$", "preferred_prefix": "kegg.drug", "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/kegg.drug:$1" } ], "publications": [ { "doi": "10.1093/nar/gkj102", "pmc": "PMC1347464", "pubmed": "16381885", "title": "From genomics to chemical genomics: new developments in KEGG", "year": 2006 } ], "synonyms": [ "KEGG DRUG", "KEGG.DRUG" ], "uri_format": "https://www.kegg.jp/entry/$1" }, "kegg.environ": { "deprecated": true, "description": "KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential oils, and other health-promoting substances, which are mostly natural products of plants. It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable.", "example": "ev:E00032", "homepage": "http://www.genome.jp/kegg/drug/environ.html", "mappings": { "biocontext": "KEGG.ENVIRON", "integbio": "nbdc01059", "miriam": "kegg.environ", "n2t": "kegg.environ" }, "name": "KEGG Environ", "part_of": "kegg", "pattern": "^(ev\\:)?E\\d+$", "preferred_prefix": "kegg.environ", "synonyms": [ "KEGG.EDRUG" ], "uri_format": "http://www.kegg.jp/entry/$1" }, "kegg.enzyme": { "description": "KEGG ENZYME is an implementation of the Enzyme Nomenclature (EC number system) produced by the IUBMB/IUPAC Biochemical Nomenclature Committee. KEGG ENZYME is based on the ExplorEnz database at Trinity College Dublin, and is maintained in the KEGG relational database with additional annotation of reaction hierarchy and sequence data links.", "homepage": "http://www.genome.jp/dbget-bin/www_bfind?enzyme", "mappings": { "biolink": "KEGG.ENZYME", "go": "KEGG_ENZYME" }, "name": "KEGG Enzyme", "part_of": "kegg", "preferred_prefix": "kegg.enzyme", "provides": "ec", "uri_format": "http://www.genome.jp/dbget-bin/www_bget?ec:$1" }, "kegg.genes": { "contact": { "email": "kanehisa@kuicr.kyoto-u.ac.jp", "name": "Minoru Kanehisa", "orcid": "0000-0001-6123-540X" }, "description": "KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources.", "example": "bsu:BSU01340", "homepage": "http://www.genome.jp/kegg/genes.html", "keywords": [ "dna", "gene", "protein" ], "mappings": { "biocontext": "KEGG.GENES", "biolink": "KEGG.GENES", "miriam": "kegg.genes", "n2t": "kegg.genes", "prefixcommons": "kegg.gene", "wikidata": "P665" }, "name": "KEGG Genes", "part_of": "kegg", "pattern": "^\\w+:[\\w\\d\\.-]*$", "preferred_prefix": "kegg.genes", "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/kegg.gene:$1" } ], "publications": [ { "doi": "10.1093/nar/gkj102", "pmc": "PMC1347464", "pubmed": "16381885", "title": "From genomics to chemical genomics: new developments in KEGG", "year": 2006 } ], "uri_format": "http://www.kegg.jp/entry/$1" }, "kegg.genome": { "contact": { "email": "kanehisa@kuicr.kyoto-u.ac.jp", "name": "Minoru Kanehisa", "orcid": "0000-0001-6123-540X" }, "description": "KEGG Genome is a collection of organisms whose genomes have been completely sequenced.", "example": "T06648", "homepage": "http://www.genome.jp/kegg/catalog/org_list.html", "license": "https://www.kegg.jp/kegg/legal.html", "mappings": { "biocontext": "KEGG.GENOME", "integbio": "nbdc00816", "miriam": "kegg.genome", "n2t": "kegg.genome", "prefixcommons": "kegg.genome", "wikidata": "P665" }, "name": "KEGG Genome", "part_of": "kegg", "pattern": "^(T0\\d+|\\w{3,5})$", "preferred_prefix": "kegg.genome", "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/kegg.genome:$1" } ], "publications": [ { "doi": "10.1093/nar/gkr988", "pmc": "PMC3245020", "pubmed": "22080510", "title": "KEGG for integration and interpretation of large-scale molecular data sets", "year": 2011 } ], "synonyms": [ "kegg_genome", "kegg_genomes" ], "uri_format": "http://www.kegg.jp/entry/$1" }, "kegg.glycan": { "contact": { "email": "kanehisa@kuicr.kyoto-u.ac.jp", "name": "Minoru Kanehisa", "orcid": "0000-0001-6123-540X" }, "description": "KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways.", "example": "G00123", "homepage": "https://www.genome.jp/kegg/glycan/", "keywords": [ "small molecule" ], "mappings": { "biocontext": "KEGG.GLYCAN", "edam": "2613", "integbio": "nbdc00533", "miriam": "kegg.glycan", "n2t": "kegg.glycan", "prefixcommons": "kegg.glycan" }, "name": "KEGG Glycan", "part_of": "kegg", "pattern": "^G\\d+$", "preferred_prefix": "kegg.glycan", "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/kegg.glycan:$1" } ], "publications": [ { "doi": "10.1093/glycob/cwj010", "pubmed": "16014746", "title": "KEGG as a glycome informatics resource", "year": 2005 } ], "uri_format": "https://www.kegg.jp/entry/$1" }, "kegg.ligand": { "comment": "This database has been discontinued by KEGG. It now lives inside the compound database", "deprecated": true, "homepage": "http://www.genome.ad.jp/kegg/docs/upd_ligand.html", "mappings": { "go": "KEGG_LIGAND" }, "name": "KEGG LIGAND", "part_of": "kegg", "preferred_prefix": "kegg.ligand", "uri_format": "http://www.genome.jp/dbget-bin/www_bget?cpd:$1" }, "kegg.metagenome": { "contact": { "email": "kanehisa@kuicr.kyoto-u.ac.jp", "name": "Minoru Kanehisa", "orcid": "0000-0001-6123-540X" }, "description": "The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species.", "example": "T30002", "homepage": "http://www.genome.jp/kegg/catalog/org_list3.html", "keywords": [ "genome" ], "mappings": { "biocontext": "KEGG.METAGENOME", "miriam": "kegg.metagenome", "n2t": "kegg.metagenome", "prefixcommons": "kegg.metagenome" }, "name": "KEGG Metagenome", "part_of": "kegg", "pattern": "^T3\\d+$", "preferred_prefix": "kegg.metagenome", "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/kegg.metagenome:$1" } ], "publications": [ { "doi": "10.1093/nar/gkr988", "pmc": "PMC3245020", "pubmed": "22080510", "title": "KEGG for integration and interpretation of large-scale molecular data sets", "year": 2011 } ], "uri_format": "http://www.kegg.jp/entry/$1" }, "kegg.module": { "description": "KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules.", "example": "M00002", "homepage": "http://www.kegg.jp/kegg/module.html", "mappings": { "biocontext": "KEGG.MODULE", "integbio": "nbdc01428", "miriam": "kegg.module", "n2t": "kegg.module" }, "name": "KEGG Module", "part_of": "kegg", "pattern": "^([a-z]{3,5}_)?M\\d{5}$", "preferred_prefix": "kegg.module", "uri_format": "http://www.kegg.jp/entry/$1" }, "kegg.orthology": { "description": "KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms.", "example": "K00001", "homepage": "http://www.genome.jp/kegg/ko.html", "keywords": [ "classification", "pathway" ], "mappings": { "biocontext": "KEGG.ORTHOLOGY", "miriam": "kegg.orthology", "n2t": "kegg.orthology", "prefixcommons": "kegg.orthology" }, "name": "KEGG Orthology", "part_of": "kegg", "pattern": "^K\\d+$", "preferred_prefix": "kegg.orthology", "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/kegg.orthology:$1" } ], "uri_format": "http://www.kegg.jp/entry/$1" }, "kegg.pathway": { "contact": { "email": "kanehisa@kuicr.kyoto-u.ac.jp", "name": "Minoru Kanehisa", "orcid": "0000-0001-6123-540X" }, "description": "KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks.", "example": "rsk00410", "homepage": "https://www.genome.jp/kegg/pathway.html", "keywords": [ "pathway" ], "mappings": { "biocontext": "KEGG.PATHWAY", "biolink": "KEGG.PATHWAY", "edam": "2343", "go": "KEGG_PATHWAY", "miriam": "kegg.pathway", "n2t": "kegg.pathway", "prefixcommons": "kegg.pathway", "wikidata": "P665" }, "name": "KEGG Pathways Database", "part_of": "kegg", "pattern": "^\\w{2,4}\\d{5}$", "preferred_prefix": "kegg.pathway", "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/kegg.pathway:$1" } ], "publications": [ { "doi": "10.1002/0471250953.bi0112s38", "pubmed": "22700311", "title": "Using the KEGG database resource", "year": 2012 } ], "synonyms": [ "KEGG-path", "KEGG_PATHWAY" ], "uri_format": "https://www.kegg.jp/entry/$1" }, "kegg.rclass": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "KEGG RCLASS contains classification of reactions based on the chemical structure transformation patterns of substrate-product pairs (reactant pairs), which are represented by the so-called RDM patterns.", "example": "RC00001", "homepage": "http://www.genome.jp/kegg/reaction/", "mappings": { "biolink": "KEGG.RCLASS", "integbio": "nbdc00860" }, "name": "KEGG Reaction Class", "part_of": "kegg", "pattern": "^RC\\d+$", "preferred_prefix": "kegg.rclass", "references": [ "https://github.com/prefixcommons/prefixes/pull/2" ], "synonyms": [ "KEGG_RCLASS", "KEGG_REACTION_CLASS" ] }, "kegg.reaction": { "contact": { "email": "kanehisa@kuicr.kyoto-u.ac.jp", "name": "Minoru Kanehisa", "orcid": "0000-0001-6123-540X" }, "description": "KEGG reaction contains our knowledge on the universe of reactions that are relevant to life.", "example": "R00100", "homepage": "https://www.genome.jp/kegg/reaction/", "keywords": [ "enzyme", "pathway" ], "mappings": { "biocontext": "KEGG.REACTION", "edam": "2608", "go": "KEGG_REACTION", "integbio": "nbdc00818", "miriam": "kegg.reaction", "n2t": "kegg.reaction", "prefixcommons": "kegg.reaction", "wikidata": "P665" }, "name": "KEGG Reaction", "part_of": "kegg", "pattern": "^R\\d+$", "preferred_prefix": "kegg.reaction", "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/kegg.reaction:$1" } ], "publications": [ { "doi": "10.1002/0471250953.bi0112s38", "pubmed": "22700311", "title": "Using the KEGG database resource", "year": 2012 } ], "rdf_uri_format": "http://www.kegg.jp/entry/$1", "synonyms": [ "KEGG_REACTION" ], "uri_format": "https://www.kegg.jp/entry/$1" }, "kerafast": { "description": "Cell line collections (Providers)", "example": "EJH014", "homepage": "https://www.kerafast.com/", "mappings": { "cellosaurus": "Kerafast" }, "name": "Kerafast cell lines", "preferred_prefix": "kerafast", "uri_format": "https://www.kerafast.com/Search?SearchTerm="$1"" }, "kestrelo": { "contact": { "email": "lindsey.anderson@pnnl.gov", "github": "lnanderson", "name": "Lindsey N. Anderson", "orcid": "0000-0002-8741-7823" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology for harmonizing and extending severeral existing resources in the vaccine and immunology domains", "example": "0000001", "homepage": "https://gitlab.pnnl.gov/kestrel/kestrel_ontology", "name": "KESTREL Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "kestrelo", "uri_format": "http://purl.obolibrary.org/obo/kestrelo_$1" }, "knapsack": { "description": "KNApSAcK provides information on metabolites and the\ntaxonomic class with which they are associated.", "example": "C00000001", "homepage": "http://www.knapsackfamily.com/KNApSAcK/", "mappings": { "biocontext": "KNAPSACK", "integbio": "nbdc00545", "miriam": "knapsack", "n2t": "knapsack", "wikidata": "P2064" }, "name": "KNApSAcK", "pattern": "^C\\d{8}$", "preferred_prefix": "knapsack", "synonyms": [ "KNApSAcK" ], "uri_format": "http://www.knapsackfamily.com/knapsack_core/information.php?word=$1" }, "kupo": { "appears_in": [ "cl" ], "comment": "Website is down, now it redirects to something else that is not related", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "example": "0001009", "homepage": "http://www.kupkb.org/", "name": "Kidney and Urinary Pathway Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "kupo", "references": [ "https://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-2-S2-S7" ] }, "kyinno": { "description": "Cell line collections (Providers)", "example": "KC-0979", "homepage": "https://www.kyinno.com/", "mappings": { "cellosaurus": "KYinno" }, "name": "KYinno cell lines", "preferred_prefix": "kyinno", "uri_format": "https://innopedia.kyinno.com/DataBase/CellLine.aspx?file=$1.pdf" }, "labo": { "contact": { "email": "paul.fabry@usherbrooke.ca", "github": "pfabry", "name": "Paul Fabry", "orcid": "0000-0002-3336-2476" }, "depends_on": [ "iao", "obi", "ogms", "omiabis", "omrse", "opmi" ], "description": "LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents.", "download_owl": "http://purl.obolibrary.org/obo/labo.owl", "example": "0000124", "homepage": "https://github.com/OpenLHS/LABO", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "LABO", "bioportal": "LABO", "obofoundry": "labo", "ols": "labo", "ontobee": "LABO" }, "name": "clinical LABoratory Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "LABO", "publications": [ { "doi": "10.5281/zenodo.6522019", "title": "LABO: An ontology for laboratory test prescription and reporting", "year": 2019 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/LABO_$1", "repository": "https://github.com/OpenLHS/LABO", "uri_format": "http://purl.obolibrary.org/obo/LABO_$1", "version": "2021-06-08" }, "langual": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Langual stands for \"langua alimentaria\" or \"language of food\". it is an automated method for describing, capturing and retrieving data about food. the work on langual was started in the late 1970's by the center for food safety and applied nutrition (cfsan) of the united states food and drug administration as an ongoing co-operative effort of specialists in food technology, information science and nutrition. the thesaurus provides a standardized language for describing foods, specifically for classifying food products for information retrieval. langual is based on the concept that: - any food (or food product) can be systematically described by a combination of characteristics - these characteristics can be categorized into viewpoints and coded for computer processing - the resulting viewpoint/characteristic codes can be used to retrieve data about the food from external databases", "example": "B2067", "github_request_issue": 507, "homepage": "https://www.langual.org", "name": "Langua aLimentaria Thesaurus", "pattern": "^B\\d+$", "preferred_prefix": "langual", "uri_format": "https://www.langual.org/langual_thesaurus.asp?termid=$1" }, "lattes": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "number for the Lattes Platform entry on the person or group. Relationship between entry and subject must be supported by a source", "example": "0061106995455595", "homepage": "https://lattes.cnpq.br", "keywords": [ "person", "researcher" ], "mappings": { "wikidata": "P1007" }, "name": "Lattes Platform number", "pattern": "^\\d{16}$", "preferred_prefix": "lattes", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1171" ], "uri_format": "https://lattes.cnpq.br/$1" }, "lbctr": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Lebanese Clinical Trials Registry is an online register of clinical trials being undertaken in Lebanon. It includes trials that target humans from the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle, devices, treatment and rehabilitation strategies and complementary therapies. (from homepage)", "example": "LBCTR2023015204", "homepage": "https://lbctr.moph.gov.lb/", "name": "Lebanon Clinical Trials Registry", "pattern": "^LBCTR\\d+$", "preferred_prefix": "lbctr", "references": [ "https://lbctr.moph.gov.lb/Trials/Details/5204" ] }, "lbo": { "contact": { "email": "caripark@iastate.edu", "github": "caripark", "name": "Carissa Park", "orcid": "0000-0002-2346-5201" }, "description": "A vocabulary for cattle, chicken, horse, pig, and sheep breeds.", "download_obo": "https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.obo", "download_owl": "https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.owl", "example": "0000487", "homepage": "http://bioportal.bioontology.org/ontologies/LBO", "keywords": [ "animal breeding", "animal husbandry", "genetics", "genomics", "ontology" ], "mappings": { "aberowl": "LBO", "agroportal": "LBO", "bioportal": "LBO", "fairsharing": "FAIRsharing.309v57", "ols": "lbo" }, "name": "Livestock Breed Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "lbo", "rdf_uri_format": "http://purl.obolibrary.org/obo/LBO_$1", "repository": "https://github.com/AnimalGenome/livestock-breed-ontology", "uri_format": "https://bioportal.bioontology.org/ontologies/LBO/?p=classes&conceptid=http://purl.obolibrary.org/obo/LBO_$1" }, "lccn": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "LCCN Permalinks are persistent URLs for bibliographic records in the LC Catalog and authority records in LC Authorities. These links are constructed using the record's LCCN (or Library of Congress Control Number), an identifier assigned by the Library of Congress to bibliographic and authority records. LCCN Permalinks are also available for citation records in the Handbook for Latin American Studies (HLAS). [from homepage]", "example": "2011488555", "github_request_issue": 1310, "homepage": "https://lccn.loc.gov", "name": "Library of Congress Control Number", "pattern": "^\\d+$", "preferred_prefix": "lccn", "uri_format": "https://lccn.loc.gov/$1" }, "lcsh": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Library of Congress Subject Headings (LCSH) has been actively maintained since 1898 to catalog materials held at the Library of Congress. (from homepage)", "example": "nb2018006591", "homepage": "https://id.loc.gov/authorities", "keywords": [ "subject agnostic" ], "mappings": { "bartoc": "454", "fairsharing": "FAIRsharing.d31795", "wikidata": "P244" }, "name": "Library of Congress Subject Headings", "pattern": "^\\w{1,2}\\d{8,10}$", "preferred_prefix": "lcsh", "rdf_uri_format": "http://id.loc.gov/authorities/names/$1", "synonyms": [ "lcnaf", "lcnafid" ], "uri_format": "https://id.loc.gov/authorities/$1" }, "leafsnap": { "description": "identifier for a tree species of the United States and Canada on the Leafsnap electronic field guide", "example": "Amelanchier laevis", "homepage": "http://leafsnap.com/", "mappings": { "wikidata": "P10538" }, "name": "Leafsnap", "preferred_prefix": "leafsnap", "uri_format": "http://leafsnap.com/species/$1/" }, "lei": { "description": "Established by the Financial Stability Board in June 2014, the Global Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen by the LEI Regulatory Oversight Committee, representing public authorities from around the globe that have come together to jointly drive forward transparency within the global financial markets. GLEIF is a supra-national not-for-profit organization headquartered in Basel, Switzerland.", "example": "HWUPKR0MPOU8FGXBT394", "homepage": "https://www.gleif.org/", "mappings": { "miriam": "lei", "n2t": "lei" }, "name": "Global LEI Index", "pattern": "^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$", "preferred_prefix": "lei", "uri_format": "https://www.gleif.org/lei/$1" }, "lepao": { "contact": { "email": "lagonzalezmo@unal.edu.co", "github": "luis-gonzalez-m", "name": "Luis A. Gonzalez-Montana", "orcid": "0000-0002-9136-9932" }, "depends_on": [ "aism", "bfo", "bspo", "caro", "pato", "ro", "uberon" ], "description": "The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research.", "download_obo": "http://purl.obolibrary.org/obo/lepao.obo", "download_owl": "http://purl.obolibrary.org/obo/lepao.owl", "example": "0000005", "homepage": "https://github.com/insect-morphology/lepao", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "LEPAO", "bioportal": "LEPAO", "obofoundry": "lepao", "ols": "lepao", "ontobee": "LEPAO" }, "name": "Lepidoptera Anatomy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "LEPAO", "rdf_uri_format": "http://purl.obolibrary.org/obo/LEPAO_$1", "repository": "https://github.com/insect-morphology/lepao", "uri_format": "http://purl.obolibrary.org/obo/LEPAO_$1", "version": "2023-02-18" }, "lgai.cede": { "description": "LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset with molecular instance level annotations (i.e. atom-bond level position annotations within an image) for molecular structure images. This dataset was designed to encourage research on detection-based pipelines for Optical Chemical Structure Recognition (OCSR).", "example": "LGCEDe-S-000002244", "homepage": "https://www.lgresearch.ai", "mappings": { "miriam": "lgai.cede" }, "name": "LG Chemical Entity Detection Dataset (LGCEDe)", "pattern": "^LGCEDe-S-\\d{9}$", "preferred_prefix": "lgai.cede", "uri_format": "https://s3.us-east-2.amazonaws.com/lg.cede/$1" }, "lgic": { "comment": "Website is gone", "deprecated": true, "description": "The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available.", "example": "5HT3Arano", "homepage": "https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php", "keywords": [ "gene", "protein", "sequence" ], "mappings": { "biocontext": "LGIC", "miriam": "lgic", "n2t": "lgic", "prefixcommons": "lgicdb" }, "name": "Ligand-Gated Ion Channel database", "pattern": "^\\w+$", "preferred_prefix": "lgic", "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/lgicdb:$1" } ], "publications": [ { "doi": "10.1093/nar/27.1.340", "pmc": "PMC148177", "pubmed": "9847222", "title": "The Ligand Gated Ion Channel Database", "year": 1999 } ], "uri_format": "https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php" }, "licebase": { "contact": { "email": "Inge.Jonassen@uib.no", "name": "Inge Jonassen", "orcid": "0000-0003-4110-0748" }, "description": "Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects.", "example": "EMLSAT00000003403", "homepage": "https://licebase.org", "keywords": [ "life science" ], "mappings": { "biocontext": "LICEBASE", "fairsharing": "FAIRsharing.c7w81a", "integbio": "nbdc02217", "miriam": "licebase", "n2t": "licebase", "re3data": "r3d100013547" }, "name": "LiceBase", "pattern": "^[A-Za-z0-9\\-\\/]+$", "preferred_prefix": "licebase", "uri_format": "https://licebase.org/?q=$1" }, "ligandbook": { "description": "Ligandbook is a public repository for force field parameters with a special emphasis on small molecules and known ligands of proteins. It acts as a warehouse for parameter files that are supplied by the community.", "example": "785", "homepage": "https://ligandbook.org/", "mappings": { "miriam": "ligandbook", "n2t": "ligandbook" }, "name": "LigandBook", "pattern": "^[0-9]+$", "preferred_prefix": "ligandbook", "uri_format": "https://ligandbook.org/package/$1" }, "ligandbox": { "description": "LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds.", "example": "D00001", "homepage": "http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en", "mappings": { "biocontext": "LIGANDBOX", "integbio": "nbdc00551", "miriam": "ligandbox", "n2t": "ligandbox" }, "name": "LigandBox", "pattern": "^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$", "preferred_prefix": "ligandbox", "uri_format": "http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id=$1" }, "ligandexpo": { "contact": { "email": "jwest@rcsb.rutgers.edu", "name": "John Westbrook", "orcid": "0000-0002-6686-5475" }, "description": "Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids.", "example": "ABC", "homepage": "http://ligand-depot.rutgers.edu/index.html", "keywords": [ "chemical", "interaction", "life science", "nucleic acid", "protein", "structure" ], "mappings": { "biocontext": "LIGANDEXPO", "fairsharing": "FAIRsharing.2ma4gq", "integbio": "nbdc01864", "miriam": "ligandexpo", "n2t": "ligandexpo", "pathguide": "154", "prefixcommons": "ligandexpo" }, "name": "Ligand Expo", "pattern": "^(\\w){3}$", "preferred_prefix": "ligandexpo", "providers": [ { "code": "CURATOR_REVIEW", "description": "Ligand Expo at Rutgers", "homepage": "http://ligand-expo.rcsb.org/", "name": "Ligand Expo at Rutgers", "uri_format": "http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid" }, { "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/ligandexpo:$1" } ], "publications": [ { "doi": "10.1093/bioinformatics/bth214", "pubmed": "15059838", "title": "Ligand Depot: a data warehouse for ligands bound to macromolecules", "year": 2004 } ], "uri_format": "http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid" }, "ligea": { "comment": "This might just be a provider for CCLE", "description": "Polymorphism and mutation databases", "example": "CCLE_867", "homepage": "http://hpc-bioinformatics.cineca.it/fusion/main", "mappings": { "cellosaurus": "LiGeA" }, "name": "Cancer cell LInes GEne fusions portAl", "preferred_prefix": "ligea", "uri_format": "http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1" }, "limore": { "description": "Cell line databases/resources", "example": "Li7", "homepage": "https://www.picb.ac.cn/limore/home", "mappings": { "cellosaurus": "LIMORE" }, "name": "Liver Cancer Model Repository", "preferred_prefix": "limore", "uri_format": "https://www.picb.ac.cn/limore/cellLines/single?para=$1" }, "lincs.cell": { "description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease.", "example": "LCL-2085", "homepage": "http://lincsportal.ccs.miami.edu/cells/", "mappings": { "biocontext": "LINCS.CELL", "cellosaurus": "LINCS_LDP", "miriam": "lincs.cell", "n2t": "lincs.cell" }, "name": "LINCS Cell", "pattern": "^(LCL|LDC|ES|LSC|LPC)-\\d+$", "preferred_prefix": "lincs.cell", "synonyms": [ "LINCS_LDP" ], "uri_format": "http://lincsportal.ccs.miami.edu/cells/#/view/$1" }, "lincs.data": { "description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level).", "example": "LDS-1110", "homepage": "http://lincsportal.ccs.miami.edu/datasets/", "mappings": { "biocontext": "LINCS.DATA", "miriam": "lincs.data", "n2t": "lincs.data" }, "name": "LINCS Data", "pattern": "^[EL]D[SG]-\\d+$", "preferred_prefix": "lincs.data", "providers": [ { "code": "omicsdi", "description": "Lincs through OmicsDI", "homepage": "https://www.omicsdi.org/", "name": "Lincs through OmicsDI", "uri_format": "https://www.omicsdi.org/dataset/lincs/$1" } ], "uri_format": "http://lincsportal.ccs.miami.edu/datasets/#/view/$1" }, "lincs.protein": { "description": "The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins.", "example": "200282", "homepage": "http://lincs.hms.harvard.edu/db/proteins/", "mappings": { "biocontext": "LINCS.PROTEIN", "miriam": "lincs.protein", "n2t": "lincs.protein" }, "name": "LINCS Protein", "pattern": "^\\d+$", "preferred_prefix": "lincs.protein", "uri_format": "https://lincs.hms.harvard.edu/db/proteins/$1" }, "lincs.smallmolecule": { "description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC).", "example": "LSM-6306", "homepage": "http://lincsportal.ccs.miami.edu/SmallMolecules/", "mappings": { "biocontext": "LINCS.SMALLMOLECULE", "miriam": "lincs.smallmolecule", "n2t": "lincs.smallmolecule" }, "name": "LINCS Small Molecule", "pattern": "^LSM-\\d+$", "preferred_prefix": "lincs.smallmolecule", "synonyms": [ "lincs" ], "uri_format": "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1" }, "linguist": { "description": "Registry of programming languages for the Linguist program for detecting and highlighting programming languages.", "example": "Python", "homepage": "https://github.com/github/linguist", "mappings": { "miriam": "linguist" }, "name": "Linguist", "pattern": "^[a-zA-Z0-9 +#'*]+$", "preferred_prefix": "linguist", "repository": "https://github.com/github/linguist", "uri_format": "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1" }, "linguist.gold": { "comment": "This resource has been deprecated and was last released in 2010. The homepage links to a zip folder that includes an OWL artifact, but it doesn't follow any typical standards. The ontology browser is not perfect, it only works for classes.", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "example": "Term", "github_request_issue": 1310, "homepage": "https://linguistlist.org/gold/", "name": "Genderal Ontology for Linguistic Description", "preferred_prefix": "linguist.gold", "rdf_uri_format": "http://purl.org/linguistics/gold/$1", "uri_format": "https://lambdamusic.github.io/ontospy-examples/gold-2010owl/class-gold$1.html" }, "linkedin": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "identifier for a person, on the LinkedIn website", "example": "deborahlehr", "homepage": "https://www.linkedin.com", "keywords": [ "person", "researcher" ], "mappings": { "wikidata": "P6634" }, "name": "LinkedIn personal profile ID", "pattern": "^[\\w0-9\\-&_'’\\.]+$", "preferred_prefix": "linkedin", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1171" ], "uri_format": "https://www.linkedin.com/in/$1" }, "linkml": { "comment": "Closes #508", "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Linkml is a flexible modeling language that allows you to author schemas in yaml that describe the structure of your data. additionally, it is a framework for working with and validating data in a variety of formats (json, rdf, tsv), with generators for compiling linkml schemas to other frameworks.", "example": "SchemaDefinition", "github_request_issue": 512, "homepage": "https://linkml.io/linkml-model/docs/SchemaDefinition/", "keywords": [ "data integration", "ontology and terminology" ], "mappings": { "biolink": "linkml", "fairsharing": "FAIRsharing.cb7086" }, "name": "LinkML", "preferred_prefix": "linkml", "publications": [ { "doi": "10.5281/zenodo.5598314", "title": "linkml/linkml-model: v1.5.2", "year": 2023 } ], "repository": "https://github.com/linkml/", "twitter": "linkml_data", "uri_format": "https://w3id.org/linkml/$1" }, "lipidbank": { "contact": { "email": "e-yasugi@umin.ac.jp", "name": "Etsuko Yasugi", "orcid": "0000-0003-1898-4426" }, "description": "LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.", "example": "BBA0001", "homepage": "http://lipidbank.jp/index.html", "keywords": [ "life science", "lipid", "molecule", "structure" ], "mappings": { "biocontext": "LIPIDBANK", "edam": "2665", "fairsharing": "FAIRsharing.bdn9br", "integbio": "nbdc00126", "miriam": "lipidbank", "n2t": "lipidbank", "prefixcommons": "lipidbank" }, "name": "LipidBank", "pattern": "^\\w+\\d+$", "preferred_prefix": "lipidbank", "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/lipidbank:$1" } ], "publications": [ { "pubmed": "12058481", "title": "[LIPIDBANK for Web, the newly developed lipid database]", "year": 2002 } ], "uri_format": "http://lipidbank.jp/cgi-bin/detail.cgi?id=$1" }, "lipidmaps": { "contact": { "email": "edennis@ucsd.edu", "name": "0000-0003-3738-3140", "orcid": "0000-0003-3738-3140" }, "description": "The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy.", "example": "LMPR0102010012", "homepage": "http://www.lipidmaps.org", "keywords": [ "biomedical science", "endocrinology", "life science", "lipid", "structure", "systems biology", "taxonomy" ], "mappings": { "biocontext": "LIPIDMAPS", "cheminf": "000564", "edam": "2625", "fairsharing": "FAIRsharing.cpneh8", "miriam": "lipidmaps", "n2t": "lipidmaps", "pathguide": "503", "prefixcommons": "lipidmaps", "re3data": "r3d100012315", "togoid": "Lipidmaps", "wikidata": "P2063" }, "name": "LIPID MAPS", "pattern": "^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$", "preferred_prefix": "lipidmaps", "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/lipidmaps:$1" }, { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", "homepage": "https://scholia.toolforge.org/", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/lipidmaps/$1" } ], "publications": [ { "doi": "10.1194/jlr.r800095-jlr200", "pmc": "PMC2674711", "pubmed": "19098281", "title": "Update of the LIPID MAPS comprehensive classification system for lipids", "year": 2008 }, { "doi": "10.1093/nar/gkm324", "pmc": "PMC1933166", "pubmed": "17584797", "title": "LIPID MAPS online tools for lipid research", "year": 2007 }, { "doi": "10.1093/nar/gkl838", "pmc": "PMC1669719", "pubmed": "17098933", "title": "LMSD: LIPID MAPS structure database", "year": 2006 }, { "doi": "10.1194/jlr.e400004-jlr200", "pubmed": "15722563", "title": "A comprehensive classification system for lipids", "year": 2005 }, { "doi": "10.1194/jlr.R800095-JLR200", "title": "Update of the LIPID MAPS comprehensive classification system for lipids." } ], "synonyms": [ "LIPID MAPS", "LIPID_MAPS_class", "LIPID_MAPS_instance" ], "twitter": "lipidmaps", "uri_format": "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1" }, "lipro": { "contact": { "email": "bakerc@unb.ca", "name": "Christopher Baker", "orcid": "0000-0003-4004-6479" }, "deprecated": true, "description": "An ontology representation of the LIPIDMAPS nomenclature classification.", "download_owl": "http://aber-owl.net/media/ontologies/LIPRO/4/lipro.owl", "keywords": [ "obo", "ontology" ], "mappings": { "aberowl": "LIPRO", "biocontext": "LIPRO", "bioportal": "LIPRO", "obofoundry": "lipro" }, "name": "Lipid Ontology", "preferred_prefix": "LIPRO", "rdf_uri_format": "http://purl.obolibrary.org/obo/LIPRO_$1", "uri_format": "http://purl.obolibrary.org/obo/LIPRO_$1" }, "lncipedia": { "contact": { "email": "pieter.mestdagh@ugent.be", "github": "OncoRNALab", "name": "Pieter Mestdagh", "orcid": "0000-0001-7821-9684" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A comprehensive compendium of human long non-coding RNAs", "example": "SNHG3", "homepage": "https://lncipedia.org", "keywords": [ "life science" ], "mappings": { "fairsharing": "FAIRsharing.84c1a7" }, "name": "LNCipedia", "preferred_prefix": "lncipedia", "publications": [ { "doi": "10.1093/nar/gkv295", "pmc": "PMC4417186", "pubmed": "25829178", "title": "An update on LNCipedia: a database for annotated human lncRNA sequences", "year": 2015 }, { "doi": "10.1093/nar/gku1060", "pmc": "PMC4383901", "pubmed": "25378313", "title": "An update on LNCipedia: a database for annotated human lncRNA sequences", "year": 2014 }, { "doi": "10.1093/nar/gks915", "pmc": "PMC3531107", "pubmed": "23042674", "title": "LNCipedia: a database for annotated human lncRNA transcript sequences and structures", "year": 2012 } ] }, "loggerhead": { "contact": { "email": "peteremidford@yahoo.com", "name": "Peter Midford", "orcid": "0000-0001-6512-3296" }, "deprecated": true, "homepage": "http://www.mesquiteproject.org/ontology/Loggerhead/index.html", "keywords": [ "obo", "ontology" ], "mappings": { "biocontext": "LOGGERHEAD", "obofoundry": "loggerhead" }, "name": "Loggerhead nesting", "preferred_prefix": "LOGGERHEAD", "rdf_uri_format": "http://purl.obolibrary.org/obo/LOGGERHEAD_$1", "uri_format": "http://purl.obolibrary.org/obo/LOGGERHEAD_$1" }, "loinc": { "contact": { "email": "loinc@regenstrief.org", "name": "LOINC Support" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The international standard for identifying health measurements, observations, and documents.", "example": "LL379-9", "homepage": "https://loinc.org/", "keywords": [ "assay", "biomedical science", "diagnosis", "genetic disorder", "genetic polymorphism", "life science", "ontology", "phenotype", "preclinical studies" ], "license": "https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf", "mappings": { "aberowl": "LOINC", "bartoc": "1897", "biolink": "LOINC", "bioportal": "LOINC", "fairsharing": "FAIRsharing.2mk2zb", "hl7": "2.16.840.1.113883.6.1", "wikidata": "P4338" }, "name": "Logical Observation Identifiers Names and Codes", "pattern": "^(\\d|\\w)+-\\d$", "preferred_prefix": "loinc", "publications": [ { "doi": "10.1016/s1386-5056(98)00089-6", "pubmed": "9749897", "title": "Combining laboratory data sets from multiple institutions using the logical observation identifier names and codes (LOINC)", "year": 1998 }, { "doi": "10.1093/jamia/ocu012", "pmc": "PMC5566197", "pubmed": "25656513", "title": "Supporting interoperability of genetic data with LOINC", "year": 2015 }, { "doi": "10.1016/j.jbi.2012.01.005", "pmc": "PMC3376691", "pubmed": "22285984", "title": "Enabling international adoption of LOINC through translation", "year": 2012 } ], "rdf_uri_format": "http://loinc.org/rdf/$1", "synonyms": [ "LNC" ], "twitter": "LOINC", "uri_format": "https://loinc.org/$1" }, "lonza": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Contains information about cells and data sheets related to transfection.", "example": "968", "homepage": "https://knowledge.lonza.com", "mappings": { "cellosaurus": "Lonza" }, "name": "Lonza", "pattern": "^\\d+$", "preferred_prefix": "lonza", "uri_format": "https://knowledge.lonza.com/cell?id=$1" }, "loop": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "identifier for a person, in the Loop database of researcher impact", "example": "1859", "homepage": "https://loop.frontiersin.org/", "keywords": [ "person", "researcher" ], "mappings": { "wikidata": "P2798" }, "name": "Loop ID", "pattern": "^[1-9]\\d*$", "preferred_prefix": "loop", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1171" ], "uri_format": "https://loop.frontiersin.org/people/$1/overview" }, "loqate": { "contact": { "email": "maya.schuldiner@weizmann.ac.il", "github": "Maya-Schuldiner-lab", "name": "Maya Schuldiner", "orcid": "0000-0001-9947-115X" }, "description": "The data presented here is a result of systematically tracking the localization and abundance of 5330 yeast proteins at single-cell resolution under three different stress conditions (DTT, H2O2 and nitrogen starvation) using the GFP-tagged yeast library", "example": "1001", "homepage": "http://www.weizmann.ac.il/molgen/loqate/", "mappings": { "prefixcommons": "loqate" }, "name": "The localization and quantitation atlas of the yeast proteome", "preferred_prefix": "loqate", "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/loqate:$1" } ], "publications": [ { "doi": "10.1093/nar/gkt933", "pmc": "PMC3965041", "pubmed": "24150937", "title": "LoQAtE--Localization and Quantitation ATlas of the yeast proteomE. A new tool for multiparametric dissection of single-protein behavior in response to biological perturbations in yeast", "year": 2013 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.weizmann.ac.il/molgen/loqate/gene/view/$1" }, "lotus": { "comment": "IDs are actually leading to the structural part of LOTUS only, which might change in the future. Will adapt the regexp in case.", "contact": { "email": "adriano.rutz@ik.me", "github": "adafede", "name": "Adriano Rutz", "orcid": "0000-0003-0443-9902" }, "contributor": { "email": "adriano.rutz@ik.me", "github": "adafede", "name": "Adriano Rutz", "orcid": "0000-0003-0443-9902" }, "description": "LOTUS, actually, represents the most exhaustive resource of documented structure-organism pairs. Within the frame of current computational approaches in Natural Produts’s research and related fields, these documented structure-organism pairs should allow a more complete understanding of organisms and their chemistry.", "example": "LTS0004651", "github_request_issue": 222, "homepage": "https://lotus.naturalproducts.net", "keywords": [ "chemistry", "drugs", "metabolites" ], "logo": "https://upload.wikimedia.org/wikipedia/commons/6/64/Lotus_initiative_logo.svg", "name": "LOTUS Initiative for Open Natural Products Research", "pattern": "^LTS\\d{7}$", "preferred_prefix": "lotus", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://lotus.naturalproducts.net/compound/lotus_id/$1" }, "lpt": { "contact": { "email": "caripark@iastate.edu", "github": "caripark", "name": "Carissa Park", "orcid": "0000-0002-2346-5201" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Livestock Product Trait Ontology (LPT) is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit.", "download_obo": "https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.obo", "download_owl": "https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.owl", "example": "0000156", "homepage": "https://github.com/AnimalGenome/livestock-product-trait-ontology", "keywords": [ "animal husbandry", "ontology", "phenotype" ], "mappings": { "aberowl": "LPT", "agroportal": "LPT", "biocontext": "LPT", "bioportal": "LPT", "fairsharing": "FAIRsharing.g78mbm" }, "name": "Livestock Product Trait Ontology", "pattern": "^\\d+$", "preferred_prefix": "lpt", "repository": "https://github.com/AnimalGenome/livestock-product-trait-ontology", "uri_format": "http://purl.obolibrary.org/obo/LPT_$1" }, "lrg": { "banana": "LRG", "banana_peel": "_", "description": "A Locus Reference Genomic (LRG) is a manually curated record that contains stable genomic, transcript and protein reference sequences for reporting clinically relevant sequence variants. All LRGs are generated and maintained by the NCBI and EMBL-EBI.", "example": "1", "homepage": "http://www.lrg-sequence.org/", "mappings": { "biocontext": "LRG", "hl7": "2.16.840.1.113883.6.283", "integbio": "nbdc02566", "miriam": "lrg", "n2t": "lrg", "togoid": "Lrg" }, "name": "Locus Reference Genomic", "pattern": "^\\d+$", "preferred_prefix": "lrg", "providers": [ { "code": "CURATOR_REVIEW", "description": "Locus Reference Genomic through Ensembl", "homepage": "http://www.ensembl.org/", "name": "Locus Reference Genomic through Ensembl", "uri_format": "http://www.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1" }, { "code": "CURATOR_REVIEW", "description": "Locus Reference Genomic through Ensembl mirror (asia)", "homepage": "http://asia.ensembl.org/", "name": "Locus Reference Genomic through Ensembl mirror (asia)", "uri_format": "http://asia.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1" }, { "code": "CURATOR_REVIEW", "description": "Locus Reference Genomic through Ensembl mirror (US east)", "homepage": "http://useast.ensembl.org/", "name": "Locus Reference Genomic through Ensembl mirror (US east)", "uri_format": "http://useast.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1" } ], "uri_format": "http://ftp.ebi.ac.uk/pub/databases/lrgex/$1.xml" }, "lspci": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Internal identifiers form the LSP for ChEBML compound classes (e.g., combining various salts and ions)", "example": "1", "homepage": "https://labsyspharm.github.io/lspci/", "keywords": [ "chemistry", "drugs", "metabolites" ], "name": "Laboratory of Systems Pharmacology Compound", "pattern": "^\\d+$", "preferred_prefix": "lspci", "uri_format": "https://labsyspharm.github.io/lspci/$1" }, "lter": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Ecological terms", "example": "182", "homepage": "https://vocab.lternet.edu/vocab/vocab/index.php", "name": "Long Term Ecological Research Controlled Vocabulary", "pattern": "^\\d+$", "preferred_prefix": "lter", "uri_format": "https://vocab.lternet.edu/vocab/vocab/index.php?tema=$1" }, "lw": { "description": "The LifeWatch Metadata Catalogues plays a crucial role in managing metadata for digital objects, including Datasets, Services, Workflows and Virtual Research Environments. This catalogue serves as the central repository, ensuring that resources are accessible and reusable by stakeholders.", "example": "6e3b1371-59d7-481a-9db4-cd0d0de98436", "homepage": "https://metadatacatalogue.lifewatch.eu/", "mappings": { "miriam": "lw" }, "name": "LifeWatch Metadata Catalogue", "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "preferred_prefix": "lw", "uri_format": "https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/$1" }, "m4i": { "contact": { "email": "dorothea.iglezakis@ub.uni-stuttgart.de", "github": "doigl", "name": "Dorothea Iglezakis", "orcid": "0000-0002-8524-0569" }, "contributor": { "email": "giacomo.lanza@ptb.de", "github": "Zack-83", "name": "Giacomo Lanza", "orcid": "0000-0002-2239-3955" }, "description": "The ontology Metadata4Ing is developed within the NFDI Consortium NFDI4Ing with the aim of providing a thorough framework for the semantic description of research data, with a particular focus on engineering sciences and neighbouring disciplines. This ontology allows a description of the whole data generation process (experiment, observation, simulation), embracing the object of investigation, all sample and data manipulation procedures, a summary of the data files and the information contained, and all personal and institutional roles. The subordinate classes and relations can be built according to the two principles of inheritance and modularity. \"Inheritance\" means that a subclass inherits all properties of its superordinate class, possibly adding some new ones. Modularity means that all expansions are independent of each other; this makes possible for instance to generate expanded ontologies for any possible combinations of method × object of research.", "download_owl": "https://nfdi4ing.pages.rwth-aachen.de/metadata4ing/metadata4ing/ontology.xml", "download_rdf": "https://nfdi4ing.pages.rwth-aachen.de/metadata4ing/metadata4ing/ontology.ttl", "example": "Method", "github_request_issue": 970, "homepage": "https://w3id.org/nfdi4ing/metadata4ing/", "keywords": [ "academy", "engineering science", "metadata", "ontology" ], "license": "CC-BY-4.0", "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaWNHIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--6435da59153a976c6b09d30ac0ee96286c50a32c/Logo.png?disposition=inline", "mappings": { "bartoc": "20402", "fairsharing": "FAIRsharing.f8b3ec", "lov": "m4i", "wikidata": "Q111516803", "zazuko": "m4i" }, "mastodon": "nfdi4ing@nfdi.social", "name": "Metadata4Ing", "owners": [ { "name": "Nationale Forschungsdateninfrastruktur", "partnered": false, "ror": "05qj6w324" } ], "pattern": "^\\w+$", "preferred_prefix": "m4i", "repository": "https://git.rwth-aachen.de/nfdi4ing/metadata4ing/metadata4ing/", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://w3id.org/nfdi4ing/metadata4ing#$1" }, "ma": { "banana": "MA", "contact": { "email": "Terry.Hayamizu@jax.org", "github": "tfhayamizu", "name": "Terry Hayamizu", "orcid": "0000-0002-0956-8634" }, "description": "A structured controlled vocabulary of the adult anatomy of the mouse (Mus)", "download_obo": "http://purl.obolibrary.org/obo/ma.obo", "download_owl": "http://purl.obolibrary.org/obo/ma.owl", "example": "0002502", "homepage": "https://github.com/obophenotype/mouse-anatomy-ontology", "keywords": [ "anatomy", "mouse", "obo", "ontology", "organ", "tissue" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "MA", "biocontext": "MA", "bioportal": "MA", "fairsharing": "FAIRsharing.pdwqcr", "go": "MA", "miriam": "ma", "n2t": "ma", "obofoundry": "ma", "ols": "ma", "ontobee": "MA", "prefixcommons": "ma" }, "name": "Mouse adult gross anatomy", "namespace_in_lui": true, "pattern": "^\\d+$", "preferred_prefix": "MA", "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/mao:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/MAO_$1", "uri_format": "http://purl.obolibrary.org/obo/MAO_$1" }, "markerdb": { "contact": { "email": "dwishart@ualberta.ca", "github": "DavidWishartLab", "name": "David S. Wishart", "orcid": "0000-0002-3207-2434" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "MarkerDB is a freely available electronic database that attempts to consolidate information on all known clinical and pre-clinical biomarkers into a single resource. It provides identifiers for known clinical and pre-clinical biomarkers. 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"omicsdi", "description": "MassIVE through OmicsDI", "homepage": "https://www.omicsdi.org/", "name": "MassIVE through OmicsDI", "uri_format": "https://www.omicsdi.org/dataset/massive/$1" } ], "publications": [ { "doi": "10.1038/s41592-020-0955-0", "pmc": "PMC7541731", "pubmed": "32929271", "title": "MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets", "year": 2020 }, { "doi": "10.1093/nar/gkz984", "pmc": "PMC7145525", "pubmed": "31686107", "title": "The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics", "year": 2020 }, { "doi": "10.1016/j.cels.2018.08.004", "pmc": "PMC6279426", "pubmed": "30172843", "title": "Assembling the Community-Scale Discoverable Human Proteome", "year": 2018 }, { "doi": "10.1093/nar/gkw936", "pmc": "PMC5210636", "pubmed": "27924013", "title": "The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition", "year": 2016 }, { "doi": "10.1038/nbt.3597", "pmc": "PMC5321674", "pubmed": "27504778", "title": "Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking", "year": 2016 } ], "repository": "https://ccms-ucsd.github.io/MassIVEDocumentation", "uri_format": "https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id=$1" }, "mastodon": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "address on the Mastodon decentralized social network (the form is 'user@server.domain' without a leading '@')", "example": "jz@mamot.fr", "homepage": "https://mastodon.social", "mappings": { "wikidata": "P4033" }, "name": "Mastodon", "pattern": "^[A-Za-z0-9_]+([A-Za-z0-9_\\.]+[A-Za-z0-9_]+)?@[\\d\\w\\.\\-]+[0-9a-z]+$", "preferred_prefix": "mastodon", "uri_format": "https://fedirect.toolforge.org/?id=$1" }, "mat": { "contact": { "email": "j.bard@ed.ac.uk", "name": "Jonathan Bard" }, 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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/matrixdb:$1" } ], "publications": [ { "doi": "10.1093/nar/gky1035", "pmc": "PMC6324007", "pubmed": "30371822", "title": "MatrixDB: integration of new data with a focus on glycosaminoglycan interactions", "year": 2019 }, { "doi": "10.1093/nar/gku1091", "pmc": "PMC4383919", "pubmed": "25378329", "title": "MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities", "year": 2014 }, { "doi": "10.1093/nar/gkq830", "pmc": "PMC3013758", "pubmed": "20852260", "title": "MatrixDB, the extracellular matrix interaction database", "year": 2010 }, { "doi": "10.1093/bioinformatics/btp025", "pmc": "PMC2647840", "pubmed": "19147664", "title": "MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions", "year": 2009 } ], "uri_format": "http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value=$1" }, "matrixdb.association": { "description": "MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations.", "example": "P00747__P07355", "homepage": "https://matrixdb.univ-lyon1.fr/", "mappings": { "biocontext": "MATRIXDB.ASSOCIATION", "miriam": "matrixdb.association", "n2t": "matrixdb.association" }, "name": "MatrixDB Association", "pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$", "preferred_prefix": "matrixdb.association", "uri_format": "https://matrixdb.univ-lyon1.fr/association/$1" }, "mavedb": { "comment": "This is an interesting one as the full IDs as they appear on the page are of the form `urn:mavedb:00000011-a` suggesting this is the preferred URI expansion for identification purposes. However, mavedb hasn't been registered with IANA https://www.iana.org/assignments/urn-namespaces/urn-namespaces.xhtml", "contact": { "email": "alan.rubin@wehi.edu.au", "github": "afrubin", "name": "Alan Rubin", "orcid": "0000-0003-1474-605X" }, "contributor": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "description": "Some IDs may represent experiment sets, e.g. https://www.mavedb.org/#/experiment-sets/urn:mavedb:00000011 Others represent genomic regions (specifically deep mutational scans thereof) e.g. https://www.mavedb.org/#/experiment-sets/urn:mavedb:00000011-a", "example": "00000011-a", "example_extras": [ "00000011" ], "github_request_issue": 1045, "homepage": "https://www.mavedb.org", "name": "Multiplexed Assays of Variant Effect Database", "pattern": "^\\S+$", "preferred_prefix": "mavedb", "publications": [ { "doi": "10.1186/s13059-025-03476-y", "pmc": "PMC11753097", "pubmed": "39838450", "title": "MaveDB 2024: a curated community database with over seven million variant effects from multiplexed functional assays", "year": 2025 }, { "doi": "10.1186/s13059-019-1845-6", "pmc": "PMC6827219", "pubmed": "31679514", "title": "MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect", "year": 2019 } ], "repository": "https://github.com/VariantEffect/mavedb-api", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.mavedb.org/#/experiments/urn:mavedb:$1" }, "maxo": { "appears_in": [ "ecto" ], "contact": { "email": "Leigh.Carmody@jax.org", "github": "LCCarmody", "name": "Leigh Carmody", "orcid": "0000-0001-7941-2961" }, "depends_on": [ "chebi", "foodon", "go", "hp", "iao", "nbo", "obi", "ro", "uberon" ], "description": "An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations.", "download_json": "http://purl.obolibrary.org/obo/maxo.json", "download_obo": "http://purl.obolibrary.org/obo/maxo.obo", "download_owl": "http://purl.obolibrary.org/obo/maxo.owl", "example": "0000008", "homepage": "https://github.com/monarch-initiative/MAxO", "keywords": [ "medicine", "obo", "ontology", "rare disease" ], "license": "CC-BY-4.0", "logo": "https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/maxo-logos/maxo_logo_black-banner.png", "mappings": { "aberowl": "MAXO", "biolink": "MAXO", "bioportal": "MAXO", "fairsharing": "FAIRsharing.945c78", "miriam": "maxo", "obofoundry": "maxo", "ols": "maxo", "ontobee": "MAXO" }, "name": "Medical Action Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MAXO", "publications": [ { "doi": "10.1101/2023.07.13.23292612", "pubmed": "37503136", "title": "The Medical Action Ontology: A Tool for Annotating and Analyzing Treatments and Clinical Management of Human Disease", "year": 2023 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/MAXO_$1", "repository": "https://github.com/monarch-initiative/MAxO", "twitter": "MonarchInit", "uri_format": "http://purl.obolibrary.org/obo/MAXO_$1", "version": "2024-07-29" }, "mba": { "contact": { "email": "cellsemantics@gmail.com", "name": "Allen Institute for Brain Science" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A controlled vocabulary to support the study of transcription in the mouse brain", "download_obo": "https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-mba.obo", "download_owl": "https://purl.brain-bican.org/ontology/mbao/releases/2025-02-10/mbao.owl", "example": "688", "homepage": "https://mouse.brain-map.org", "keywords": [ "ontology" ], "mappings": { "bioportal": "ABA-AMB", "ols": "mba" }, "name": "Mouse Brain Atlas", "pattern": "^\\d+$", "preferred_prefix": "MBA", "providers": [ { "code": "biopragmatics", "description": "Biopragmatics provider for MBA", "homepage": "https://biopragmatics.github.io/providers/mba", "name": "MBA from Biopragmatics", "uri_format": "https://biopragmatics.github.io/providers/mba/$1" } ], "uri_format": "https://purl.brain-bican.org/ontology/mbao/MBA_$1", "version": "2025-02-10" }, "mcc": { "contact": { "email": "usha@molecularconnections.com", "name": "Usha Mahadevan" }, "deprecated": true, "description": "Ontologies provide a common platform of controlled vocabulary for researchers who need to share information across a particular domain, inclusive of machine-interpretable definitions of basic concepts in the domain and relations among them. The need for ontologies that provide a systematic arrangement of available data and allow cross talk across various related domains is gaining momentum. In this backdrop, we have developed a comprehensive ontology on primary and established cell lines-both normal and pathologic. It covers around 400 cell lines. This ontology has been built to include the major domains in the field of biology like anatomy, bio-molecules, chemicals and drugs, pathological conditions and genetic variations around the cell lines. An extensive network of relations has been built across these concepts to enable different combinations of queries. The ontology covers all cell lines from major sources like ATCC, DSMZ, ECACC, ICLC etc. and is built in OWL format.", "example": "ThoracicArtery", "homepage": "http://www.molecularconnections.com", "keywords": [ "ontology" ], "mappings": { "bioportal": "MCCL" }, "name": "Cell Line Ontology [derivative]", "preferred_prefix": "mcc", "uri_format": "http://www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#$1" }, "mco": { "contact": { "email": "citlalli.mejiaalmonte@gmail.com", "github": "citmejia", "name": "Citlalli Mejía-Almonte", "orcid": "0000-0002-0142-5591" }, "depends_on": [ "bfo", "chebi", "cl", "clo", "micro", "ncbitaxon", "ncit", "obi", "omit", "omp", "pato", "peco", "uberon", "zeco" ], "description": "Microbial Conditions Ontology is an ontology...", "download_obo": "http://purl.obolibrary.org/obo/mco.obo", "download_owl": "http://purl.obolibrary.org/obo/mco.owl", "example": "0000858", "homepage": "https://github.com/microbial-conditions-ontology/microbial-conditions-ontology", "keywords": [ "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "MCO", "bioportal": "MCO", "obofoundry": "mco", "ols": "mco", "ontobee": "MCO" }, "name": "Microbial Conditions Ontology", "pattern": "^\\d+$", "preferred_prefix": "MCO", "rdf_uri_format": "http://purl.obolibrary.org/obo/MCO_$1", "repository": "https://github.com/microbial-conditions-ontology/microbial-conditions-ontology", "uri_format": "http://purl.obolibrary.org/obo/MCO_$1", "version": "2019-05-15" }, "mcro": { "banana": "MCRO", "contact": { "email": "muamith@utmb.edu", "github": "ProfTuan", "name": "Tuan Amith", "orcid": "0000-0003-4333-1857" }, "depends_on": [ "iao", "swo" ], "description": "An ontology representing the model card structure, he aim of this work is to describe machine learning models to communicate information about specific details about the model (trade offs, intended users, licensing, etc.). ", "download_owl": "http://purl.obolibrary.org/obo/mcro.owl", "example": "0000001", "homepage": "https://github.com/UTHealth-Ontology/MCRO", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "MCRO", "bioportal": "MCRO", "miriam": "mcro", "obofoundry": "mcro", "ontobee": "MCRO" }, "name": "Model Card Report Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "MCRO", "publications": [ { "doi": "10.1186/s12859-022-04797-6", "title": "Toward a standard formal semantic representation of the model card report" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/MCRO_$1", "repository": "https://github.com/UTHealth-Ontology/MCRO", "uri_format": "https://www.ebi.ac.uk/ols4/ontologies/mcro/classes?obo_id=MCRO:$1" }, "mdl": { "appears_in": [ "xlmod" ], "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The MDL number contains a unique identification number for each reaction and variation. The format is RXXXnnnnnnnn. R indicates a reaction, XXX indicates which database contains the reaction record. The numeric portion, nnnnnnnn, is an 8-digit number. [wikipedia]", "example": "MFCD00011659", "github_request_issue": 1311, "homepage": "https://en.wikipedia.org/wiki/Chemical_file_format#MDL_number", "name": "Molecular Design Limited Hash", "pattern": "^\\w{4}\\d{8}$", "preferred_prefix": "mdl", "references": [ "https://en.wikipedia.org/wiki/Chemical_file_format#MDL_number" ] }, "mdm": { "contact": { "email": "bernd.mueller@zbmed.de", "name": "Bernd Müller", "orcid": "0000-0003-3062-8192" }, "description": "The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems.", "download_owl": "http://aber-owl.net/media/ontologies/MDM/4/mdm.owl", "example": "4776", "homepage": "https://medical-data-models.org/", "keywords": [ "biomedical science", "medicine", "ontology", "translational medicine" ], "mappings": { "aberowl": "MDM", "biocontext": "MDM", "bioportal": "MDM", "fairsharing": "FAIRsharing.wnk2eq", "miriam": "mdm", "n2t": "mdm", "re3data": "r3d100013816" }, "name": "Medical Data Models", "pattern": "^\\d+$", "preferred_prefix": "mdm", "publications": [ { "doi": "10.1093/database/bav121", "pmc": "PMC4750548", "pubmed": "26868052", "title": "Portal of medical data models: information infrastructure for medical research and healthcare", "year": 2016 } ], "uri_format": "https://medical-data-models.org/forms/$1" }, "meddra": { "contact": { "email": "mssohelp@meddra.org", "name": "MedDRA MSSO" }, "description": "The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT).", "example": "10015919", "homepage": "http://bioportal.bioontology.org/ontologies/MEDDRA", "keywords": [ "biomedical science", "disease", "medicine", "ontology", "preclinical studies" ], "mappings": { "aberowl": "MEDDRA", "bartoc": "1237", "biocontext": "MEDDRA", "bioportal": "MEDDRA", "fairsharing": "FAIRsharing.ad3137", "hl7": "2.16.840.1.113883.6.163", "integbio": "nbdc02564", "miriam": "meddra", "n2t": "meddra", "togoid": "Meddra", "wikidata": "P3201" }, "name": "Medical Dictionary for Regulatory Activities Terminology", "pattern": "^\\d+$", "preferred_prefix": "meddra", "publications": [ { "doi": "10.1016/s1386-5056(00)00062-9", "pubmed": "10961570", "title": "The use of a medical dictionary for regulatory activities terminology (MedDRA) in prescription-event monitoring in Japan (J-PEM)", "year": 2000 }, { "doi": "10.2165/00002018-199920020-00002", "pubmed": "10082069", "title": "The medical dictionary for regulatory activities (MedDRA)", "year": 1999 } ], "rdf_uri_format": "http://purl.bioontology.org/ontology/MDRFRE/$1", "synonyms": [ "MEDRA", "MeDRA", "MedDRA", "Medical Dictionary for Regulatory Activities" ], "uri_format": "http://bioportal.bioontology.org/ontologies/MEDDRA?p=classes&conceptid=$1" }, "medgen": { "description": "MedGen is a portal for information about conditions and phenotypes related to Medical Genetics. Terms from multiple sources are aggregated into concepts, each of which is assigned a unique identifier and a preferred name and symbol. The core content of the record may include names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder.", "example": "760050", "homepage": "https://www.ncbi.nlm.nih.gov/medgen/", "mappings": { "biocontext": "MedGen", "biolink": "medgen", "integbio": "nbdc02560", "miriam": "medgen", "n2t": "medgen", "ncbi": "MedGen", "togoid": "Medgen" }, "name": "Human Medical Genetics", "pattern": "^[CN]*\\d{4,7}$", "preferred_prefix": "medgen", "uri_format": "https://www.ncbi.nlm.nih.gov/medgen/$1" }, "mediadive.ingredient": { "contact": { "email": "joerg.overmann@dsmz.de", "name": "Jörg Overmann", "orcid": "0000-0003-3909-7201" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about]", "example": "13", "github_request_issue": 941, "homepage": "https://mediadive.dsmz.de/solutions", "license": "CC-BY-4.0", "name": "MediaDive Ingredient", "pattern": "^\\d+$", "preferred_prefix": "mediadive.ingredient", "uri_format": "https://mediadive.dsmz.de/ingredients/$1" }, "mediadive.medium": { "contact": { "email": "joerg.overmann@dsmz.de", "name": "Jörg Overmann", "orcid": "0000-0003-3909-7201" }, "contributor": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "description": "The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about]", "example": "77", "example_extras": [ "54b" ], "github_request_issue": 941, "homepage": "https://mediadive.dsmz.de/media", "license": "CC-BY-4.0", "mappings": { "miriam": "mediadive.medium" }, "name": "MediaDive Medium", "pattern": "^\\d+\\w?$", "preferred_prefix": "mediadive.medium", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://mediadive.dsmz.de/medium/$1" }, "mediadive.solution": { "contact": { "email": "joerg.overmann@dsmz.de", "name": "Jörg Overmann", "orcid": "0000-0003-3909-7201" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about]", "example": "S6", "github_request_issue": 941, "homepage": "https://mediadive.dsmz.de/solutions", "license": "CC-BY-4.0", "name": "MediaDive Solution", "pattern": "^S\\d+$", "preferred_prefix": "mediadive.solution", "uri_format": "https://mediadive.dsmz.de/solutions/$1" }, "medlineplus": { "contact": { "email": "custserv@nlm.nih.gov", "name": "NLM Customer Service" }, "description": "MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language.", "example": "002804", "homepage": "http://www.nlm.nih.gov/medlineplus/", "keywords": [ "biomedical science", "disease", "health science", "medicine", "ontology" ], "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaEFGIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--611e307f6ed5ae6a6f06017953d913cdcacc490b/Screenshot%20from%202024-10-04%2017-49-50.png?disposition=inline", "mappings": { "aberowl": "MEDLINEPLUS", "biocontext": "MEDLINEPLUS", "bioportal": "MEDLINEPLUS", "fairsharing": "FAIRsharing.bf8dsb", "hl7": "2.16.840.1.113883.6.173", "integbio": "nbdc00836", "miriam": "medlineplus", "n2t": "medlineplus" }, "name": "MedlinePlus Health Topics", "pattern": "^\\d+$", "preferred_prefix": "medlineplus", "providers": [ { "code": "medlineplus.fp", "description": "First-party version of medline plus.", "homepage": "https://medlineplus.gov", "name": "MedLine Plus home page", "uri_format": "https://medlineplus.gov/ency/article/$1.htm" } ], "uri_format": "http://www.nlm.nih.gov/medlineplus/ency/article/$1.htm" }, "merops.clan": { "contact": { "email": "ndr@ebi.ac.uk", "name": "Neil D Rawlings", "orcid": "0000-0001-5557-7665" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.", "example": "IA", "homepage": "https://www.ebi.ac.uk/merops", "name": "MEROPS Clan", "part_of": "merops", "preferred_prefix": "merops.clan", "publications": [ { "doi": "10.1093/nar/gkx1134", "pmc": "PMC5753285", "pubmed": "29145643", "title": "The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database", "year": 2018 } ], "references": [ "https://github.com/biopragmatics/bioregistry/issues/439" ], "uri_format": "https://www.ebi.ac.uk/merops/cgi-bin/clansum?clan=$1" }, "merops.entry": { "contact": { "email": "ndr@ebi.ac.uk", "name": "Neil D Rawlings", "orcid": "0000-0001-5557-7665" }, "description": "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. This collections references inhibitors.", "example": "I31.952", "example_extras": [ "S01.001", "XM02.001" ], "homepage": "https://www.ebi.ac.uk/merops/", "keywords": [ "biomedical science", "enzyme", "life science", "protein", "structure" ], "mappings": { "biocontext": "MEROPS.INHIBITOR", "edam": "2629", "fairsharing": "FAIRsharing.2s4n8r", "go": "MEROPS", "miriam": "merops.inhibitor", "n2t": "merops.inhibitor", "prefixcommons": "merops" }, "name": "MEROPS Entry", "pattern": "^[SCTAGMNUIX]{1,2}\\d{2}\\.([AB]\\d{2}|\\d{3})$", "preferred_prefix": "merops.entry", "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/merops:$1" } ], "publications": [ { "doi": "10.1093/nar/27.1.325", "pmc": "PMC148173", "pubmed": "9847218", "title": "MEROPS: the peptidase database", "year": 1999 }, { "doi": "10.1042/bj2900205", "pmc": "PMC1132403", "pubmed": "8439290", "title": "Evolutionary families of peptidases", "year": 1993 }, { "doi": "10.1093/nar/gkx1134", "pmc": "PMC5753285", "pubmed": "29145643", "title": "The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database", "year": 2018 }, { "doi": "10.1093/nar/gkv1118", "pmc": "PMC4702814", "pubmed": "26527717", "title": "Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors", "year": 2015 }, { "doi": "10.1016/j.biochi.2015.10.003", "pmc": "PMC4756867", "pubmed": "26455268", "title": "Peptidase specificity from the substrate cleavage collection in the MEROPS database and a tool to measure cleavage site conservation", "year": 2015 }, { "doi": "10.1093/nar/gkr987", "pmc": "PMC3245014", "pubmed": "22086950", "title": "MEROPS: the database of proteolytic enzymes, their substrates and inhibitors", "year": 2011 }, { "doi": "10.1093/nar/gkm954", "pmc": "PMC2238837", "pubmed": "17991683", "title": "MEROPS: the peptidase database", "year": 2007 } ], "references": [ "https://github.com/biopragmatics/bioregistry/issues/439" ], "synonyms": [ "merops.inhibitor" ], "uri_format": "https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=$1" }, "merops.family": { "contact": { "email": "ndr@ebi.ac.uk", "name": "Neil D Rawlings", "orcid": "0000-0001-5557-7665" }, "description": "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families.", "example": "S1", "homepage": "https://www.ebi.ac.uk/merops/", "mappings": { "biocontext": "MEROPS.FAMILY", "miriam": "merops.family", "n2t": "merops.family" }, "name": "MEROPS Family", "part_of": "merops", "pattern": "^[SCTAGMNU]\\d+$", "preferred_prefix": "merops.family", "publications": [ { "doi": "10.1093/nar/gkx1134", "pmc": "PMC5753285", "pubmed": "29145643", "title": "The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database", "year": 2018 } ], "references": [ "https://github.com/biopragmatics/bioregistry/issues/439" ], "uri_format": "https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=$1" }, "merriamwebster": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Online Dictionary", "example": "buccal_gland", "github_request_issue": 1310, "homepage": "https://www.merriam-webster.com", "name": "Merriam Webster Dictionary", "preferred_prefix": "merriamwebster", "synonyms": [ "merriam_webster" ], "uri_format": "https://www.merriam-webster.com/dictionary/$1" }, "mesh": { "contact": { "email": "custserv@nlm.nih.gov", "name": "NLM Customer Service" }, "contributor_extras": [ { "github": "rombaum", "name": "Roman Baum", "orcid": "0000-0001-5246-9351" } ], "description": "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc.", "example": "C063233", "example_extras": [ "D000001" ], "homepage": "http://id.nlm.nih.gov/mesh/", "keywords": [ "bioinformatics", "biomedical science", "classification", "data model", "data retrieval", "life science", "literature curation", "metascience", "ontology", "topics" ], "license": "CC0-1.0", "logo": "https://meshb.nlm.nih.gov/public/img/meshLogo.jpg", "mappings": { "aberowl": "MESH", "bartoc": "391", "biocontext": "MESH", "biolink": "MESH", "bioportal": "MESH", "cellosaurus": "MeSH", "edam": "1177", "fairsharing": "FAIRsharing.qnkw45", "go": "MeSH", "hl7": "2.16.840.1.113883.6.177", "integbio": "nbdc00132", "miriam": "mesh", "n2t": "mesh", "prefixcommons": "mesh", "togoid": "Mesh", "wikidata": "P486" }, "name": "Medical Subject Headings", "pattern": "^(C|D|M)\\d{6,9}$", "preferred_prefix": "mesh", "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/mesh:$1" }, { "code": "bioportal.purl", "description": "The BioPortal version of MeSH. Should be re-coded to `bioportal`, see https://github.com/biopragmatics/bioregistry/pull/1066.", "homepage": "https://bioportal.bioontology.org/ontologies/MESH", "name": "BioPortal", "uri_format": "http://purl.bioontology.org/ontology/MESH/$1" }, { "code": "mesh.2008", "description": "Appears in birnlex", "homepage": "http://id.nlm.nih.gov/mesh/", "name": "Legacy 2008 MeSH URL", "uri_format": "http://www.nlm.nih.gov/cgi/mesh/2008/MB_cgi?field=uid&term=$1" }, { "code": "mesh.json-ld", "description": "The MeSH version in JSON-LD.", "first_party": true, "homepage": "http://id.nlm.nih.gov/mesh/", "name": "Medical Subject Headings (JSON-LD)", "uri_format": "https://id.nlm.nih.gov/mesh/$1.json-ld" }, { "code": "mesh.n3", "description": "The MeSH version in N3.", "first_party": true, "homepage": "http://id.nlm.nih.gov/mesh/", "name": "Medical Subject Headings (N3)", "uri_format": "https://id.nlm.nih.gov/mesh/$1.n3" }, { "code": "mesh.ttl", "description": "The MeSH version in TTL.", "first_party": true, "homepage": "http://id.nlm.nih.gov/mesh/", "name": "Medical Subject Headings (TTL)", "uri_format": "https://id.nlm.nih.gov/mesh/$1.ttl" }, { "code": "ncbi", "description": "MeSH via National Library of Medicine", "homepage": "https://www.nlm.nih.gov/", "name": "MeSH via National Library of Medicine", "uri_format": "https://www.ncbi.nlm.nih.gov/mesh/?term=$1" } ], "publications": [ { "pmc": "PMC197951", "pubmed": "13982385", "title": "Medical subject headings", "year": 1963 } ], "rdf_uri_format": "http://id.nlm.nih.gov/mesh/$1", "synonyms": [ "MESH", "MESHA", "MESHC", "MESHCS", "MESHD", "MESHPP", "MESH_DESCRIPTOR_UI", "MESH_SUPPLEMENTAL_RECORD_UI", "MSH", "MSH2010_2010_02_22", "MeSH", "meshUID" ], "uri_format": "https://meshb.nlm.nih.gov/record/ui?ui=$1" }, "mesh.2012": { "description": "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2012.", "example": "17186", "homepage": "http://www.nlm.nih.gov/mesh/", "mappings": { "biocontext": "MESH.2012", "miriam": "mesh.2012", "n2t": "mesh.2012" }, "name": "MeSH 2012", "pattern": "^[A-Za-z0-9]+$", "preferred_prefix": "mesh.2012", "provides": "mesh", "uri_format": "http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=$1&view=expanded" }, "mesh.2013": { "description": "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013.", "example": "17165", "homepage": "http://www.nlm.nih.gov/mesh/", "mappings": { "biocontext": "MESH.2013", "miriam": "mesh.2013", "n2t": "mesh.2013" }, "name": "MeSH 2013", "pattern": "^[A-Za-z0-9]+$", "preferred_prefix": "mesh.2013", "provides": "mesh", "uri_format": "http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$1&view=expanded" }, "mesh.vocab": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Medical Subject Headings vocabulary is the set of predicates used in the MeSH RDF dump", "example": "term", "homepage": "https://hhs.github.io/meshrdf/", "name": "Medical Subject Headings Vocabulary", "part_of": "mesh", "preferred_prefix": "mesh.vocab", "references": [ "https://id.nlm.nih.gov/mesh/query" ], "repository": "https://github.com/HHS/meshrdf", "uri_format": "http://id.nlm.nih.gov/mesh/vocab#$1" }, "metabolights": { "description": "MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies.", "example": "MTBLS1", "homepage": "https://www.ebi.ac.uk/metabolights/", "mappings": { "biocontext": "METABOLIGHTS", "cellosaurus": "MetaboLights", "integbio": "nbdc02124", "miriam": "metabolights", "n2t": "metabolights", "re3data": "r3d100011556", "wikidata": "P3890" }, "name": "MetaboLights Compound", "pattern": "^MTBLS\\d+$", "preferred_prefix": "metabolights", "providers": [ { "code": "omicsdi", "description": "MataboLights through OmicsDI", "homepage": "https://www.omicsdi.org/", "name": "MataboLights through OmicsDI", "uri_format": "https://www.omicsdi.org/dataset/metabolights_dataset/$1" } ], "uri_format": "https://www.ebi.ac.uk/metabolights/$1" }, "metacyc.compound": { "contact": { "email": "pkarp@ai.sri.com", "github": "pkarp111", "name": "Peter Karp", "orcid": "0000-0002-5876-6418" }, "description": "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.", "example": "CPD-10330", "homepage": "https://metacyc.org", "keywords": [ "life science", "metabolomics", "systems biology" ], "mappings": { "biocontext": "METACYC.COMPOUND", "biolink": "MetaCyc", "fairsharing": "FAIRsharing.yytevr", "go": "MetaCyc", "integbio": "nbdc00907", "miriam": "metacyc.compound", "n2t": "metacyc.compound", "pathguide": "10", "re3data": "r3d100011294" }, "name": "Metabolic Encyclopedia of metabolic and other pathways", "pattern": "^[A-Za-z0-9+_.%-:]+$", "preferred_prefix": "metacyc.compound", "publications": [ { "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/gkt1103", "pmc": "PMC3964957", "pubmed": "24225315", "title": "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases", "year": 2013 }, { "doi": "10.1093/nar/gkr1014", "pmc": "PMC3245006", "pubmed": "22102576", "title": "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases", "year": 2011 } ], "synonyms": [ "MetaCyc" ], "twitter": "BioCyc", "uri_format": "https://metacyc.org/compound?orgid=META&id=$1" }, "metacyc.pathway": { "contact": { "email": "pkarp@ai.sri.com", "github": "pkarp111", "name": "Peter Karp", "orcid": "0000-0002-5876-6418" }, "contributor": { "github": "hrshdhgd", "name": "Harshad Hegde", "orcid": "0000-0002-2411-565X" }, "description": "MetaCyc is a database of non-redundant, experimentally elucidated metabolic pathways and enzymes. It also contains reactions, chemical compounds, and genes. It stores predominantly qualitative information rather than quantitative data, although it does contain some quantitative data such as enzyme kinetics data.\n\nMetaCyc is [curated](http://www.biocyc.org/glossary.shtml?sid=biocyc14-3908554027#Curation) from the scientific experimental literature according to an [extensive process](https://metacyc.org/MetaCycUserGuide.shtml#TAG:__tex2page_sec_4)]. The majority of pathways occurring in it are from microorganisms and plants. MetaCyc stores thousands of additional enzyme-catalyzed reactions that have not yet been assigned an EC number", "example": "12DICHLORETHDEG-PWY", "github_request_issue": 1012, "homepage": "https://metacyc.org", "name": "Metabolic Encyclopedia for Pathway/Genome Databases", "preferred_prefix": "metacyc.pathway", "publications": [ { "pubmed": "31586394", "title": "The MetaCyc database of metabolic pathways and enzymes - a 2019 update", "year": 2019 }, { "pubmed": "23746312", "title": "The challenge of constructing, classifying, and representing metabolic pathways", "year": 2013 }, { "pubmed": "21523460", "title": "A survey of metabolic databases emphasizing the MetaCyc family", "year": 2011 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://metacyc.org/META/NEW-IMAGE?object=$1" }, "metacyc.reaction": { "contact": { "email": "pkarp@ai.sri.com", "github": "pkarp111", "name": "Peter Karp", "orcid": "0000-0002-5876-6418" }, "description": "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.", "example": "RXN-14904", "homepage": "https://metacyc.org", "mappings": { "biocontext": "METACYC.REACTION", "biolink": "metacyc.reaction", "miriam": "metacyc.reaction", "n2t": "metacyc.reaction" }, "name": "MetaCyc Reaction", "pattern": "^[A-Za-z0-9+_.%-:]+$", "preferred_prefix": "metacyc.reaction", "uri_format": "https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1" }, "metanetx.chemical": { "description": "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components.", "example": "MNXM1723", "homepage": "https://www.metanetx.org/", "mappings": { "biocontext": "METANETX.CHEMICAL", "miriam": "metanetx.chemical", "n2t": "metanetx.chemical" }, "name": "MetaNetX chemical", "pattern": "^(MNXM\\d+|BIOMASS|WATER)$", "preferred_prefix": "metanetx.chemical", "uri_format": "https://www.metanetx.org/chem_info/$1" }, "metanetx.compartment": { "description": "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments.", "example": "MNXC15", "homepage": "https://www.metanetx.org/", "mappings": { "biocontext": "METANETX.COMPARTMENT", "miriam": "metanetx.compartment", "n2t": "metanetx.compartment" }, "name": "MetaNetX compartment", "pattern": "^(MNX[CD]\\d+|BOUNDARY|IN|OUT)$", "preferred_prefix": "metanetx.compartment", "uri_format": "https://www.metanetx.org/comp_info/$1" }, "metanetx.reaction": { "description": "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions.", "example": "MNXR101574", "homepage": "https://www.metanetx.org/", "mappings": { "biocontext": "METANETX.REACTION", "biolink": "METANETX.REACTION", "miriam": "metanetx.reaction", "n2t": "metanetx.reaction" }, "name": "MetaNetX reaction", "pattern": "^(MNXR\\d+|EMPTY)$", "preferred_prefix": "metanetx.reaction", "uri_format": "https://www.metanetx.org/equa_info/$1" }, "metatlas": { "contact": { "email": "mihail.anton@chalmers.se", "github": "mihai-sysbio", "name": "Mihail Anton", "orcid": "0000-0002-7753-9042" }, "contributor": { "email": "mihail.anton@chalmers.se", "github": "mihai-sysbio", "name": "Mihail Anton", "orcid": "0000-0002-7753-9042" }, "description": "A resource for exploring metabolism, starting with a set of of community-curated genome-scale metabolic models of human and model organisms, enriched with pathway maps and other tools for easy browsing and analysis.", "example": "MAM01234c", "example_decoys": [ "MAR11851c" ], "example_extras": [ "MAR11851" ], "github_request_issue": 495, "homepage": "https://metabolicatlas.org", "keywords": [ "chemistry", "metabolites", "reactions" ], "mappings": { "miriam": "metatlas" }, "name": "Metabolic Atlas", "pattern": "^(MAM\\d{5}\\w)|(MAR\\d{5})$", "preferred_prefix": "metatlas", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://metabolicatlas.org/identifier/MetabolicAtlas/$1" }, "metatlas.metabolite": { "contact": { "email": "mihail.anton@chalmers.se", "github": "mihai-sysbio", "name": "Mihail Anton", "orcid": "0000-0002-7753-9042" }, "contributor": { "email": "mihail.anton@chalmers.se", "github": "mihai-sysbio", "name": "Mihail Anton", "orcid": "0000-0002-7753-9042" }, "description": "A subspace of Metabolic Atlas for compartment-specific records for metabolites.", "example": "MAM01234c", "github_request_issue": 495, "homepage": "https://metabolicatlas.org", "keywords": [ "chemistry", "metabolites" ], "name": "Metabolic Atlas Metabolite", "part_of": "metatlas", "pattern": "^MAM\\d{5}\\w$", "preferred_prefix": "metatlas.metabolite", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://metabolicatlas.org/identifier/MetabolicAtlas/$1" }, "metatlas.reaction": { "contact": { "email": "mihail.anton@chalmers.se", "github": "mihai-sysbio", "name": "Mihail Anton", "orcid": "0000-0002-7753-9042" }, "contributor": { "email": "mihail.anton@chalmers.se", "github": "mihai-sysbio", "name": "Mihail Anton", "orcid": "0000-0002-7753-9042" }, "description": "A subspace of Metabolic Atlas for reactions.", "example": "MAR11851", "github_request_issue": 495, "homepage": "https://metabolicatlas.org", "keywords": [ "chemistry", "reactions" ], "name": "Metabolic Atlas Reaction", "part_of": "metatlas", "pattern": "^MAR\\d{5}$", "preferred_prefix": "metatlas.reaction", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://metabolicatlas.org/identifier/MetabolicAtlas/$1" }, "metlin": { "deprecated": true, "description": "The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry.", "example": "1455", "homepage": "http://masspec.scripps.edu/", "mappings": { "biocontext": "METLIN", "miriam": "metlin", "n2t": "metlin", "re3data": "r3d100012311" }, "name": "Metabolite and Tandem Mass Spectrometry Database", "pattern": "^\\d{4}$", "preferred_prefix": "metlin", "uri_format": "http://metlin.scripps.edu/metabo_info.php?molid=$1" }, "metnetdb": { "description": "The MetNet database (MetNetDB) contains information on networks of metabolic and regulatory and interactions in Arabidopsis. Types of interactions in MetNetDB include transcription, translation, protein modification, assembly, allosteric regulation, translocation from one subcellular compartment to another.", "example": "377369", "homepage": "http://www.metnetdb.org/MetNet_db.htm", "keywords": [ "dna", "interaction", "pathway", "protein", "regulation", "rna", "small molecule" ], "mappings": { "pathguide": "234", "prefixcommons": "metnetdb" }, "name": "Metabolic Network Exchange Database", "preferred_prefix": "metnetdb", "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/metnetdb:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://metnetonline.org/browse_pathway2.php?pthID=$1" }, "mex": { "description": "A public place to process, interpret and share GC/MS metabolomics datasets.", "example": "36", "homepage": "https://www.metabolome-express.org/", "mappings": { "biocontext": "MEX", "miriam": "mex", "n2t": "mex" }, "name": "Metabolome Express", "pattern": "^\\d+$", "preferred_prefix": "mex", "providers": [ { "code": "omicsdi", "description": "Metabolome Express through OmicsDI", "homepage": "https://www.omicsdi.org/", "name": "Metabolome Express through OmicsDI", "uri_format": "https://www.omicsdi.org/dataset/metabolome_express/MEX$1" } ], "uri_format": "https://www.metabolome-express.org/datasetview.php?datasetid=$1" }, "mf": { "contact": { "email": "janna.hastings@gmail.com", "github": "jannahastings", "name": "Janna Hastings", "orcid": "0000-0002-3469-4923" }, "description": "The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning.", "download_owl": "http://purl.obolibrary.org/obo/mf.owl", "example": "0000091", "homepage": "https://github.com/jannahastings/mental-functioning-ontology", "keywords": [ "biomedical science", "cognition", "cognitive neuroscience", "mental health", "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "MF", "biocontext": "MF", "bioportal": "MF", "fairsharing": "FAIRsharing.4gm9gt", "obofoundry": "mf", "ols": "mf", "ontobee": "MF" }, "name": "Mental Functioning Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MF", "rdf_uri_format": "http://purl.obolibrary.org/obo/MF_$1", "repository": "https://github.com/jannahastings/mental-functioning-ontology", "uri_format": "http://purl.obolibrary.org/obo/MF_$1", "version": "2022-07-19" }, "mfmo": { "contact": { "email": "druzinsk@uic.edu", "github": "RDruzinsky", "name": "Robert Druzinsky", "orcid": "0000-0002-1572-1316" }, "depends_on": [ "uberon" ], "deprecated": true, "description": "The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors.", "download_owl": "http://purl.obolibrary.org/obo/mfmo.owl", "example": "0000208", "homepage": "https://github.com/rdruzinsky/feedontology", "keywords": [ "anatomy", "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "MFMO", "biocontext": "MFMO", "bioportal": "MFMO", "fairsharing": "FAIRsharing.669cnk", "obofoundry": "mfmo", "ols": "mfmo", "ontobee": "MFMO" }, "name": "Mammalian Feeding Muscle Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MFMO", "providers": [ { "code": "conflated", "description": "A conflated URL with parts.", "homepage": "http://purl.obolibrary.org", "name": "OBO PURL Parts", "uri_format": "http://purl.obolibrary.org/obo/mfmo.owl#MFMO_$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/MFMO_$1", "repository": "https://github.com/RDruzinsky/feedontology", "uri_format": "http://purl.obolibrary.org/obo/MFMO_$1", "version": "2013-11-16" }, "mfo": { "contact": { "email": "henrich@embl.de", "github": "ThorstenHen", "name": "Thorsten Henrich", "orcid": "0000-0002-1548-3290" }, "deprecated": true, "description": "A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes.", "download_obo": "http://aber-owl.net/media/ontologies/MFO/14/mfo.obo", "download_owl": "http://purl.obolibrary.org/obo/mfo.owl", "example": "0000001", "homepage": "http://ani.embl.de:8080/mepd/", "keywords": [ "anatomy", "development", "fish", "obo", "ontology" ], "mappings": { "aberowl": "MFO", "biocontext": "MFO", "bioportal": "MFO", "obofoundry": "mfo", "prefixcommons": "mfo" }, "name": "Medaka fish anatomy and development", "pattern": "^\\d{7}$", "preferred_prefix": "MFO", "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/mfo:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/MFO_$1", "uri_format": "http://purl.obolibrary.org/obo/MFO_$1" }, "mfoem": { "contact": { "email": "janna.hastings@gmail.com", "github": "jannahastings", "name": "Janna Hastings", "orcid": "0000-0002-3469-4923" }, "description": "An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings.", "download_owl": "http://purl.obolibrary.org/obo/mfoem.owl", "example": "000204", "homepage": "https://github.com/jannahastings/emotion-ontology", "keywords": [ "biomedical science", "emotion", "mental health", "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "MFOEM", "biocontext": "MFOEM", "bioportal": "MFOEM", "fairsharing": "FAIRsharing.dx30m8", "obofoundry": "mfoem", "ols": "mfoem", "ontobee": "MFOEM" }, "name": "Emotion Ontology", "pattern": "^\\d{6}$", "preferred_prefix": "MFOEM", "publications": [ { "doi": "10.1186/2041-1480-5-38", "pmc": "PMC4417517", "pubmed": "25937879", "title": "Evaluating the Emotion Ontology through use in the self-reporting of emotional responses at an academic conference", "year": 2014 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/MFOEM_$1", "repository": "https://github.com/jannahastings/emotion-ontology", "uri_format": "http://purl.obolibrary.org/obo/MFOEM_$1", "version": "2025-01-06" }, "mfomd": { "contact": { "email": "janna.hastings@gmail.com", "github": "jannahastings", "name": "Janna Hastings", "orcid": "0000-0002-3469-4923" }, "description": "The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF).", "download_owl": "http://purl.obolibrary.org/obo/mfomd.owl", "example": "0000046", "homepage": "https://github.com/jannahastings/mental-functioning-ontology", "keywords": [ "disease", "obo", "ontology", "psychiatry" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "MFOMD", "biocontext": "MFOMD", "bioportal": "MFOMD", "fairsharing": "FAIRsharing.q053vb", "obofoundry": "mfomd", "ols": "mfomd", "ontobee": "MFOMD" }, "name": "Mental Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MFOMD", "rdf_uri_format": "http://purl.obolibrary.org/obo/MFOMD_$1", "repository": "https://github.com/jannahastings/mental-functioning-ontology", "uri_format": "http://purl.obolibrary.org/obo/MFOMD_$1", "version": "2020-04-26" }, "mge": { "banana": "mge", "deprecated": true, "description": "ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.", "example": "2", "homepage": "http://aclame.ulb.ac.be/", "keywords": [ "gene", "genome", "life science" ], "mappings": { "biocontext": "ACLAME", "edam": "2631", "fairsharing": "FAIRsharing.5tfcy8", "integbio": "nbdc00355", "miriam": "mge", "n2t": "mge", "prefixcommons": "aclame" }, "name": "Aclame", "namespace_in_lui": true, "pattern": "^\\d+$", "preferred_prefix": "mge", "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/aclame:$1" } ], "publications": [ { "doi": "10.1093/nar/gkp938", "pmc": "PMC2808911", "pubmed": "19933762", "title": "ACLAME: a CLAssification of Mobile genetic Elements, update 2010", "year": 2009 }, { "doi": "10.1093/nar/gkh084", "pmc": "PMC308818", "pubmed": "14681355", "title": "ACLAME: a CLAssification of Mobile genetic Elements", "year": 2004 } ], "synonyms": [ "aclame" ], "uri_format": "http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1" }, "mgi": { "banana": "MGI", "contact": { "email": "joel.richardson@jax.org", "github": "JoelRichardson", "name": "Joel Richardson", "orcid": "0000-0003-3342-5753" }, "description": "The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data.", "example": "6017782", "homepage": "http://www.informatics.jax.org/", "keywords": [ "animal model", "blast", "data analysis service", "expression", "function", "gene", "gene expression", "genetics", "genome", "genotype", "gold standard", "human disease", "human health", "image", "life science", "model", "molecular neuroanatomy resource", "ontology and terminology", "orthology", "pathology", "pathway", "phenotype", "recombinase", "sequence", "single nucleotide polymorphism", "strain", "tumor" ], "license": "CC-BY-4.0", "mappings": { "biocontext": "MGI", "cellosaurus": "MGI", "edam": "3274", "fairsharing": "FAIRsharing.fcwyhz", "go": "MGI", "integbio": "nbdc00568", "miriam": "mgi", "n2t": "mgi", "ncbi": "MGI", "prefixcommons": "mgi", "re3data": "r3d100010266", "rrid": "MGI", "uniprot": "DB-0060", "wikidata": "P671" }, "name": "Mouse Genome Informatics", "namespace_in_lui": true, "pattern": "^\\d+$", "preferred_prefix": "MGI", "providers": [ { "code": "agr", "description": "MGI through the Alliance of Genome Resources", "homepage": "https://www.alliancegenome.org", "name": "MGI through the Alliance of Genome Resources", "uri_format": "https://www.alliancegenome.org/gene/MGI:$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/mgi:$1" }, { "code": "mgi.marker", "description": "MGI Marker", "homepage": "http://www.informatics.jax.org/marker", "name": "MGI Marker", "uri_format": "http://www.informatics.jax.org/marker/MGI:$1" } ], "publications": [ { "doi": "10.1126/science.8091224", "pubmed": "8091224", "title": "A database for mouse development", "year": 1994 }, { "doi": "10.1093/nar/gky1056", "pmc": "PMC6323923", "pubmed": "30407599", "title": "Mouse Genome Database (MGD) 2019", "year": 2019 }, { "doi": "10.1093/nar/gky922", "pmc": "PMC6324054", "pubmed": "30335138", "title": "The mouse Gene Expression Database (GXD): 2019 update", "year": 2019 }, { "doi": "10.1093/ilar/ilx013", "pmc": "PMC5886341", "pubmed": "28838066", "title": "Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse", "year": 2017 }, { "doi": "10.1007/978-1-4939-6427-7_3", "pubmed": "27933520", "title": "Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research", "year": 2017 }, { "doi": "10.1093/nar/gkw1040", "pmc": "PMC5210536", "pubmed": "27899570", "title": "Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse", "year": 2016 }, { "doi": "10.1093/nar/gkt1225", "pmc": "PMC3964950", "pubmed": "24285300", "title": "The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse", "year": 2013 }, { "doi": "10.1093/nar/gks1115", "pmc": "PMC3531104", "pubmed": "23175610", "title": "The mouse genome database: genotypes, phenotypes, and models of human disease", "year": 2012 }, { "doi": "10.1093/nar/gkr974", "pmc": "PMC3245042", "pubmed": "22075990", "title": "The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse", "year": 2011 }, { "pubmed": "19274630" }, { "pubmed": "18428715" }, { "doi": "10.1093/nar/gki113", "pmc": "PMC540067", "pubmed": "15608240", "title": "The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology", "year": 2005 } ], "synonyms": [ "MGD", "MGI" ], "twitter": "mgi_mouse", "uri_format": "http://www.informatics.jax.org/accession/MGI:$1" }, "mgnify.analysis": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Analyses of microbiome data within MGnify", "example": "MGYA00002270", "homepage": "https://www.ebi.ac.uk/metagenomics/", "name": "MGnify Analysis", "pattern": "^MGYA\\d+$", "preferred_prefix": "mgnify.analysis", "uri_format": "https://www.ebi.ac.uk/metagenomics/analyses/$1" }, "mgnify.proj": { "description": "MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis.", "example": "ERP004492", "homepage": "https://www.ebi.ac.uk/metagenomics", "mappings": { "miriam": "mgnify.proj", "n2t": "mgnify.proj" }, "name": "MGnify Project", "pattern": "^[A-Z]+[0-9]+$", "preferred_prefix": "mgnify.proj", "uri_format": "https://www.ebi.ac.uk/metagenomics/projects/$1" }, "mgnify.samp": { "description": "The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples.", "example": "SRS086444", "homepage": "https://www.ebi.ac.uk/metagenomics", "mappings": { "miriam": "mgnify.samp", "n2t": "mgnify.samp" }, "name": "MGnify Sample", "pattern": "^[A-Z]+[0-9]+$", "preferred_prefix": "mgnify.samp", "uri_format": "https://www.ebi.ac.uk/metagenomics/samples/$1" }, "mi": { "banana": "MI", "contact": { "email": "luana.licata@gmail.com", "github": "luanalicata", "name": "Luana Licata", "orcid": "0000-0001-5084-9000" }, "description": "The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative.", "download_obo": "http://purl.obolibrary.org/obo/mi.obo", "download_owl": "http://purl.obolibrary.org/obo/mi.owl", "example": "0058", "homepage": "https://github.com/HUPO-PSI/psi-mi-CV", "keywords": [ "interaction", "life science", "molecular interaction", "molecule", "obo", "ontology", "protein", "protein interaction" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "MI", "biocontext": "PSIMI", "biolink": "MI", "bioportal": "MI", "fairsharing": "FAIRsharing.8qzmtr", "go": "PSI-MI", "miriam": "mi", "n2t": "psimi", "obofoundry": "mi", "ols": "mi", "ontobee": "MI", "prefixcommons": "psi.mi" }, "name": "Molecular Interactions Controlled Vocabulary", "namespace_in_lui": true, "pattern": "^\\d{4}$", "preferred_prefix": "MI", "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/psi.mi:$1" } ], "publications": [ { "doi": "10.1038/nbt926", "pubmed": "14755292", "title": "The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data", "year": 2004 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/MI_$1", "repository": "https://github.com/HUPO-PSI/psi-mi-CV", "synonyms": [ "PSI-MI" ], "uri_format": "http://purl.obolibrary.org/obo/MI_$1" }, "miaa": { "comment": "same as MAT", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "name": "Minimal Information About Anatomy ontology", "preferred_prefix": "miaa", "references": [ "https://bioconductor.statistik.tu-dortmund.de/packages/3.1/bioc/vignettes/rols/inst/doc/rols.pdf" ] }, "miapa": { "contact": { "email": "hilmar.lapp@duke.edu", "github": "hlapp", "name": "Hilmar Lapp", "orcid": "0000-0001-9107-0714" }, "description": "The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies.\n\nThis ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA.", "download_owl": "http://purl.obolibrary.org/obo/miapa.owl", "example": "0000010", "homepage": "http://www.evoio.org/wiki/MIAPA", "keywords": [ "life science", "obo", "ontology", "phylogenetics", "phylogeny" ], "license": "CC0-1.0", "mappings": { "aberowl": "MIAPA", "biocontext": "MIAPA", "bioportal": "MIAPA", "fairsharing": "FAIRsharing.ca48xs", "obofoundry": "miapa", "ols": "miapa", "ontobee": "MIAPA" }, "name": "Minimum Anformation About a Phylogenetic Analysis Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MIAPA", "publications": [ { "doi": "10.1089/omi.2006.10.231", "pmc": "PMC3167193", "pubmed": "16901231", "title": "Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)", "year": 2006 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/MIAPA_$1", "repository": "https://github.com/evoinfo/miapa", "uri_format": "http://purl.obolibrary.org/obo/MIAPA_$1" }, "mibig": { "contact": { "email": "kblin@biosustain.dtu.dk", "github": "kblin", "name": "Kai Blin", "orcid": "0000-0003-3764-6051" }, "contributor": { "email": "zdoucmm@gmail.com", "github": "mmzdouc", "name": "Mitja M. Zdouc", "orcid": "0000-0001-6534-6609" }, "description": "MIBiG (Minimum Information about a Biosynthetic Gene Cluster) is a data repository and associated data standard designed to describe biosynthetic gene clusters involved in the production of specialized metabolites. It also stores data on measured biological activities and links to other resources such as NCBI, NPAtlas, and ChEBI. MIBiG is used as a reference database, knowledgebase, and training dataset for machine learning.", "example": "BGC0000001", "github_request_issue": 1407, "homepage": "https://mibig.secondarymetabolites.org", "license": "CC-BY-4.0", "name": "Minimum Information about a Biosynthetic Gene Cluster data repository", "pattern": "^BGC\\d{7}$", "preferred_prefix": "mibig", "publications": [ { "doi": "10.1093/nar/gkae1115", "pmc": "PMC11701617", "pubmed": "39657789", "title": "MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration", "year": 2024 } ], "repository": "https://github.com/mibig-secmet/mibig-json", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://mibig.secondarymetabolites.org/go/$1" }, "micro": { "appears_in": [ "mco" ], "contact": { "email": "carrine.blank@umontana.edu", "github": "carrineblank", "name": "Carrine Blank", "orcid": "0000-0002-2100-6351" }, "deprecated": true, "description": "An ontology of prokaryotic phenotypic and metabolic characters", "download_owl": "http://purl.obolibrary.org/obo/micro.owl", "example": "0002999", "homepage": "https://github.com/carrineblank/MicrO", "keywords": [ "assay", "bioinformatics", "cell culture", "microbiology", "obo", "ontology", "phenotype" ], "license": "CC BY 2.0", "mappings": { "aberowl": "MICRO", "biocontext": "MICRO", "fairsharing": "FAIRsharing.brhpb0", "obofoundry": "micro", "ols": "micro", "ontobee": "MICRO" }, "name": "Ontology of Prokaryotic Phenotypic and Metabolic Characters", "pattern": "^\\d{7}$", "preferred_prefix": "MICRO", "publications": [ { "doi": "10.1186/s13326-016-0060-6", "pmc": "PMC4830071", "pubmed": "27076900", "title": "MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions", "year": 2016 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/MICRO_$1", "repository": "https://github.com/carrineblank/MicrO", "uri_format": "http://purl.obolibrary.org/obo/MICRO_$1", "version": "1.5.1" }, "microscope": { "contact": { "email": "cmedigue@genoscope.cns.fr", "name": "MEDIGUE Claudine", "orcid": "0000-0002-3905-1054" }, "description": "MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis.", "example": "5601141", "homepage": "http://www.genoscope.cns.fr/agc/microscope", "keywords": [ "comparative genomics", "life science" ], "mappings": { "biocontext": "MICROSCOPE", "fairsharing": "FAIRsharing.3t5qc3", "miriam": "microscope", "n2t": "microscope", "re3data": "r3d100012928" }, "name": "MicroScope", "pattern": "^\\d+$", "preferred_prefix": "microscope", "publications": [ { "doi": "10.1093/nar/gks1194", "pmc": "PMC3531135", "pubmed": "23193269", "title": "MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data", "year": 2012 } ], "uri_format": "http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1" }, "microsporidia": { "contact": { "email": "oharb@upenn.edu", "github": "ramobrah", "name": "Omar Harb", "orcid": "0000-0003-4446-6200" }, "description": "MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", "example": "ECU03_0820i", "homepage": "http://microsporidiadb.org/micro/", "keywords": [ "eukaryotic", "genome" ], "mappings": { "biocontext": "MICROSPORIDIA", "miriam": "microsporidia", "n2t": "microsporidia", "prefixcommons": "microsporidia" }, "name": "MicrosporidiaDB", "pattern": "^\\w+$", "preferred_prefix": "microsporidia", "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/microsporidia:$1" } ], "publications": [ { "doi": "10.1093/nar/gkp941", "pmc": "PMC2808945", "pubmed": "19914931", "title": "EuPathDB: a portal to eukaryotic pathogen databases", "year": 2009 } ], "uri_format": "http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1" }, "millipore": { "description": "Cell line collections (Providers)", "example": "SCC111", "homepage": "https://www.merckmillipore.com/", "mappings": { "cellosaurus": "Millipore" }, "name": "Merck Millipore (EMD Millipore)", "preferred_prefix": "millipore", "uri_format": "https://www.merckmillipore.com/catalogue/item/$1" }, "mimodb": { "contact": { "email": "hj@uestc.edu.cn", "name": "Jian Huang", "orcid": "0000-0003-2314-7104" }, "description": "MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank.", "example": "1", "homepage": "http://immunet.cn/bdb/", "keywords": [ "interaction", "life science", "protein" ], "mappings": { "biocontext": "MIMODB", "fairsharing": "FAIRsharing.bv0zjz", "miriam": "mimodb", "n2t": "mimodb", "prefixcommons": "mimodb" }, "name": "MimoDB", "pattern": "^\\d+$", "preferred_prefix": "mimodb", "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/mimodb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkv1100", "pmc": "PMC4702802", "pubmed": "26503249", "title": "BDB: biopanning data bank", "year": 2015 }, { "doi": "10.1093/nar/gkr922", "pmc": "PMC3245166", "pubmed": "22053087", "title": "MimoDB 2.0: a mimotope database and beyond", "year": 2011 }, { "doi": "10.3390/molecules15118279", "pmc": "PMC6259156", "pubmed": "21079566", "title": "MimoDB: a new repository for mimotope data derived from phage display technology", "year": 2010 } ], "uri_format": "http://immunet.cn/bdb/index.php/mimoset/$1" }, "minid": { "contact": { "email": "foster@uchicago.edu", "name": "Ian Foster", "orcid": "0000-0003-2129-5269" }, "description": "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation.", "example": "b97957", "homepage": "https://fair-research.org", "keywords": [ "citation", "data retrieval", "publication", "subject agnostic" ], "mappings": { "biocontext": "MINID", "fairsharing": "FAIRsharing.d099fb", "miriam": "minid", "n2t": "minid" }, "name": "Minimal Viable Identifier", "pattern": "^[A-Za-z0-9]+$", "preferred_prefix": "minid", "publications": [ { "doi": "10.1371/journal.pone.0213013", "pubmed": "30973881", "title": "Reproducible big data science: A case study in continuous FAIRness", "year": 2019 }, { "doi": "10.1371/journal.pone.0294883", "title": "Correction: Reproducible big data science: A case study in continuous FAIRness", "year": 2023 } ], "uri_format": "https://hdl.handle.net/hdl:20.500.12582/$1" }, "minid.test": { "description": "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. This is a prefix for referencing identifiers in the minid test namespace. ", "example": "3SBPLMKKVEVR", "homepage": "https://fair-research.org", "mappings": { "miriam": "minid.test" }, "name": "MINID Test", "pattern": "^[A-Za-z0-9]+$", "preferred_prefix": "minid.test", "uri_format": "https://hdl.handle.net/hdl:20.500.12633/$1" }, "mint": { "banana": "MINT", "banana_peel": "-", "contact": { "email": "luana.licata@gmail.com", "name": "Luana Licata", "orcid": "0000-0001-5084-9000" }, "description": "The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals.", "example": "6978836", "homepage": "https://mint.bio.uniroma2.it", "keywords": [ "interaction", "life science", "protein", "proteomics" ], "mappings": { "biocontext": "MINT", "edam": "2615", "fairsharing": "FAIRsharing.2bdvmk", "miriam": "mint", "n2t": "mint", "pathguide": "17", "prefixcommons": "mint", "re3data": "r3d100010414", "uniprot": "DB-0158" }, "name": "Molecular Interaction Database", "pattern": "^\\d{1,7}$", "preferred_prefix": "mint", "providers": [ { "code": "CURATOR_REVIEW", "description": "The Molecular INTeraction database (MINT)", "homepage": "http://mint.bio.uniroma2.it/mint/", "name": "The Molecular INTeraction database (MINT)", "uri_format": "https://mint.bio.uniroma2.it/index.php/results-interactions/?id=$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/mint:$1" } ], "publications": [ { "doi": "10.1093/nar/gkr930", "pmc": "PMC3244991", "pubmed": "22096227", "title": "MINT, the molecular interaction database: 2012 update", "year": 2011 }, { "doi": "10.1093/nar/gkp983", "pmc": "PMC2808973", "pubmed": "19897547", "title": "MINT, the molecular interaction database: 2009 update", "year": 2009 }, { "doi": "10.1093/nar/gkl950", "pmc": "PMC1751541", "pubmed": "17135203", "title": "MINT: the Molecular INTeraction database", "year": 2006 }, { "doi": "10.1016/s0014-5793(01)03293-8", "pubmed": "11911893", "title": "MINT: a Molecular INTeraction database", "year": 2002 } ], "twitter": "MINT_database", "uri_format": "https://mint.bio.uniroma2.it/index.php/detailed-curation/?id=MINT-$1" }, "mipmod": { "contact": { "email": "rsankar@iitk.ac.in", "name": "Ramasubbu Sankararamakrishnan", "orcid": "0000-0002-8527-5614" }, "description": "MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures.", "example": "HOSAPI0399", "homepage": "http://bioinfo.iitk.ac.in/MIPModDB", "keywords": [ "protein", "structure" ], "mappings": { "biocontext": "MIPMOD", "miriam": "mipmod", "n2t": "mipmod", "prefixcommons": "mipmod" }, "name": "MIPModDB", "pattern": "^\\w+$", "preferred_prefix": "mipmod", "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/mipmod:$1" } ], "publications": [ { "doi": "10.1093/nar/gkr914", "pmc": "PMC3245135", "pubmed": "22080560", "title": "MIPModDB: a central resource for the superfamily of major intrinsic proteins", "year": 2011 } ], "uri_format": "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1" }, "mir": { "banana": "MIR", "description": "The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections. These prefixes are used in web resolution of compact identifiers of the form “PREFIX:ACCESSION” or \"PROVIDER/PREFIX:ACCESSION” commonly used to specify bioinformatics and other data resources.", "example": "00100037", "homepage": "https://registry.identifiers.org/registry", "mappings": { "biocontext": "MIR", "miriam": "mir", "n2t": "mir" }, "name": "Identifiers.org Registry", "namespace_in_lui": true, "pattern": "^\\d{8}$", "preferred_prefix": "mir", "uri_format": "https://registry.identifiers.org/registry?query=MIR:$1" }, "mirbase": { "contact": { "email": "sam.griffiths-jones@manchester.ac.uk", "github": "samgriffithsjones", "name": "Sam Griffiths-Jones", "orcid": "0000-0001-6043-807X" }, "description": "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR).", "example": "MI0026471", "homepage": "http://www.mirbase.org/", "keywords": [ "biology", "gene", "rna" ], "license": "public domain", "mappings": { "biocontext": "MIRBASE", "biolink": "mirbase", "edam": "2642", "fairsharing": "FAIRsharing.hmgte8", "integbio": "nbdc00136", "miriam": "mirbase", "n2t": "mirbase", "ncbi": "miRBase", "pathguide": "210", "prefixcommons": "mirbase", "re3data": "r3d100010566", "togoid": "Mirbase", "wikidata": "P2870" }, "name": "miRBase pre-miRNA", "pattern": "^MI\\d{7}$", "preferred_prefix": "mirbase", "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/mirbase:$1" } ], "publications": [ { "doi": "10.1093/nar/gky1141", "pmc": "PMC6323917", "pubmed": "30423142", "title": "miRBase: from microRNA sequences to function", "year": 2019 }, { "doi": "10.1093/nar/gkt1181", "pmc": "PMC3965103", "pubmed": "24275495", "title": "miRBase: annotating high confidence microRNAs using deep sequencing data", "year": 2013 }, { "doi": "10.1093/nar/gkq1027", "pmc": "PMC3013655", "pubmed": "21037258", "title": "miRBase: integrating microRNA annotation and deep-sequencing data", "year": 2010 }, { "doi": "10.1093/nar/gkm952", "pmc": "PMC2238936", "pubmed": "17991681", "title": "miRBase: tools for microRNA genomics", "year": 2007 }, { "doi": "10.1093/nar/gkj112", "pmc": "PMC1347474", "pubmed": "16381832", "title": "miRBase: microRNA sequences, targets and gene nomenclature", "year": 2006 }, { "doi": "10.1093/nar/gkh023", "pmc": "PMC308757", "pubmed": "14681370", "title": "The microRNA Registry", "year": 2004 } ], "uri_format": "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1" }, "mirbase.family": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download.", "example": "MIPF0000002", "homepage": "http://www.mirbase.org/", "license": "public domain", "name": "miRBase Families", "preferred_prefix": "mirbase.family", "synonyms": [ "MIRBASE_FAMILY" ], "uri_format": "http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=$1" }, "mirbase.mature": { "description": "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence.", "example": "MIMAT0046872", "homepage": "http://www.mirbase.org/", "keywords": [ "nucleotide", "sequence" ], "license": "public domain", "mappings": { "biocontext": "MIRBASE.MATURE", "miriam": "mirbase.mature", "n2t": "mirbase.mature", "prefixcommons": "mirbase.mature", "wikidata": "P2871" }, "name": "miRBase mature miRNA", "pattern": "^MIMAT\\d{7}$", "preferred_prefix": "mirbase.mature", "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/mirbase.mature:$1" } ], "synonyms": [ "MIRBASEM" ], "uri_format": "http://mirbase.org/cgi-bin/mature.pl?mature_acc=$1" }, "mirex": { "contact": { "email": "wmk@amu.edu.pl", "name": "Wojciech M. Karlowski", "orcid": "0000-0002-8086-5404" }, "description": "mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data, storing RT–qPCR-based gene expression profile over seven development stages of Arabidopsis. It also provides RNA structural models, publicly available deep sequencing results and experimental procedure details. This collection provides profile information for a single microRNA over all development stages.", "example": "165a", "homepage": "http://comgen.pl/mirex/?page=home", "keywords": [ "life science" ], "mappings": { "biocontext": "MIREX", "fairsharing": "FAIRsharing.q3b39v", "integbio": "nbdc02064", "miriam": "mirex", "n2t": "mirex" }, "name": "mirEX", "pattern": "^\\d+(\\w+)?$", "preferred_prefix": "mirex", "publications": [ { "doi": "10.1186/s12870-015-0533-2", "pmc": "PMC4490709", "pubmed": "26141515", "title": "mirEX 2.0 - an integrated environment for expression profiling of plant microRNAs", "year": 2015 }, { "doi": "10.1093/nar/gkr878", "pmc": "PMC3245179", "pubmed": "22013167", "title": "mirEX: a platform for comparative exploration of plant pri-miRNA expression data", "year": 2011 } ], "uri_format": "http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes" }, "mirgenedb": { "contact": { "email": "BastianFromm@gmail.com", "name": "Bastian Fromm", "orcid": "0000-0003-0352-3037" }, "contributor": { "email": "palayoor.n@northeastern.edu", "github": "nalikapalayoor", "name": "Nalika Palayoor", "orcid": "0009-0008-8406-631X" }, "description": "mircoRNA Gene Database is a collection of animal microRNA genes. This database allows researchers to analyze mircoRNA properties like secondary structure and features in a phylogenetic context.", "example": "Hsa-Let-7-P2a3", "github_request_issue": 1393, "homepage": "https://mirgenedb.org/", "name": "microRNA Gene Database", "pattern": "^[a-zA-Z0-9]+(-[a-zA-Z0-9]+)+$", "preferred_prefix": "mirgenedb", "publications": [ { "doi": "10.1093/nar/gkae1094", "pmc": "PMC11701709", "pubmed": "39673268", "title": "MirGeneDB 3.0: improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models", "year": 2025 }, { "doi": "10.1093/nar/gkab1101", "pmc": "PMC8728216", "pubmed": "34850127", "title": "MirGeneDB 2.1: toward a complete sampling of all major animal phyla", "year": 2022 }, { "doi": "10.1093/nar/gkz885", "pmc": "PMC6943042", "pubmed": "31598695", "title": "MirGeneDB 2.0: the metazoan microRNA complement", "year": 2020 }, { "doi": "10.1146/annurev-genet-120213-092023", "pmc": "PMC4743252", "pubmed": "26473382", "title": "A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome", "year": 2015 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://mirgenedb.org/browse?qtype=mgid&org=ALL&query=$1" }, "miriam": { "contact": { "email": "n.lenovere@gmail.com", "name": "Nicolas Le Novère", "orcid": "0000-0002-6309-7327" }, "description": "Identifiers.org is an established resolving system that enables the referencing of data for the scientific community, with a current focus on the Life Sciences domain.", "example": "pubmed", "homepage": "https://www.ebi.ac.uk", "keywords": [ "biochemistry", "biomedical science", "life science" ], "mappings": { "edam": "1162", "fairsharing": "FAIRsharing.ap169a", "miriam": "identifiers.namespace" }, "name": "Identifiers.org namespace", "pattern": "^[0-9a-z_:\\.-]+$", "preferred_prefix": "miriam", "publications": [ { "doi": "10.1093/nar/gkr1097", "pmc": "PMC3245029", "pubmed": "22140103", "title": "Identifiers.org and MIRIAM Registry: community resources to provide persistent identification", "year": 2011 }, { "doi": "10.1186/1752-0509-1-58", "pmc": "PMC2259379", "pubmed": "18078503", "title": "MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology", "year": 2007 }, { "doi": "10.1038/nbt1156", "pubmed": "16333295", "title": "Minimum information requested in the annotation of biochemical models (MIRIAM)", "year": 2005 } ], "synonyms": [ "identifiers.namespace" ], "uri_format": "https://registry.identifiers.org/registry/$1" }, "miriam.collection": { "banana": "MIR", "deprecated": true, "description": "MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections.", "example": "00000008", "homepage": "https://www.ebi.ac.uk/miriam/", "mappings": { "biocontext": "MIRIAM.COLLECTION", "miriam": "miriam.collection", "n2t": "miriam.collection" }, "name": "MIRIAM Registry collection", "part_of": "miriam", "pattern": "^000\\d{5}$", "preferred_prefix": "miriam.collection", "uri_format": "https://www.ebi.ac.uk/miriam/main/$1" }, "miriam.resource": { "banana": "MIR", "deprecated": true, "description": "MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases.", "example": "00100005", "homepage": "https://www.ebi.ac.uk/miriam/", "keywords": [ "registry" ], "mappings": { "biocontext": "MIRIAM.RESOURCE", "miriam": "miriam.resource", "n2t": "miriam.resource", "prefixcommons": "miriam.resource" }, "name": "MIRIAM Legacy Registry Identifier", "part_of": "miriam", "pattern": "^001\\d{5}$", "preferred_prefix": "miriam.resource", "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/miriam.resource:$1" } ], "publications": [ { "doi": "10.1186/1752-0509-1-58", "pmc": "PMC2259379", "pubmed": "18078503", "title": "MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology", "year": 2007 } ], "uri_format": "https://resolver.api.identifiers.org/resolveMirId/$1" }, "mirnao": { "contact": { "email": "topalis@imbb.forth.gr", "name": "Pantelis Topalis", "orcid": "0000-0002-1635-4810" }, "deprecated": true, "description": "An application ontology for use with miRNA databases.", "download_owl": "http://aber-owl.net/media/ontologies/MIRNAO/11/mirnao.owl", "homepage": "http://code.google.com/p/mirna-ontology/", "keywords": [ "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "MIRNAO", "biocontext": "MIRNAO", "bioportal": "MIRNAO", "obofoundry": "mirnao", "ontobee": "miRNAO" }, "name": "microRNA Ontology", "preferred_prefix": "MIRNAO", "rdf_uri_format": "http://purl.obolibrary.org/obo/MIRNAO_$1", "uri_format": "http://purl.obolibrary.org/obo/MIRNAO_$1" }, "mirnest": { "contact": { "email": "miszcz@amu.edu.pl", "name": "Michael Szcześniak", "orcid": "0000-0002-6050-9525" }, "description": "miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species.", "example": "MNEST029358", "homepage": "http://rhesus.amu.edu.pl/mirnest/copy/", "keywords": [ "expression", "genomics", "life science", "prediction" ], "mappings": { "biocontext": "MIRNEST", "fairsharing": "FAIRsharing.5pfx4r", "integbio": "nbdc01703", "miriam": "mirnest", "n2t": "mirnest", "prefixcommons": "mirnest" }, "name": "miRNEST", "pattern": "^MNEST\\d+$", "preferred_prefix": "mirnest", "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/mirnest:$1" } ], "publications": [ { "doi": "10.1093/nar/gkt1156", "pmc": "PMC3965105", "pubmed": "24243848", "title": "miRNEST 2.0: a database of plant and animal microRNAs", "year": 2013 }, { "doi": "10.1093/nar/gkr1159", "pmc": "PMC3245016", "pubmed": "22135287", "title": "miRNEST database: an integrative approach in microRNA search and annotation", "year": 2011 } ], "uri_format": "http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1" }, "miro": { "contact": { "email": "louis@imbb.forth.gr", "name": "Christos Louis", "orcid": "0000-0003-2497-2210" }, "deprecated": true, "description": "Application ontology for entities related to insecticide resistance in mosquitos", "download_obo": "http://purl.obolibrary.org/obo/miro.obo", "download_owl": "http://purl.obolibrary.org/obo/miro.owl", "example": "40000617", "homepage": "https://github.com/VEuPathDB-ontology/MIRO", "keywords": [ "insecticide resistance", "life science", "mutation", "obo", "ontology", "phenotype" ], "mappings": { "aberowl": "MIRO", "biocontext": "MIRO", "bioportal": "MIRO", "fairsharing": "FAIRsharing.sjf113", "obofoundry": "miro", "ols": "miro", "ontobee": "MIRO" }, "name": "Mosquito insecticide resistance", "pattern": "^\\d{8}$", "preferred_prefix": "MIRO", "publications": [ { "doi": "10.1371/journal.pntd.0000465", "pmc": "PMC2694272", "pubmed": "19547750", "title": "MIRO and IRbase: IT tools for the epidemiological monitoring of insecticide resistance in mosquito disease vectors", "year": 2009 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/MIRO_$1", "repository": "https://github.com/VEuPathDB-ontology/MIRO", "uri_format": "http://purl.obolibrary.org/obo/MIRO_$1", "version": "2014-05-14" }, "mirtarbase": { "contact": { "email": "ken.sd.hsu@gmail.com", "name": "Sheng-Da Hsu", "orcid": "0000-0002-8214-1696" }, "contributor_extras": [ { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } ], "deprecated": true, "description": "miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments.", "example": "MIRT000002", "homepage": "https://mirtarbase.cuhk.edu.cn/", "keywords": [ "life science" ], "mappings": { "biocontext": "MIRTARBASE", "fairsharing": "FAIRsharing.f0bxfg", "integbio": "nbdc01217", "miriam": "mirtarbase", "n2t": "mirtarbase", "pathguide": "715", "wikidata": "P2646" }, "name": "mirTarBase", "pattern": "^MIRT\\d{6}$", "preferred_prefix": "mirtarbase", "publications": [ { "doi": "10.1093/nar/gkab1079", "pmc": "PMC8728135", "pubmed": "34850920", "title": "miRTarBase update 2022: an informative resource for experimentally validated miRNA–target interactions", "year": 2022 }, { "doi": "10.1093/nar/gkz896", "pmc": "PMC7145596", "pubmed": "31647101", "title": "miRTarBase 2020: updates to the experimentally validated microRNA-target interaction database", "year": 2020 }, { "doi": "10.1093/nar/gkx1067", "pmc": "PMC5753222", "pubmed": "29126174", "title": "miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions", "year": 2018 }, { "doi": "10.1093/nar/gkv1258", "pmc": "PMC4702890", "pubmed": "26590260", "title": "miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database", "year": 2016 }, { "doi": "10.1093/nar/gkt1266", "pmc": "PMC3965058", "pubmed": "24304892", "title": "miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions", "year": 2014 }, { "doi": "10.1093/nar/gkq1107", "pmc": "PMC3013699", "pubmed": "21071411", "title": "miRTarBase: a database curates experimentally validated microRNA-target interactions", "year": 2010 } ], "references": [ "https://github.com/biopragmatics/bioregistry/pull/940" ], "uri_format": "https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/detail.php?mirtid=$1" }, "mirte": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs", "example": "miR-1", "homepage": "http://www.russelllab.org/miRNAs/", "name": "miRNA Target Prediction at EMBL", "preferred_prefix": "mirte" }, "mite": { "contact": { "email": "zdoucmm@gmail.com", "github": "mmzdouc", "name": "Mitja M. Zdouc", "orcid": "0000-0001-6534-6609" }, "contributor": { "email": "zdoucmm@gmail.com", "github": "mmzdouc", "name": "Mitja M. Zdouc", "orcid": "0000-0001-6534-6609" }, "description": "MITE (Minimum Information about a Tailoring Enzyme) is a data repository and associated data standard designed to capture the reaction- and substrate-specificities of tailoring enzymes. Community-driven and fully expert-reviewed, it represents enzymatic reactions using reaction SMARTS and links to established resources such as UniProt, NCBI GenPept, Rhea, and MIBiG. MITE serves as a knowledgebase for enzyme and pathway annotation, in silico biosynthesis, and machine learning applications.", "example": "MITE0000001", "github_request_issue": 1405, "homepage": "https://mite.bioinformatics.nl", "license": "CC0-1.0", "name": "Minimum Information about a Tailoring Enzyme data repository", "pattern": "^MITE\\d{7}$", "preferred_prefix": "mite", "publications": [ { "doi": "10.26434/chemrxiv-2024-78mtl", "title": "The Minimum Information about a Tailoring Enzyme/Maturase data standard for capturing natural product biosynthesis", "year": 2024 } ], "repository": "https://github.com/mite-standard/mite_data", "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://mite.bioinformatics.nl/repository/$1" }, "mixs": { "comment": "Some things to be decided before granting - [ ] should the prefix be mixs, gsc.mixs, MIxS, MIXS, ...? - [ ] MIxS terms are most commonly identified by a short computable stable label, e.g ph_regm. The GSC CIG team are creating numeric identifiers, e.g. MIXS:0001056 - Should we support both schemes? - If we do, should these be different prefixes? I would strongly recommend this. E.g. mixs.term:ph_regm, mixs:0001056. We can then have different regex patterns for both Additional notes: - The http://gensc.org/ns/mixs/ will likely changes to a w3id.org URI that will also serve as a semweb identifier - It currently redirects to the tdwg wiki but this is I assume temporary", "contact": { "email": "rlwalls2008@gmail.com", "github": "ramonawalls", "name": "Ramona Walls", "orcid": "0000-0001-8815-0078" }, "contributor": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "contributor_extras": [ { "email": "chris@gigasciencejournal.com", "github": "only1chunts", "name": "Chris Hunter", "orcid": "0000-0002-1335-0881" }, { "email": "lindsey.anderson@pnnl.gov", "github": "lnanderson", "name": "Lindsey N. Anderson", "orcid": "0000-0002-8741-7823" } ], "description": "The GSC family of minimum information standards (checklists) – Minimum Information about any (x) Sequence (MIxS). MIxS identifiers are for terms describing an aspect of an environmental sample.", "download_owl": "http://aber-owl.net/media/ontologies/MIXS/5/mixs.owl", "example": "0001056", "github_request_issue": 151, "homepage": "https://www.gensc.org/pages/standards/all-terms.html", "keywords": [ "ontology" ], "mappings": { "aberowl": "MIXS", "bioportal": "MIXS", "fairsharing": "FAIRsharing.9aa0zp" }, "name": "Minimal Information about any Sequence", "pattern": "^\\d{7}$", "preferred_prefix": "mixs", "providers": [ { "code": "github", "description": "MIxS LinkML schema", "homepage": "https://genomicsstandardsconsortium.github.io/mixs", "name": "MIxS LinkML schema", "uri_format": "https://genomicsstandardsconsortium.github.io/mixs/$1" } ], "publications": [ { "doi": "10.1038/nbt.1823", "pmc": "PMC3367316", "pubmed": "21552244", "title": "Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications", "year": 2011 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://w3id.org/mixs/$1" }, "mlc": { "description": "MLCommons Association artifacts, including benchmark results, datasets, and saved models.", "example": "0.7-123", "homepage": "https://mlcommons.org/en/", "mappings": { "miriam": "mlc" }, "name": "MLCommons Association", "pattern": "^[0-9a-zA-Z\\.\\-\\_]+$", "preferred_prefix": "mlc", "uri_format": "https://www.mlcommons.org/mlc-id/$1" }, "mmdb": { "contact": { "email": "siqian.he@nih.gov", "name": "Siqian He", "orcid": "0000-0002-1707-4167" }, "description": "The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites.", "example": "50885", "homepage": "http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure", "keywords": [ "dna", "interaction", "protein", "small molecule", "structure" ], "mappings": { "biocontext": "MMDB", "edam": "2667", "miriam": "mmdb", "n2t": "mmdb", "pathguide": "508", "prefixcommons": "mmdb" }, "name": "Molecular Modeling Database", "pattern": "^\\d{1,5}$", "preferred_prefix": "mmdb", "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/mmdb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkl952", "pmc": "PMC1751549", "pubmed": "17135201", "title": "MMDB: annotating protein sequences with Entrez's 3D-structure database", "year": 2006 } ], "uri_format": "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1" }, "mmmp.biomaps": { "description": "A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma.", "example": "37", "homepage": "http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp", "keywords": [ "interaction", "molecule", "pathway" ], "mappings": { "biocontext": "MMMP:BIOMAPS", "biolink": "mmmp.biomaps", "miriam": "mmmp.biomaps", "n2t": "biomaps", "prefixcommons": "mmmp" }, "name": "Melanoma Molecular Map Project Biomaps", "pattern": "^\\d+$", "preferred_prefix": "mmmp.biomaps", "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/mmmp:$1" } ], "synonyms": [ "mmmp:biomaps" ], "uri_format": "http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1" }, "mmo": { "contact": { "email": "jrsmith@mcw.edu", "github": "jrsjrs", "name": "Jennifer Smith", "orcid": "0000-0002-6443-9376" }, "description": "A representation of the variety of methods used to make clinical and phenotype measurements.", "download_obo": "http://purl.obolibrary.org/obo/mmo.obo", "download_owl": "http://purl.obolibrary.org/obo/mmo.owl", "example": "0000574", "homepage": "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000", "keywords": [ "biomedical science", "life science", "model organism", "obo", "ontology", "phenotype", "preclinical studies" ], "license": "CC0-1.0", "mappings": { "aberowl": "MMO", "biocontext": "MMO", "bioportal": "MMO", "fairsharing": "FAIRsharing.bgkyd7", "obofoundry": "mmo", "ols": "mmo", "ontobee": "MMO" }, "name": "Measurement method ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MMO", "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/MMO_$1", "repository": "https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology", "twitter": "ratgenome", "uri_format": "http://purl.obolibrary.org/obo/MMO_$1", "version": "2.146" }, "mmp.cat": { "description": "MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples.", "example": "MMP743597.11", "homepage": "https://mmp.sfb.uit.no/databases/marcat/", "mappings": { "biocontext": "MMP.CAT", "miriam": "mmp.cat", "n2t": "mmp.cat" }, "name": "MarCat", "pattern": "^MMP\\d+.\\d+$", "preferred_prefix": "mmp.cat", "uri_format": "https://mmp.sfb.uit.no/databases/marcat/#/records/$1" }, "mmp.db": { "description": "MarDB includes all sequenced marine microbial genomes regardless of level of completeness.", "example": "MMP02954345.1", "homepage": "https://mmp.sfb.uit.no/databases/mardb/", "mappings": { "biocontext": "MMP.DB", "miriam": "mmp.db", "n2t": "mmp.db" }, "name": "MarDB", "pattern": "^MMP\\d+.\\d+$", "preferred_prefix": "mmp.db", "uri_format": "https://mmp.sfb.uit.no/databases/mardb/#/records/$1" }, "mmp.fun": { "description": "MarFun is manually curated database for marine fungi which is a part of the MAR databases.", "example": "MMP3888430", "homepage": "https://mmp.sfb.uit.no/databases/marfun", "mappings": { "miriam": "mmp.fun" }, "name": "MarFun", "pattern": "^MMP\\d+.\\d+$", "preferred_prefix": "mmp.fun", "uri_format": "https://mmp.sfb.uit.no/databases/marfun/#/records/$1" }, "mmp.ref": { "description": "MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes.", "example": "MMP3312982.2", "homepage": "https://mmp.sfb.uit.no/databases/marref/", "mappings": { "biocontext": "MMP.REF", "miriam": "mmp.ref", "n2t": "mmp.ref" }, "name": "MarRef", "pattern": "^MMP\\d+.\\d+$", "preferred_prefix": "mmp.ref", "uri_format": "https://mmp.sfb.uit.no/databases/marref/#/records/$1" }, "mmrrc": { "contact": { "email": "f.grieder@nih.gov", "name": "Franziska B. Grieder", "orcid": "0000-0002-3070-8224" }, "description": "The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections.", "example": "70", "homepage": "https://www.mmrrc.org", "keywords": [ "biology", "cryopreserved", "database", "embryonic stem cell", "embryonic stem cell line", "faseb list", "mouse strain", "mutant", "mutant mouse strain", "stem cell", "transgenic" ], "mappings": { "biocontext": "MMRRC", "cellosaurus": "MMRRC", "fairsharing": "FAIRsharing.9dpd18", "miriam": "mmrrc", "n2t": "mmrrc", "re3data": "r3d100013715", "rrid": "MMRRC" }, "name": "Mutant Mouse Resource and Research Centers", "pattern": "^\\d+$", "preferred_prefix": "mmrrc", "publications": [ { "pubmed": "12102564", "title": "Mutant Mouse Regional Resource Center Program: a resource for distribution of mouse models for biomedical research", "year": 2002 } ], "twitter": "mmrc", "uri_format": "http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1" }, "mmsinc": { "description": "MMSsINC is a database of commercially-available compounds for virtual screening and chemoinformatic applications. MMsINC contains over 4 million non-redundant chemical compounds in 3D formats.", "example": "MMs00000001", "homepage": "http://mms.dsfarm.unipd.it/MMsINC", "keywords": [ "small molecule", "structure" ], "mappings": { "prefixcommons": "mmsinc" }, "name": "MMsINC", "preferred_prefix": "mmsinc", "providers": [ { "code": "bio2rdf", "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. 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This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways.", "download_json": "http://purl.obolibrary.org/obo/mp.json", "download_obo": "http://purl.obolibrary.org/obo/mp.obo", "download_owl": "http://purl.obolibrary.org/obo/mp.owl", "example": "0005452", "homepage": "https://www.informatics.jax.org/vocab/mp_ontology/", "keywords": [ "behavior", "developmental biology", "life science", "mammalian", "obo", "ontology", "phenotype", "physiology" ], "license": "CC-BY-4.0", "logo": "https://raw.githubusercontent.com/mgijax/mammalian-phenotype-ontology/main/logo/2024_MP_logo_RGB_ICON_color.png", "mappings": { "aberowl": "MP", "biocontext": "MP", "bioportal": "MP", "fairsharing": "FAIRsharing.kg1x4z", "miriam": "mp", "n2t": "mp", "obofoundry": "mp", "ols": "mp", "ontobee": "MP", "prefixcommons": "mp", "togoid": "Mp" }, "name": "Mammalian Phenotype Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "MP", "providers": [ { "code": "CURATOR_REVIEW", "description": "Mammalian Phenotype Ontology at The Jackson Lab", "homepage": "http://www.informatics.jax.org/", "name": "Mammalian Phenotype Ontology at The Jackson Lab", "uri_format": "http://www.informatics.jax.org/searches/Phat.cgi?id=MP:$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/mp:$1" }, { "code": "nextprot", "description": "The neXtProt endpoint for exploring MP", "homepage": "https://www.nextprot.org", "name": "neXtProt MP Browser", "uri_format": "https://www.nextprot.org/term/MP:$1" } ], "publications": [ { "doi": "10.1186/s13326-015-0009-1", "pmc": "PMC4378007", "pubmed": "25825651", "title": "Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens", "year": 2015 }, { "doi": "10.1007/s00335-012-9421-3", "pmc": "PMC3463787", "pubmed": "22961259", "title": "The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data", "year": 2012 }, { "doi": "10.1002/wsbm.44", "pmc": "PMC2801442", "pubmed": "20052305", "title": "The mammalian phenotype ontology: enabling robust annotation and comparative analysis", "year": 2009 }, { "doi": "10.1186/gb-2004-6-1-r7", "pmc": "PMC549068", "pubmed": "15642099", "title": "The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information", "year": 2004 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/MP_$1", "repository": "https://github.com/mgijax/mammalian-phenotype-ontology", "uri_format": "http://purl.obolibrary.org/obo/MP_$1", "version": "2025-01-30" }, "mpath": { "contact": { "email": "pns12@hermes.cam.ac.uk", "github": "PaulNSchofield", "name": "Paul Schofield", "orcid": "0000-0002-5111-7263" }, "description": "A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes", "download_obo": "https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo", "download_owl": "http://purl.obolibrary.org/obo/mpath.owl", "example": "728", "homepage": "http://www.pathbase.net", "keywords": [ "anatomy", "biomedical science", "disease", "genetic strain", "histology", "mouse", "mutation", "obo", "ontology", "phenotype" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "MPATH", "biocontext": "MPATH", "bioportal": "MPATH", "fairsharing": "FAIRsharing.3wbgm0", "integbio": "nbdc01568", "obofoundry": "mpath", "ols": "mpath", "ontobee": "MPATH", "prefixcommons": "mpath" }, "name": "Mouse pathology ontology", "pattern": "^\\d+$", "preferred_prefix": "MPATH", "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/mpath:$1" } ], "publications": [ { "doi": "10.1177/0300985810374845", "pmc": "PMC3038412", "pubmed": "20587689", "title": "Pathbase and the MPATH ontology. Community resources for mouse histopathology", "year": 2010 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/MPATH_$1", "repository": "https://github.com/PaulNSchofield/mpath", "synonyms": [ "MPATH" ], "uri_format": "http://purl.obolibrary.org/obo/MPATH_$1", "version": "2020-05-19" }, "mpid": { "contact": { "email": "jgoll@emmes.com", "name": "Johannes B. Goll", "orcid": "0000-0002-9968-4080" }, "description": "The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts.", "example": "172", "homepage": "https://www.ebi.ac.uk/intact/", "keywords": [ "interaction", "life science", "protein", "small molecule" ], "mappings": { "biocontext": "MPID", "fairsharing": "FAIRsharing.eyjkws", "miriam": "mpid", "n2t": "mpid", "pathguide": "559", "prefixcommons": "mpi" }, "name": "Microbial Protein Interaction Database", "pattern": "^\\d+$", "preferred_prefix": "mpid", "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/mpi:$1" } ], "publications": [ { "doi": "10.1093/bioinformatics/btn285", "pmc": "PMC2638870", "pubmed": "18556668", "title": "MPIDB: the microbial protein interaction database", "year": 2008 } ], "synonyms": [ "mpidb" ], "uri_format": "https://www.ebi.ac.uk/intact/query/interaction_id:MPIDB-INT-$1" }, "mpio": { "contact": { "email": "mbrochhausen@uams.edu", "github": "mbrochhausen", "name": "Mathias Brochhausen", "orcid": "0000-0003-1834-3856" }, "description": "An ontology of minimum information regarding potential drug-drug interaction information.", "download_owl": "http://purl.obolibrary.org/obo/mpio.owl", "example": "0000004", "homepage": "https://github.com/MPIO-Developers/MPIO", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "MPIO", "biocontext": "MPIO", "bioportal": "MPIO", "obofoundry": "mpio", "ols": "mpio", "ontobee": "MPIO" }, "name": "Minimum PDDI Information Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MPIO", "rdf_uri_format": "http://purl.obolibrary.org/obo/MPIO_$1", "repository": "https://github.com/MPIO-Developers/MPIO", "uri_format": "http://purl.obolibrary.org/obo/MPIO_$1", "version": "2023-10-17" }, "mro": { "contact": { "email": "bpeters@lji.org", "github": "bpeters42", "name": "Bjoern Peters", "orcid": "0000-0002-8457-6693" }, "description": "The MHC Restriction Ontology is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions.", "download_owl": "http://purl.obolibrary.org/obo/mro.owl", "example": "0000634", "homepage": "https://github.com/IEDB/MRO", "keywords": [ "immune system", "immunology", "major histocompatibility complex", "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "MRO", "biocontext": "MRO", "fairsharing": "FAIRsharing.k893xa", "obofoundry": "mro", "ols": "mro", "ontobee": "MRO" }, "name": "MHC Restriction Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MRO", "publications": [ { "doi": "10.1186/s13326-016-0045-5", "pmc": "PMC4709943", "pubmed": "26759709", "title": "An ontology for major histocompatibility restriction", "year": 2016 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/MRO_$1", "repository": "https://github.com/IEDB/MRO", "uri_format": "http://purl.obolibrary.org/obo/MRO_$1", "version": "2025-02-13" }, "ms": { "banana": "MS", "contact": { "email": "joshua.adam.klein@gmail.com", "github": "mobiusklein", "name": "Joshua Klein", "orcid": "0000-0003-1279-6838" }, "depends_on": [ "pato", "uo" ], "description": "The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance.", "download_obo": "http://purl.obolibrary.org/obo/ms.obo", "download_owl": "http://purl.obolibrary.org/obo/ms.owl", "example": "1000560", "homepage": "http://www.psidev.info/groups/controlled-vocabularies", "keywords": [ "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "MS", "biocontext": "MS", "bioportal": "MS", "miriam": "ms", "n2t": "ms", "obofoundry": "ms", "ols": "ms", "ontobee": "MS" }, "name": "Mass spectrometry ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "MS", "publications": [ { "doi": "10.1093/database/bat009", "pmc": "PMC3594986", "pubmed": "23482073", "title": "The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary", "year": 2013 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/MS_$1", "repository": "https://github.com/HUPO-PSI/psi-ms-CV", "uri_format": "http://purl.obolibrary.org/obo/MS_$1", "version": "4.1.191" }, "msigdb": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can", "example": "M1", "homepage": "https://www.gsea-msigdb.org", "license": "CC-BY-4.0", "mappings": { "biolink": "MSigDB", "integbio": "nbdc02550" }, "name": "Molecular Signatures Database", "pattern": "^M\\d+$", "preferred_prefix": "msigdb", "providers": [ { "code": "biopragmatics", "description": "An OBO to Website of MMSigDB", "homepage": "https://biopragmatics.github.io/providers/msigdb/", "name": "MMSigDB from Biopragmatics", "uri_format": "https://biopragmatics.github.io/providers/msigdb/$1" } ], "synonyms": [ "msig" ], "uri_format": "https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/$1" }, "msio": { "contact": { "email": "philippe.rocca-serra@oerc.ox.ac.uk", "name": "Philippe Rocca-Serra", "orcid": "0000-0001-9853-5668" }, "description": "an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies.", "download_owl": "https://raw.githubusercontent.com/MSI-Metabolomics-Standards-Initiative/MSIO/master/releases/latest_release/MSIO-merged-reasoned.owl", "example": "0000111", "homepage": "https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO", "keywords": [ "annotation", "experimental measurement", "functional magnetic resonance imaging", "mass spectrum", "metabolomics", "nmr", "nuclear magnetic resonance (nmr) spectroscopy", "omics", "omics data analysis", "ontology" ], "mappings": { "fairsharing": "FAIRsharing.4c7f91", "ols": "msio" }, "name": "Metabolomics Standards Initiative Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "msio", "publications": [ { "doi": "10.1007/s11306-007-0069-z", "title": "Metabolomics standards initiative: ontology working group work in progress", "year": 2007 } ], "repository": "https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO", "uri_format": "http://purl.obolibrary.org/obo/MSIO_$1", "version": "1.0.1" }, "mtbd": { "description": "The Mouse Tumor Biology (MTB) Database supports the use of the mouse as a model system of hereditary cancer by providing electronic access to Information on endogenous spontaneous and induced tumors in mice, including tumor frequency & latency data, information on genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice) in which tumors arise, and information on genetic factors associated with tumor susceptibility in mice and somatic genetic-mutations observed in the tumors.", "example": "1374", "homepage": "http://tumor.informatics.jax.org", "keywords": [ "dna", "gene expression" ], "mappings": { "prefixcommons": "mtbd" }, "name": "Mouse Tumor Biology Database", "preferred_prefix": "mtbd", "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/mtbd:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://tumor.informatics.jax.org/mtbwi/strainDetails.do?key=$1" }, "multicellds": { "contact": { "email": "samuel.friedman@cammlab.org", "name": "Samuel Friedman", "orcid": "0000-0001-8003-6860" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata.", "example": "MCDS_S_0000000001", "homepage": "http://multicellds.org/MultiCellDB.php", "keywords": [ "life science" ], "mappings": { "fairsharing": "FAIRsharing.pqzyd5" }, "name": "MultiCellDS", "preferred_prefix": "multicellds", "uri_format": "http://multicellds.org/MultiCellDB/$1" }, "multicellds.cell_line": { "description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata.", "example": "MCDS_L_0000000001", "homepage": "http://multicellds.org/MultiCellDB.php", "mappings": { "biocontext": "MULTICELLDS.CELL_LINE", "miriam": "multicellds.cell_line", "n2t": "multicellds.cell_line" }, "name": "MultiCellDS Digital Cell Line", "part_of": "multicellds", "pattern": "^MCDS_L_[a-zA-Z0-9]{1,10}$", "preferred_prefix": "multicellds.cell_line", "uri_format": "http://multicellds.org/MultiCellDB/$1" }, "multicellds.collection": { "description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections).", "example": "MCDS_C_0000000001", "homepage": "http://multicellds.org/MultiCellDB.php", "mappings": { "biocontext": "MULTICELLDS.COLLECTION", "miriam": "multicellds.collection", "n2t": "multicellds.collection" }, "name": "MultiCellDS collection", "part_of": "multicellds", "pattern": "^MCDS_C_[a-zA-Z0-9]{1,10}$", "preferred_prefix": "multicellds.collection", "uri_format": "http://multicellds.org/MultiCellDB/$1" }, "multicellds.snapshot": { "description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data.", "example": "MCDS_S_0000000001", "homepage": "http://multicellds.org/MultiCellDB.php", "mappings": { "biocontext": "MULTICELLDS.SNAPSHOT", "miriam": "multicellds.snapshot", "n2t": "multicellds.snapshot" }, "name": "MultiCellDS Digital snapshot", "part_of": "multicellds", "pattern": "^MCDS_S_[a-zA-Z0-9]{1,10}$", "preferred_prefix": "multicellds.snapshot", "uri_format": "http://multicellds.org/MultiCellDB/$1" }, "mvx": { "contributor": { "email": "lindsey.anderson@pnnl.gov", "github": "lnanderson", "name": "Lindsey Anderson", "orcid": "0000-0002-8741-7823" }, "description": "The CDC's National Center for Immunization and Respiratory Diseases ([NCIRD](https://www.cdc.gov/ncird/)) developed and maintains HL7 Table 0227, Manufacturers of Vaccines (MVX). It includes both active and inactive manufacturers of vaccines in the US. Inactive MVX codes allow transmission of historical immunization records. When [MVX code is paired with a CVX code](https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=tradename) (vaccine administered code), the specific trade named vaccine may be indicated.", "example": "ASZ", "github_request_issue": 986, "homepage": "https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=mvx", "mappings": { "hl7": "2.16.840.1.113883.6.60" }, "name": "Manufacturers of Vaccines", "pattern": "^\\w+$", "preferred_prefix": "mvx", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://phinvads.cdc.gov/vads/ViewCodeSystemConcept.action?oid=2.16.840.1.113883.12.227&code=$1" }, "mw.project": { "description": "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).", "example": "PR000001", "homepage": "http://www.metabolomicsworkbench.org/", "mappings": { "biocontext": "MW.PROJECT", "miriam": "mw.project", "n2t": "mw.project" }, "name": "Metabolomics Workbench Project", "pattern": "^PR[0-9]{6}$", "preferred_prefix": "mw.project", "uri_format": "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1" }, "mw.study": { "description": "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).", "example": "ST000900", "homepage": "http://www.metabolomicsworkbench.org/", "mappings": { "biocontext": "MW.STUDY", "miriam": "mw.study", "n2t": "mw.study" }, "name": "Metabolomics Workbench Study", "pattern": "^ST[0-9]{6}$", "preferred_prefix": "mw.study", "providers": [ { "code": "omicsdi", "description": "Metabolomics Workbench Study through OmicsDI", "homepage": "https://www.omicsdi.org/", "name": "Metabolomics Workbench Study through OmicsDI", "uri_format": "https://www.omicsdi.org/dataset/metabolomics_workbench/$1" } ], "uri_format": "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1" }, "myco": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information.", "example": "ML0224", "example_extras": [ "MMAR_2462", "MSMEG_3769", "Rv1908c" ], "homepage": "https://mycobrowser.epfl.ch", "name": "MycoBrowser", "preferred_prefix": "myco", "uri_format": "https://mycobrowser.epfl.ch/genes/$1" }, "myco.lepra": { "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information.", "example": "ML0224", "homepage": "https://mycobrowser.epfl.ch", "keywords": [ "genome", "sequence" ], "mappings": { "biocontext": "MYCO.LEPRA", "miriam": "myco.lepra", "n2t": "myco.lepra", "prefixcommons": "myco.lepra" }, "name": "MycoBrowser leprae", "part_of": "myco", "pattern": "^ML\\w+$", "preferred_prefix": "myco.lepra", "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/myco.lepra:$1" } ], "uri_format": "https://mycobrowser.epfl.ch/genes/$1" }, "myco.marinum": { "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information.", "example": "MMAR_2462", "homepage": "https://mycobrowser.epfl.ch", "keywords": [ "genome", "sequence" ], "mappings": { "biocontext": "MYCO.MARINUM", "miriam": "myco.marinum", "n2t": "myco.marinum", "prefixcommons": "myco.marinum" }, "name": "MycoBrowser marinum", "part_of": "myco", "pattern": "^MMAR\\_\\d+$", "preferred_prefix": "myco.marinum", "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/myco.marinum:$1" } ], "uri_format": "https://mycobrowser.epfl.ch/genes/$1" }, "myco.smeg": { "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information.", "example": "MSMEG_3769", "homepage": "https://mycobrowser.epfl.ch/", "keywords": [ "genome", "sequence" ], "mappings": { "biocontext": "MYCO.SMEG", "miriam": "myco.smeg", "n2t": "myco.smeg", "prefixcommons": "myco.smeg" }, "name": "MycoBrowser smegmatis", "part_of": "myco", "pattern": "^MSMEG\\w+$", "preferred_prefix": "myco.smeg", "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/myco.smeg:$1" } ], "uri_format": "https://mycobrowser.epfl.ch/genes/$1" }, "myco.tuber": { "contact": { "email": "stewart.cole@epfl.ch", "name": "Stewart Thomas Cole", "orcid": "0000-0003-1400-5585" }, "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information.", "example": "Rv1908c", "homepage": "https://mycobrowser.epfl.ch/", "keywords": [ "dna", "genome", "protein" ], "mappings": { "biocontext": "MYCO.TUBER", "miriam": "myco.tuber", "n2t": "myco.tuber", "ncbi": "TubercuList", "prefixcommons": "tuberculist", "uniprot": "DB-0106" }, "name": "TubercuList knowledge base", "part_of": "myco", "pattern": "^Rv\\d{4}(A|B|c)?$", "preferred_prefix": "myco.tuber", "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/tuberculist:$1" } ], "publications": [ { "doi": "10.1016/j.tube.2010.09.006", "pubmed": "20980200", "title": "The MycoBrowser portal: a comprehensive and manually annotated resource for mycobacterial genomes", "year": 2010 } ], "synonyms": [ "TubercuList" ], "uri_format": "https://mycobrowser.epfl.ch/genes/$1" }, "mycobank": { "contact": { "email": "vrobert@unistra.fr", "name": "Vincent Robert", "orcid": "0000-0002-9370-4677" }, "contributor_extras": [ { "email": "carlosm@ebi.ac.uk", "github": "CarMoreno", "name": "Carlos Moreno", "orcid": "0000-0003-0066-1717" } ], "description": "MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations.", "example": "349124", "homepage": "http://www.mycobank.org/", "keywords": [ "biology", "classification", "taxonomy" ], "mappings": { "biocontext": "MYCOBANK", "fairsharing": "FAIRsharing.v8se8r", "integbio": "nbdc01815", "miriam": "mycobank", "n2t": "mycobank", "ncbi": "MycoBank", "prefixcommons": "mycobank", "re3data": "r3d100011222" }, "name": "Fungal Nomenclature and Species Bank", "pattern": "^\\d+$", "preferred_prefix": "mycobank", "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/mycobank:$1" } ], "publications": [ { "doi": "10.5598/imafungus.2013.04.02.16", "pmc": "PMC3905949", "pubmed": "24563843", "title": "MycoBank gearing up for new horizons", "year": 2013 } ], "uri_format": "https://www.mycobank.org/page/Name%20details%20page/$1" }, "mzspec": { "banana": "mzspec", "contact": { "email": "gerhard.mayer@rub.de", "github": "germa", "name": "Gerhard Mayer", "orcid": "0000-0002-1767-2343" }, "contributor_extras": [ { "email": "lindsey.anderson@pnnl.gov", "github": "lnanderson", "name": "Lindsey N. Anderson", "orcid": "0000-0002-8741-7823" } ], "description": "The Universal Spectrum Identifier (USI) is a compound identifier that provides an abstract path to refer to a single spectrum generated by a mass spectrometer, and potentially the ion that is thought to have produced it.", "example": "PXD002255:ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2", "homepage": "http://www.psidev.info/usi", "keywords": [ "data governance", "data identity and mapping", "data retrieval", "lipidomics", "mass spectrum", "metabolomics", "omics data analysis", "proteomics" ], "mappings": { "biocontext": "MZSPEC", "fairsharing": "FAIRsharing.b549b8", "miriam": "mzspec", "n2t": "mzspec" }, "name": "Universal Spectrum Identifier", "namespace_in_lui": true, "pattern": "^.+$", "preferred_prefix": "mzspec", "providers": [ { "code": "CURATOR_REVIEW", "description": "Universal Spectrum Identifier through Peptide Atlas", "homepage": "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum", "name": "Universal Spectrum Identifier through Peptide Atlas", "uri_format": "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum?usi=mzspec:$1" }, { "code": "ebi", "description": "PRIDE is a database of PRoteomics IDEntifications. It contains protein and peptide identifications (including details of post-translational modifications) together with the mass spectrometric evidence supporting these identifications. PRIDE acts as a repository for mass spectrometry data, specifically the fragment ion spectra used to identify peptide sequences.", "homepage": "https://www.ebi.ac.uk/pride", "name": "PRIDE", "uri_format": "https://www.ebi.ac.uk/pride/archive/usi?usi=mzspec:$1" } ], "publications": [ { "doi": "10.1038/s41592-021-01184-6", "pmc": "PMC8405201", "pubmed": "34183830", "title": "Universal Spectrum Identifier for mass spectra", "year": 2021 } ], "repository": "https://github.com/HUPO-PSI/usi", "uri_format": "http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:$1" }, "n2t": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ARK resolver as well as resolver built with common prefixes as in Identifiers.org", "example": "chebi", "homepage": "https://n2t.net", "name": "Name-to-Thing", "preferred_prefix": "n2t", "uri_format": "https://n2t.net/$1:" }, "namerxn": { "contact": { "email": "gregory.landrum@phys.chem.ethz.ch", "github": "greglandrum", "name": "Gregory Landrum", "orcid": "0000-0001-6279-4481" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The nomenclature used for named reactions in text mining software from NextMove. While it's proprietary, there are a few publications listing parts. 487/1,855 have mappings to the Reaction Ontology (RXNO).", "example": "4.2.78", "homepage": "https://www.nextmovesoftware.com/namerxn.html", "keywords": [ "chemistry", "reactions", "text mining" ], "name": "NameRXN", "preferred_prefix": "namerxn", "proprietary": true, "publications": [ { "doi": "10.1021/acs.jmedchem.6b00153", "pubmed": "27028220", "title": "Big Data from Pharmaceutical Patents: A Computational Analysis of Medicinal Chemists' Bread and Butter", "year": 2016 }, { "doi": "10.1038/s42256-020-00284-w", "title": "Mapping the space of chemical reactions using attention-based neural networks", "year": 2021 } ], "references": [ "https://www.nextmovesoftware.com/products/HazELNutPoster.pdf", "https://twitter.com/cthoyt/status/1443929184745758723" ] }, "nando": { "banana": "NANDO", "contact": { "email": "takatter@dbcls.rois.ac.jp", "name": "Terue Takatsuki" }, "description": "Nanbyo Disease Ontology (NANDO) is the ontology creating a comprehensive hierarchical controlled vocabulary for intractable and rare disease (i.e., nanbyo) representation in Japan.", "download_owl": "http://aber-owl.net/media/ontologies/NANDO/16/nando.owl", "example": "1200031", "homepage": "https://nanbyodata.jp/", "keywords": [ "ontology" ], "mappings": { "aberowl": "NANDO", "bioportal": "NANDO", "miriam": "nando", "togoid": "Nando" }, "name": "Nanbyo Disease Ontology", "namespace_in_lui": true, "pattern": "^\\d+$", "preferred_prefix": "nando", "uri_format": "https://nanbyodata.jp/disease/NANDO:$1" }, "napdi": { "contact": { "email": "rdb20@pitt.edu", "name": "Richard Boyce", "orcid": "0000-0002-2993-2085" }, "description": "The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs).", "example": "28", "homepage": "https://repo.napdi.org/", "keywords": [ "biomedical science", "pharmacology" ], "mappings": { "biocontext": "NAPDI", "fairsharing": "FAIRsharing.y9x8wk", "miriam": "napdi", "n2t": "napdi" }, "name": "Natural Product-Drug Interaction Research Data Repository", "pattern": "^[0-9]+$", "preferred_prefix": "napdi", "publications": [ { "doi": "10.1186/s13326-018-0183-z", "pmc": "PMC5944177", "pubmed": "29743102", "title": "Extending the DIDEO ontology to include entities from the natural product drug interaction domain of discourse", "year": 2018 } ], "uri_format": "https://repo.napdi.org/study/$1" }, "napp": { "contact": { "email": "daniel.gautheret@u-psud.fr", "name": "Daniel Gautheret", "orcid": "0000-0002-1508-8469" }, "description": "NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. 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A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information.", "example": "00001234", "homepage": "http://www.nbrc.nite.go.jp/e/index.html", "keywords": [ "microbial", "microbiology", "taxonomy" ], "mappings": { "biocontext": "NBRC", "fairsharing": "FAIRsharing.ftamrc", "miriam": "nbrc", "n2t": "nbrc", "ncbi": "NBRC", "prefixcommons": "nbrc" }, "name": "NITE Biological Resource Center", "pattern": "^\\d+$", "preferred_prefix": "nbrc", "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/nbrc:$1" } ], "uri_format": "http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1" }, "ncats.bioplanet": { "contact": { "email": "ruili.huang@nih.gov", "name": "Ruili Huang", "orcid": "0000-0001-8886-8311" }, "contributor": { "github": "sierra-moxon", "name": "Sierra Moxon", "orcid": "0000-0002-8719-7760" }, "description": "The NCATS BioPlanet is a comprehensive, publicly accessible informatics resource that catalogs all pathways, their healthy and disease state annotations, and targets within and relationships among them. The BioPlanet integrates pathway annotations from publicly available, manually curated sources subjected to thorough redundancy and consistency cross-evaluation via extensive manual curation. The browser supports interactive browsing, retrieval and analysis of pathways, exploration of pathway connections, and pathway search by gene targets, category, and availability of bioactivity assays.", "example": "3", "github_request_issue": 445, "homepage": "https://tripod.nih.gov/bioplanet/", "mappings": { "biolink": "ncats.bioplanet" }, "name": "National Center for Advancing Translation Sciences BioPlanet", "pattern": "^\\d+$", "preferred_prefix": "ncats.bioplanet", "publications": [ { "doi": "10.3389/fphar.2019.00445", "pmc": "PMC6524730", "pubmed": "31133849", "title": "The NCATS BioPlanet - An Integrated Platform for Exploring the Universe of Cellular Signaling Pathways for Toxicology, Systems Biology, and Chemical Genomics", "year": 2019 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "twitter": "ncats_nih_gov", "uri_format": "https://tripod.nih.gov/bioplanet/detail.jsp?pid=bioplanet_$1" }, "ncats.drug": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, { "github": "vdancik", "name": "Vlado Dancik", "orcid": "0000-0002-5970-6660" }, { "github": "sierra-moxon", "name": "Sierra Moxon", "orcid": "0000-0002-8719-7760" } ], "description": "The National Center for Advancing Translational Sciences](http://www.ncats.nih.gov/) (NCATS) has developed Inxight Drugs as a comprehensive portal for drug development information. NCATS Inxight Drugs contains information on ingredients in medicinal products, including:\n\n- US Approved Drugs\n- Marketed Drugs\n- Investigational Drugs\n- Other Substances", "example": "44259", "example_extras": [ "1IJV77EI07" ], "homepage": "https://drugs.ncats.io/", "mappings": { "biolink": "ncats.drug" }, "name": "NCATS Drugs", "preferred_prefix": "ncats.drug", "synonyms": [ "inxight", "inxight-drugs" ], "uri_format": "https://drugs.ncats.io/drug/$1" }, "ncbi.assembly": { "description": "A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data.", "example": "GCF_000005845.2", "homepage": "https://www.ncbi.nlm.nih.gov/", "mappings": { "biocontext": "NCBIAssembly", "miriam": "assembly", "re3data": "r3d100012688" }, "name": "Assembly", "pattern": "^[a-zA-Z0-9_\\.]+$", "preferred_prefix": "ncbi.assembly", "uri_format": "https://www.ncbi.nlm.nih.gov/datasets/genome/$1" }, "ncbi.gc": { "comment": "see comment here: https://github.com/obophenotype/ncbitaxon/issues/47", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries.", "example": "11", "homepage": "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html", "license": "public domain", "name": "Genetic Code", "pattern": "^\\d+$", "preferred_prefix": "ncbi.gc", "references": [ "https://github.com/obophenotype/ncbitaxon/issues/47" ], "synonyms": [ "gc", "gc_id" ], "uri_format": "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG$1" }, "ncbi.genome": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations.", "example": "51", "homepage": "https://www.ncbi.nlm.nih.gov/genome", "mappings": { "biocontext": "NCBIGenome", "edam": "2787", "re3data": "r3d100010785" }, "name": "NCBI Genome", "pattern": "^\\d+$", "preferred_prefix": "ncbi.genome", "uri_format": "https://www.ncbi.nlm.nih.gov/genome/$1" }, "ncbi.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 NCBI GenBank and related NCBI resources", "example": "ECOCYC", "homepage": "https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/", "name": "NCBI Registry", "preferred_prefix": "ncbi.resource", "uri_format": "https://bioregistry.io/metaregistry/ncbi/$1" }, "ncbibook": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The NCBI Bookshelf provides free online access to books and documents in life science and healthcare. Search, read, and discover. ", "example": "NBK331", "homepage": "https://www.ncbi.nlm.nih.gov/books", "name": "NCBI Bookshelf", "pattern": "^NBK\\d+$", "preferred_prefix": "ncbibook", "uri_format": "https://www.ncbi.nlm.nih.gov/books/$1" }, "ncbidrs": { "description": "This is the namespace for the archive of sequence and other files provided by NCBI e.g. in SRA and dbGaP. These files are related to objects in the sequencing data model managed under the insdc.sra namespace. ", "example": "72ff6ff882ec447f12df018e6183de59", "homepage": "https://www.ncbi.nlm.nih.gov/", "mappings": { "miriam": "ncbidrs" }, "name": "NCBI Data Repository Service", "pattern": "^[0-9a-fA-F]{32}$", "preferred_prefix": "ncbidrs", "uri_format": "https://locate.be-md.ncbi.nlm.nih.gov/ga4gh/drs/v1/objects/$1" }, "ncbigene": { "contact": { "email": "murphyte@ncbi.nlm.nih.gov", "name": "Terence D. 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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/ncbigene:$1" }, { "code": "marrvel", "description": "Helps browse potential orthologs in model organisms for a given gene", "homepage": "http://marrvel.org", "name": "Model organism Aggregated Resources for Rare Variant ExpLoration", "uri_format": "http://marrvel.org/model/gene/$1" }, { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", "homepage": "https://scholia.toolforge.org/", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/ncbi-gene/$1" } ], "publications": [ { "doi": "10.1093/nar/gku1055", "pubmed": "25355515" }, { "doi": "10.1093/nar/gkq1237", "pmc": "PMC3013746", "pubmed": "21115458", "title": "Entrez Gene: gene-centered information at NCBI", "year": 2010 }, { "doi": "10.1093/nar/gki031", "pmc": "PMC539985", "pubmed": "15608257", "title": "Entrez Gene: gene-centered information at NCBI", "year": 2005 } ], "rdf_uri_format": "http://purl.uniprot.org/geneid/$1", "references": [ "https://github.com/biopragmatics/bioregistry/issues/983" ], "synonyms": [ "EGID", "EntrezGene", "GeneID", "NCBIGene", "NCBI_GeneID", "entrez", "entrez gene/locuslink", "nihgeneid" ], "uri_format": "https://www.ncbi.nlm.nih.gov/gene/$1" }, "ncbigi": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A GI number (for GenInfo Identifier, sometimes written in lower case, _gi_) is a simple series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Version number of the sequence record. 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We are now in the process of adding this tag to the INSDC list for use in annotations, so I'd like to mirror that tag in bioregistry.", "contact": { "email": "murphyte@ncbi.nlm.nih.gov", "github": "murphyte", "name": "Terence Murphy", "orcid": "0000-0001-9311-9745" }, "contributor": { "email": "murphyte@ncbi.nlm.nih.gov", "github": "murphyte", "name": "Terence Murphy", "orcid": "0000-0001-9311-9745" }, "description": "Database of one-to-one ortholog information provided by the NCBI as a subset of their Gene resource. Used for users to access ortholog information for over 1000 species of vertebrates and arthropods.", "example": "2", "github_request_issue": 1181, "homepage": "https://www.ncbi.nlm.nih.gov/gene/", "license": "US gov't public domain", "name": "NCBI Orthologs", "pattern": "^\\d+$", "preferred_prefix": "ncbiortholog", "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. 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Represented in a formal, machine-interpretable ontology language, OntoCAPE captures consensual knowledge of the process engineering domain in a generic way such that it can be reused and shared by groups of people and across software systems. On the basis of OntoCAPE, novel software support for various engineering activities can be developed; possible applications include the systematic management and retrieval of simulation models and design documents, electronic procurement of plant equipment, mathematical modeling, as well as the integration of design data from distributed sources.", "homepage": "https://www.avt.rwth-aachen.de/cms/AVT/Forschung/Software/~ipts/OntoCape/", "license": "GPL-2.0", "name": "Ontology for computer aided process engineering", "preferred_prefix": "nfdi4chem.ontocape" }, "nfdi4chem.osmo": { "comment": "locked behind a private GitLab instance", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "description": "OSMO is an ontologization and extension of MODA, a workflow metadata standard that constitutes a mandatory requirement within a number of European calls and projects in the context of materials modelling. OSMO was developed within the Horizon 2020 project VIMMP (Virtual Materials Marketplace) and is part of a larger effort in ontology engineering driven by the European Materials Modelling Council, with the European Materials and Modelling Ontology (EMMO) as its core. (from https://nfdi4cat.org/services/ontologie-sammlung/)", "homepage": "https://zenodo.org/record/5237774#.YXq72hxCRGo", "name": "Ontology for simulation, modelling, and optimization", "preferred_prefix": "nfdi4chem.osmo" }, "ngbo": { "contact": { "email": "dal.alghamdi92@gmail.com", "github": "dalalghamdi", "name": "Dalia Alghamdi", "orcid": "0000-0002-2801-0767" }, "description": "Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management.", "download_owl": "http://purl.obolibrary.org/obo/ngbo.owl", "example": "6000122", "homepage": "https://github.com/Dalalghamdi/NGBO", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "NGBO", "bioportal": "NGBO", "obofoundry": "ngbo", "ols": "ngbo", "ontobee": "NGBO" }, "name": "Next Generation Biobanking Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "NGBO", "rdf_uri_format": "http://purl.obolibrary.org/obo/NGBO_$1", "repository": "https://github.com/Dalalghamdi/NGBO", "uri_format": "http://purl.obolibrary.org/obo/NGBO_$1", "version": "2024-08-27" }, "ngl": { "description": "NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing databases for expanded research, will offer tools to conduct data analysis, and is in the process of creating a place online where scientists, researchers, teachers and students can connect with their peers, share their results, and communicate with NASA.", "example": "GLDS-141", "homepage": "https://genelab-data.ndc.nasa.gov/genelab/", "mappings": { "biocontext": "NGL", "miriam": "ngl", "n2t": "ngl" }, "name": "NASA GeneLab", "pattern": "^GLDS-\\d+$", "preferred_prefix": "ngl", "uri_format": "https://genelab-data.ndc.nasa.gov/genelab/accession/$1" }, "nhcdr": { "description": "Cell line collections (Providers)", "example": "ND50028", "homepage": "https://stemcells.nindsgenetics.org", "mappings": { "cellosaurus": "NHCDR" }, "name": "NINDS Human Cell and Data Repository", "preferred_prefix": "nhcdr", "uri_format": "https://stemcells.nindsgenetics.org?line=$1" }, "niaest": { "contact": { "email": "dawood@helix.nih.gov", "name": "Dawood B. Dudekula", "orcid": "0000-0002-4054-1827" }, "deprecated": true, "description": "A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute on Aging) assembled.This collection represents the name and sequence from individual cDNA clones.", "example": "J0705A10", "homepage": "http://lgsun.grc.nia.nih.gov/cDNA/", "keywords": [ "dna", "life science" ], "mappings": { "biocontext": "NIAEST", "fairsharing": "FAIRsharing.xwqg9h", "miriam": "niaest", "n2t": "niaest", "ncbi": "niaEST", "prefixcommons": "niaest" }, "name": "NIA Mouse cDNA Project", "pattern": "^\\w\\d{4}\\w\\d{2}(\\-[35])?$", "preferred_prefix": "niaest", "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/niaest:$1" } ], "publications": [ { "doi": "10.1016/j.crvi.2003.09.008", "pubmed": "14744099", "title": "The NIA cDNA project in mouse stem cells and early embryos", "year": 2003 } ], "uri_format": "http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1" }, "niaid.chemdb": { "description": "ID in NIAID ChemDB", "example": "059486", "homepage": "http://chemdb.niaid.nih.gov", "mappings": { "wikidata": "P2065" }, "name": "NIAID ChemDB ID", "preferred_prefix": "niaid.chemdb", "uri_format": "http://chemdb.niaid.nih.gov/CompoundDetails.aspx?AIDSNO=$1" }, "nif.cell": { "contact": { "email": "smtifahim@gmail.com", "name": "Fahim Imam", "orcid": "0000-0003-4752-543X" }, "deprecated": true, "description": "Neuronal cell types", "download_owl": "http://aber-owl.net/media/ontologies/NIFCELL/15/nifcell.owl", "homepage": "http://neuinfo.org/", "keywords": [ "obo", "ontology" ], "mappings": { "aberowl": "NIFCELL", "biocontext": "NIF_CELL", "bioportal": "NIFCELL", "obofoundry": "nif_cell" }, "name": "NIF Cell", "part_of": "nif", "preferred_prefix": "NIF_CELL", "rdf_uri_format": "http://purl.obolibrary.org/obo/NIF_CELL_$1", "uri_format": "http://purl.obolibrary.org/obo/NIF_CELL_$1" }, "nif.dysfunction": { "contact": { "email": "smtifahim@gmail.com", "name": "Fahim Imam", "orcid": "0000-0003-4752-543X" }, "deprecated": true, "homepage": "http://neuinfo.org/", "keywords": [ "obo", "ontology" ], "mappings": { "biocontext": "NIF_DYSFUNCTION", "obofoundry": "nif_dysfunction" }, "name": "NIF Dysfunction", "part_of": "nif", "preferred_prefix": "NIF_DYSFUNCTION", "rdf_uri_format": "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1", "uri_format": "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1" }, "nif.ext": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NIFEXT covers IRIs that were \"external\" identifiers that were brought into the ontology at some point in time. This was done before most of the current standard ontology and identifier management practices had been developed.", "example": "7123", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "license": "CC BY-4.0", "name": "NIF Standard Ontology: External", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nif.ext", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NIFEXT" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nifext_$1" }, "nif.grossanatomy": { "contact": { "email": "smtifahim@gmail.com", "name": "Fahim Imam", "orcid": "0000-0003-4752-543X" }, "deprecated": true, "homepage": "http://neuinfo.org/", "keywords": [ "obo", "ontology" ], "mappings": { "biocontext": "NIF_GROSSANATOMY", "obofoundry": "nif_grossanatomy" }, "name": "NIF Gross Anatomy", "part_of": "nif", "preferred_prefix": "NIF_GROSSANATOMY", "rdf_uri_format": "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1", "uri_format": "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1" }, "nif.std": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NIFSTD is a base namespace (like obo:) which houses many other prefixes. Sometimes NIFSTD prefixed identifiers appear undifferentiated, but usually if it shows up it means that another prefix definition is missing when serializing.", "download_owl": "http://aber-owl.net/media/ontologies/NIFSTD/23/nifstd.owl", "example": "BAMSC981", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "keywords": [ "brain", "disease", "neuroscience", "ontology" ], "license": "CC BY-4.0", "mappings": { "aberowl": "NIFSTD", "bioportal": "NIFSTD", "fairsharing": "FAIRsharing.vgw1m6" }, "name": "NIF Standard Ontology", "part_of": "nif", "pattern": "^BAMSC\\d+$", "preferred_prefix": "nif.std", "publications": [ { "doi": "10.1007/s12021-008-9032-z", "pmc": "PMC2743139", "pubmed": "18975148", "title": "The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience", "year": 2008 } ], "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NIFSTD" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/$1" }, "nihhesc": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The NIH registration number should be used on all NIH competing applications and annual progress reports to identify the stem cell line proposed for use. Identify the specific line(s) from the Registry using the NIH Registration Number (e.g., 0001), in the specified location in the application (from homepage)", "example": "NIHhESC-10-0083", "homepage": "https://grants.nih.gov/stem_cells/registry/current.htm", "mappings": { "cellosaurus": "NIHhESC" }, "name": "NIH Human Embryonic Stem Cell Registry", "preferred_prefix": "nihhesc", "uri_format": "https://grants.nih.gov/stem_cells/registry/current.htm?ID=$1" }, "nihreporter.project": { "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "RePORTER is an electronic tool that allows users to search a repository of both intramural and extramural NIH-funded research projects and access publications and patents resulting from NIH funding.", "example": "10343835", "github_request_issue": 400, "homepage": "https://reporter.nih.gov/", "name": "NIH RePORTER", "pattern": "^\\d+$", "preferred_prefix": "nihreporter.project", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://reporter.nih.gov/project-details/$1" }, "nist": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The NIST Chemistry WebBook provides users with easy access to chemical and physical property data for chemical species through the internet. The data provided in the site are from collections maintained by the NIST Standard Reference Data Program and outside contributors. Data in the WebBook system are organized by chemical species.", "homepage": "https://webbook.nist.gov/chemistry/", "name": "NIST Chemistry WebBook", "no_own_terms": true, "preferred_prefix": "nist", "synonyms": [ "NIST", "NIST Chemistry WebBook" ] }, "nist.codata": { "description": "identifier for a physical constant", "example": "c", "homepage": "http://physics.nist.gov/cuu/Constants/index.html", "mappings": { "wikidata": "P1645" }, "name": "NIST/CODATA ID", "preferred_prefix": "nist.codata", "uri_format": "http://physics.nist.gov/cgi-bin/cuu/Value?$1" }, "nkos": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "NKOS is devoted to the discussion of the functional and data model for enabling knowledge organization systems/services (KOS), such as classification systems, thesauri, gazetteers, and ontologies, as networked interactive information services to support the description and retrieval of diverse information resources through the Internet.\n\nKnowledge Organization Systems/Services (KOS) model the underlying semantic structure of a domain. Embodied as Web-based services, they can facilitate resource discovery and retrieval. They act as semantic road maps and make possible a common orientation by indexers and future users (whether human or machine). -- Douglas Tudhope, Traugott Koch (2004).", "download_rdf": "https://nkos.dublincore.org/nkos.rdf", "example": "alignedWith", "homepage": "http://w3id.org/nkos", "name": "Networked Knowledge Organization Systems/Services/Structures", "preferred_prefix": "nkos", "uri_format": "http://w3id.org/nkos/$1" }, "nlfff": { "description": "Nonlinear Force-Free Field Three-Dimensional Magnetic Fields Data of Solar Active Regions Database", "example": "345201101230312003", "homepage": "https://nlfff.dataset.deepsolar.space/en/", "mappings": { "miriam": "nlfff" }, "name": "NLFFF Database", "pattern": "^[0-9]+$", "preferred_prefix": "nlfff", "uri_format": "http://database.deepsolar.space:18080/dbs/nlfff/$1" }, "nlm": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The NLM Catalog provides access to NLM bibliographic data for journals, books, audiovisuals, computer software, electronic resources and other materials. Links to the library's holdings in LocatorPlus, NLM's online public access catalog, are also provided. [from homepage]", "example": "101775319", "homepage": "https://www.ncbi.nlm.nih.gov/nlmcatalog", "license": "public domain", "mappings": { "bartoc": "528", "biolink": "NLMID" }, "name": "National Library of Medicine Catalog", "pattern": "^\\d+$", "preferred_prefix": "nlm", "uri_format": "https://www.ncbi.nlm.nih.gov/nlmcatalog/$1" }, "nlm.publisher": { "appears_in": [ "nlm" ], "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Publisher short codes appearin in the NLM Catalog.", "example": "wiley", "github_request_issue": 1318, "homepage": "https://ftp.ncbi.nlm.nih.gov/pubmed/xmlprovidernames.txt", "license": "public domain", "name": "NLM Publisher Codes", "preferred_prefix": "nlm.publisher" }, "nlx.anat": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "NLXANAT covers anatomy terms. Almost all terms are also in Uberon.", "example": "090201", "homepage": "https://scicrunch.org/scicrunch/interlex/dashboard", "keywords": [ "anatomy" ], "name": "NeuroLex Anatomy", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nlx.anat", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_anat_$1" }, "nlx.br": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NLXBR covers brain regions from the PHT00 macaque parcellation, Paxinos, Huang, and Tog The Rhesus Monkey Brain In Stereotaxic Coordinates (1999).", "example": "145", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "keywords": [ "anatomy", "brain regions", "neuroscience" ], "license": "CC BY-4.0", "name": "NIF Standard Ontology: Brain Regions", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nlx.br", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXBR" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_br_$1" }, "nlx.cell": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NLXCELL conatins cell types with a focus on neuron types.", "example": "091005", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "keywords": [ "cell lines", "cell types", "cells", "neuroscience" ], "license": "CC BY-4.0", "name": "NIF Standard Ontology: Cell Types", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nlx.cell", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXCELL" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_cell_$1" }, "nlx.chem": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NLXCHEM covers chemicals. Most classes are also in ChEBI.", "example": "090801", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "keywords": [ "chemistry" ], "license": "CC BY-4.0", "name": "NIF Standard Ontology: Chemical", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nlx.chem", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXCHEM" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_chem_$1" }, "nlx.dys": { "appears_in": [ "mondo" ], "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "NLXDYS covers dysfunction, diseases, and disorders. Most classes are also in Disease Ontology (DOID), Monarch Disease Ontology (MONDO), Human Phenotype Ontology (HPO), etc.", "example": "20090602", "homepage": "https://scicrunch.org/scicrunch/interlex/dashboard", "keywords": [ "disease", "disorders", "phenotypes" ], "name": "NeuroLex Dysfunction", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nlx.dys", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_dys_$1" }, "nlx.func": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NLXFUNC covers terms for cognitive function.", "example": "90801", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "keywords": [ "neuroscience" ], "license": "CC BY-4.0", "name": "NIF Standard Ontology: Cognitive Function", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nlx.func", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXFUNC" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_func_$1" }, "nlx.inv": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NLXINV includes funding agencies and some terms related to documenting scientific investigations data acquisition and analysis.", "example": "90901", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "keywords": [ "data analysis", "funding agencies" ], "license": "CC BY-4.0", "name": "NIF Standard Ontology: Investigations", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nlx.inv", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXINV" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_inv_$1" }, "nlx.mol": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NLXMOL covers molecules, proteins, and molecular roles, similar to entities in the Protein Ontology, UniProt, and ChEBI, with a focus on those of particular relevance in the nervous system.", "example": "90806", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "keywords": [ "biology", "chemistry", "neuroscience", "proteins" ], "license": "CC BY-4.0", "name": "NIF Standard Ontology: Molecules", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nlx.mol", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXMOL" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_mol_$1" }, "nlx.oen": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NLXOEN prefixed identifiers are from the version of the Ontology for Experimental Neurophysiology (OEN; https://github.com/G-Node/OEN) that were originally deposited in Neurolex (for examples, see https://scicrunch.org/scicrunch/interlex/search?q=NLXOEN results).", "example": "0001000", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "keywords": [ "neuroscience" ], "license": "CC BY-4.0", "name": "NIF Standard Ontology: OEN Terms in Neurolex", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nlx.oen", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXOEN" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/oen_$1" }, "nlx.org": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NLXORG covers organisms.", "example": "090701", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "keywords": [ "taxonomy" ], "license": "CC BY-4.0", "name": "NIF Standard Ontology: Organisms", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nlx.org", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXORG" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_organ_$1" }, "nlx.qual": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NLXQUAL covers qualities and dispositions similar to the Phenotype And Trait Ontology (PATO).", "example": "100810", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "keywords": [ "dispositions", "qualities" ], "license": "CC BY-4.0", "name": "NIF Standard Ontology: Qualities", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nlx.qual", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXQUAL" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_qual_$1" }, "nlx.res": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NLXRES covers digital resources. Most classes are high level types covering everything from databases and sourcecode to source code licenses and instrument supplier websites", "example": "090924", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "keywords": [ "software and information systems" ], "license": "CC BY-4.0", "name": "NIF Standard Ontology: Digital Resources", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nlx.res", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXRES" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_res_$1" }, "nlx.sub": { "contact": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", "orcid": "0000-0002-7509-4801" }, "description": "NLXSUB covers subcellular entities similar to the cellular component branch of the Gene Ontology (GO).", "example": "090803", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "keywords": [ "cellular components" ], "license": "CC BY-4.0", "mappings": { "go": "NIF_Subcellular" }, "name": "NIF Standard Ontology: Subcellular Entities", "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "nlx.sub", "repository": "https://github.com/SciCrunch/NIF-Ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "NLXSUB", "nif_subcellular" ], "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_subcell_$1" }, "nmdc": { "contact": { "email": "donny@polyneme.xyz", "github": "dwinston", "name": "Donny Winston", "orcid": "0000-0002-8424-0604" }, "contributor": { "email": "donny@polyneme.xyz", "github": "dwinston", "name": "Donny Winston", "orcid": "0000-0002-8424-0604" }, "contributor_extras": [ { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } ], "description": "An initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem.", "example": "y3ax-8bq3-60", "github_request_issue": 130, "homepage": "https://microbiomedata.org/", "keywords": [ "microbiome" ], "mappings": { "miriam": "nmdc" }, "name": "National Microbiome Data Collaborative", "pattern": "^.{2,}$", "preferred_prefix": "nmdc", "providers": [ { "code": "web", "description": "Direct link", "homepage": "https://drs.microbiomedata.org", "name": "NMDC Web Page", "uri_format": "https://drs.microbiomedata.org/objects/$1" } ], "rdf_uri_format": "https://w3id.org/nmdc/$1", "references": [ "https://github.com/biopragmatics/bioregistry/pull/982" ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://w3id.org/nmdc/$1" }, "nmpdr": { "comment": "This resource doesn't exist on the web anymore", "deprecated": true, "description": "The NMPDR provided curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio; as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma.", "example": "fig|306254.1.peg.183", "homepage": "http://www.nmpdr.org", "keywords": [ "genome" ], "mappings": { "ncbi": "NMPDR", "prefixcommons": "nmpdr" }, "name": "National Microbial Pathogen Data Resource", "preferred_prefix": "nmpdr", "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/nmpdr:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.nmpdr.org/FIG/wiki/rest.cgi/NmpdrPlugin/SeedViewer?page=Annotation;feature=$1" }, "nmr": { "banana": "NMR", "contact": { "email": "schober@imbi.uni-freiburg.de", "github": "DSchober", "name": "Daniel Schober", "orcid": "0000-0001-8014-6648" }, "deprecated": true, "description": "nmrCV is a controlled vocabulary to deliver standardized descriptors for the open mark-up language for NMR raw and spectrum data, sanctioned by the metabolomics standards initiative msi.", "download_owl": "https://nmrml.org/cv/stable/nmrCV.owl", "example": "1000003", "homepage": "http://msi-ontology.sourceforge.net/", "keywords": [ "nmr", "obo", "ontology", "owl" ], "mappings": { "aberowl": "NMR", "biocontext": "NMR", "bioportal": "NMR", "miriam": "nmr", "n2t": "nmr", "obofoundry": "nmr", "ols": "nmrcv", "prefixcommons": "nmr" }, "name": "NMR-instrument specific component of metabolomics investigations", "namespace_in_lui": true, "pattern": "^\\d+$", "preferred_prefix": "NMR", "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/nmr:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/NMR_$1", "synonyms": [ "nmrcv" ], "uri_format": "https://www.ebi.ac.uk/ols4/ontologies/nmrcv/terms?curie=NMR:$1", "version": "1.1.0" }, "nmrshiftdb2": { "contact": { "email": "stefan.kuhn@dmu.ac.uk", "name": "Stefan Kuhn", "orcid": "0000-0002-5990-4157" }, "contributor_extras": [ { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" } ], "description": "NMR database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties.", "example": "234", "homepage": "https://nmrshiftdb.nmr.uni-koeln.de", "keywords": [ "analytical chemistry" ], "mappings": { "fairsharing": "FAIRsharing.nYaZ1N", "miriam": "nmrshiftdb2", "re3data": "r3d100010316", "wikidata": "P9405" }, "name": "NMRShiftDB structure", "pattern": "^[0-9]+$", "preferred_prefix": "nmrshiftdb2", "publications": [ { "doi": "10.1002/mrc.4263", "pubmed": "25998807", "title": "Facilitating quality control for spectra assignments of small organic molecules: nmrshiftdb2--a free in-house NMR database with integrated LIMS for academic service laboratories", "year": 2015 }, { "doi": "10.1016/j.phytochem.2004.08.027", "pubmed": "15464159", "title": "NMRShiftDB -- compound identification and structure elucidation support through a free community-built web database", "year": 2004 }, { "doi": "10.1021/ci0341363", "pubmed": "14632418", "title": "NMRShiftDB-constructing a free chemical information system with open-source components", "year": 2003 } ], "synonyms": [ "NMRShiftDB" ], "uri_format": "https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1" }, "noaa": { "contributor": { "email": "meghan.balk@gmail.com", "github": "megbalk", "name": "Meghan Balk", "orcid": "0000-0003-2699-3066" }, "description": "Identifier for a species on the noaa fisheries website", "example": "long-finned-pilot-whale", "github_request_issue": 456, "homepage": "https://www.fisheries.noaa.gov/species-directory", "mappings": { "wikidata": "P6049" }, "name": "NOAA Fisheries Species Directory", "pattern": "^[a-z]+(\\-[a-z]+)*$", "preferred_prefix": "noaa", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.fisheries.noaa.gov/species/$1" }, "noaa.cameo": { "description": "CAMEO Chemicals is a database of hazardous chemical datasheets that emergency responders and planners can use to get response recommendations and predict hazards—such as explosions or toxic fumes.", "example": "19757", "homepage": "https://cameochemicals.noaa.gov", "mappings": { "wikidata": "P11931" }, "name": "CAMEO Chemicals ID", "pattern": "^\\d*$", "preferred_prefix": "noaa.cameo", "uri_format": "https://cameochemicals.noaa.gov/chemical/$1" }, "nomen": { "contact": { "email": "diapriid@gmail.com", "github": "mjy", "name": "Matt Yoder", "orcid": "0000-0002-5640-5491" }, "description": "NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature.", "download_owl": "http://purl.obolibrary.org/obo/nomen.owl", "example": "0000295", "homepage": "https://github.com/SpeciesFileGroup/nomen", "keywords": [ "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "NOMEN", "bioportal": "NOMEN", "obofoundry": "nomen", "ols": "nomen", "ontobee": "NOMEN" }, "name": "A nomenclatural ontology for biological names", "pattern": "^\\d{7}$", "preferred_prefix": "NOMEN", "rdf_uri_format": "http://purl.obolibrary.org/obo/NOMEN_$1", "repository": "https://github.com/SpeciesFileGroup/nomen", "uri_format": "http://purl.obolibrary.org/obo/NOMEN_$1" }, "noncodev3": { "contact": { "email": "biozy@ict.ac.cn", "name": "Yi Zhao", "orcid": "0000-0001-6049-8347" }, "deprecated": true, "description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4.", "example": "377550", "homepage": "http://www.noncode.org/", "keywords": [ "expression", "nucleotide" ], "mappings": { "biocontext": "NONCODEV3", "miriam": "noncodev3", "n2t": "noncodev3", "prefixcommons": "noncode" }, "name": "NONCODE v3", "pattern": "^\\d+$", "preferred_prefix": "noncodev3", "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/noncode:$1" } ], "publications": [ { "doi": "10.1093/nar/gkr1175", "pmc": "PMC3245065", "pubmed": "22135294", "title": "NONCODE v3.0: integrative annotation of long noncoding RNAs", "year": 2011 } ], "uri_format": "http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1" }, "noncodev4.gene": { "deprecated": true, "description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions.", "example": "NONHSAG00001", "homepage": "http://www.bioinfo.org/NONCODEv4/", "mappings": { "biocontext": "NONCODEV4.GENE", "miriam": "noncodev4.gene", "n2t": "noncodev4.gene" }, "name": "NONCODE v4 Gene", "pattern": "^NONHSAG\\d{5}$", "preferred_prefix": "noncodev4.gene", "uri_format": "http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$1" }, "noncodev4.rna": { "deprecated": true, "description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to individual transcripts.", "example": "NONHSAT000001", "homepage": "http://www.bioinfo.org/NONCODEv4/", "mappings": { "biocontext": "NONCODEV4.RNA", "miriam": "noncodev4.rna", "n2t": "noncodev4.rna" }, "name": "NONCODE v4 Transcript", "pattern": "^NONHSAT\\d{6}$", "preferred_prefix": "noncodev4.rna", "uri_format": "http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$1" }, "nord": { "appears_in": [ "mondo" ], "contact": { "email": "sean@skm.digital", "github": "skm16", "name": "Sean Roberts" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A website containing information about rare diseases, powered by Wordpress.", "example": "1693", "github_request_issue": 1375, "homepage": "https://rarediseases.org", "name": "National Organization for Rare Disorders", "pattern": "^\\d+$", "preferred_prefix": "nord", "references": [ "https://github.com/monarch-initiative/mondo/issues/8588" ], "uri_format": "https://rarediseases.org/?p=$1" }, "norine": { "contact": { "email": "maude.pupin@univ-lille.fr", "name": "Maude Pupin", "orcid": "0000-0003-3197-0715" }, "description": "Norine is a database dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids whose primary structure is not always linear, often being more complex and containing cycles and branchings.", "example": "NOR00681", "homepage": "http://bioinfo.lifl.fr/norine/", "keywords": [ "life science", "protein" ], "mappings": { "biocontext": "NORINE", "fairsharing": "FAIRsharing.gf8yhy", "miriam": "norine", "n2t": "norine", "prefixcommons": "norine" }, "name": "Nonribosomal Peptides Database", "pattern": "^NOR\\d+$", "preferred_prefix": "norine", "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/norine:$1" } ], "publications": [ { "doi": "10.1093/nar/gkz1000", "pmc": "PMC7145658", "pubmed": "31691799", "title": "Norine: update of the nonribosomal peptide resource", "year": 2020 }, { "doi": "10.1093/nar/gkm792", "pmc": "PMC2238963", "pubmed": "17913739", "title": "NORINE: a database of nonribosomal peptides", "year": 2007 } ], "uri_format": "http://bioinfo.lifl.fr/norine/result.jsp?ID=$1" }, "novus": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A vendor of antibodies and other biologics", "example": "nb100-56351", "homepage": "https://www.novusbio.com", "name": "Novus Biologicals", "preferred_prefix": "novus", "uri_format": "https://www.novusbio.com/products/$1" }, "npass": { "comment": "This resource does not have an explicit license. The [lotus database](https://github.com/lotusnprod/lotus-processor/blob/main/docs/licenses/npass.md) inferred that the CC-BY-NC license from the paper might be good enough for applying to the data itself.", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Database for integrating species source of natural products & connecting natural products to biological targets via experimental-derived quantitative activity data.\n", "example": "NPC139585", "homepage": "http://bidd.group/NPASS/", "license": "CC-BY-NC", "name": "Natural Product Activity and Species Source Database", "pattern": "^NPC\\d+$", "preferred_prefix": "npass", "uri_format": "https://bidd.group/NPASS/compound.php?compoundID=$1" }, "npatlas": { "contact": { "email": "rliningt@sfu.ca", "name": "Roger Linington", "orcid": "0000-0003-1818-4971" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "Identifiers for microbially derived natural products that contains compound structures, producing organism taxonomy, biosynthetic and chemical properties.", "example": "NPA000001", "github_request_issue": 1295, "homepage": "https://www.npatlas.org", "name": "The Natural Products Atlas", "pattern": "^NPA\\d{6}$", "preferred_prefix": "npatlas", "publications": [ { "doi": "10.1093/nar/gkae1093", "pubmed": "39588755", "title": "The Natural Products Atlas 3.0: extending the database of microbially derived natural products", "year": 2024 }, { "doi": "10.1093/nar/gkab941", "pmc": "PMC8728154", "pubmed": "34718710", "title": "The Natural Products Atlas 2.0: a database of microbially-derived natural products", "year": 2021 }, { "doi": "10.1021/acscentsci.9b00806", "pmc": "PMC6891855", "pubmed": "31807684", "title": "The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery", "year": 2019 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://www.npatlas.org/explore/compounds/$1" }, "npm": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A repository of software packages written in Javascript, TypeScript, and related.", "example": "@biopragmatics/curies", "example_extras": [ "ansi-pad" ], "homepage": "https://www.npmjs.com", "name": "Node Package Manager", "preferred_prefix": "npm", "uri_format": "https://www.npmjs.com/package/$1" }, "npo": { "contact": { "email": "nathan.baker@pnnl.gov", "github": "sobolevnrm", "name": "Nathan Baker", "orcid": "0000-0002-5892-6506" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy.", "download_owl": "http://aber-owl.net/media/ontologies/NPO/31/npo.owl", "example": "1731", "homepage": "https://bioportal.bioontology.org/ontologies/NPO", "keywords": [ "life science", "molecular entity", "nanoparticle", "ontology", "structure" ], "mappings": { "aberowl": "NPO", "bioportal": "NPO", "fairsharing": "FAIRsharing.vy0p71" }, "name": "NanoParticle Ontology", "pattern": "^\\d+$", "preferred_prefix": "npo", "publications": [ { "doi": "10.1016/j.jbi.2010.03.001", "pmc": "PMC3042056", "pubmed": "20211274", "title": "NanoParticle Ontology for cancer nanotechnology research", "year": 2010 } ], "repository": "https://github.com/sobolevnrm/npo", "uri_format": "http://purl.bioontology.org/ontology/npo#NPO_$1" }, "nrfc": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The NRFC was established at ICAR-National Bureau of Fish Genetic Resources, Lucknow in the form of a research project entitled ‘Establishment of a National Repository at NBFGR, Lucknow for conservation and characterization of fish cell lines’ during 09 November, 2010 to 08 November, 2014 with the financial support from Department of Biotechnology, Govt. of India, New Delhi. NRFC aims to receive, authenticate, store and supply the fish cell lines to the researchers and academicians for Research & Development works and to serve as a National Referral Centre for fish cell lines in the country. NRFC also aims to provide need-based support for training and education to stakeholders. (from homepage)", "example": "NRFC051", "homepage": "https://mail.nbfgr.res.in/nrfc/index.php", "mappings": { "cellosaurus": "NRFC" }, "name": "National Repository of Fish Cell Lines", "pattern": "^NRFC\\d+$", "preferred_prefix": "nrfc" }, "nsc": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Identifier used by the Cancer Chemotherapy National Service Center.", "example": "27223", "homepage": "https://wiki.nci.nih.gov/display/NCIDTPdata/Chemical+Data", "mappings": { "cheminf": "000565" }, "name": "USA National Service Center Number", "pattern": "^\\d+$", "preferred_prefix": "nsc", "references": [ "https://pubchem.ncbi.nlm.nih.gov/source/DTP/NCI" ], "uri_format": "https://dtp.cancer.gov/dtpstandard/servlet/ChemData?searchtype=NSC&searchlist=$1" }, "nsf.award": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Information about research projects that NSF has funded since 1989 can be found by searching the Award Abstracts database. The information includes abstracts that describe the research, and names of principal investigators and their institutions. The database includes both completed and in-process research.", "example": "1458400", "homepage": "https://www.nsf.gov/awards/about.jsp", "name": "National Science Foundation Award", "pattern": "^\\d+$", "preferred_prefix": "nsf.award", "uri_format": "https://www.nsf.gov/awardsearch/showAward?AWD_ID=$1" }, "nsrrc": { "description": "Provides access to critically needed swine models of human health and disease as well as a central resource for reagents, creation of new genetically modified swine, and information and training related to use of swine models in biomedical research. [from RRID]", "example": "0005", "homepage": "http://www.nsrrc.missouri.edu/", "keywords": [ "biomaterial manufacture", "breeding", "consulting", "cryopreservation", "fetal fibroblast", "fetus", "fibroblast", "genetically modified pig", "genetics", "genome", "genotyping", "health monitoring", "live animal", "phenotyping", "pig", "reproduction", "tissue" ], "mappings": { "rrid": "NSRRC" }, "name": "National Swine Resource and Research Center", "pattern": "^\\d+$", "preferred_prefix": "nsrrc", "uri_format": "https://nsrrc.missouri.edu/nsrrc$1info/" }, "nucc.characteristic": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Provider Characteristics code set is for use with health care provider information for enrollment and credentialing transactions and their corresponding responses. It is intended to provide codified responses to questions presented to a health care provider applying to or registering with an entity and to report the outcome of such application or registration. It may also be used for responses to inquiries regarding provider participation or registration in a program or plan.", "example": "2A", "example_extras": [ "10", "11" ], "homepage": "https://nucc.org/index.php/code-sets-mainmenu-41/provider-characteristics-mainmenu-39", "name": "National Uniform Claim Committee Characteristic", "pattern": "^\\d(\\d|\\w)$", "preferred_prefix": "nucc.characteristic" }, "nucc.taxonomy": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Health Care Provider Taxonomy code set is an external, nonmedical data code set designed for use in an electronic environment, specifically within the ASC X12N Health Care transactions. This includes the transactions mandated under HIPAA.\n\nThe taxonomy code is a unique alphanumeric code, ten characters in length. The code set is structured into three distinct \"Levels\" including Provider Grouping, Classification, and Area of Specialization.\n\n - **Level I, Provider Grouping** A major grouping of service(s) or occupation(s) of health care providers. For example: Allopathic & Osteopathic Physicians, Dental Providers, Hospitals, etc.\n - **Level II, Classification** A more specific service or occupation related to the Provider Grouping. For example, the Classification for Allopathic & Osteopathic Physicians is based upon the General Specialty Certificates as issued by the appropriate national boards. The following boards will however, have their general certificates appear as Level III areas of specialization strictly due to display limitations of the code set for Boards that have multiple general certificates: Medical Genetics, Preventive Medicine, Psychiatry & Neurology, Radiology, Surgery, Otolaryngology, Pathology.\n - **Level III, Area of Specialization** A more specialized area of the Classification in which a provider chooses to practice or make services available. For example, the Area of Specialization for provider grouping Allopathic & Osteopathic Physicians is based upon the Subspecialty Certificates as issued by the appropriate national boards.", "example": "207LH0002X", "homepage": "https://taxonomy.nucc.org", "name": "National Uniform Claim Committee Taxonomy", "pattern": "^\\d{3}\\w(\\w|\\d_)\\d{4}X$", "preferred_prefix": "nucc.taxonomy", "references": [ "https://www.nucc.org/images/stories/CSV/nucc_taxonomy_221.csv", "https://www.nucc.org" ] }, "nucleardb": { "comment": "Note that the typo from MIRIAM has spread to several other sources", "contact": { "email": "vriend@cmbi.ru.nl", "name": "Gert Vriend", "orcid": "0000-0002-1067-7053" }, "description": "NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs.", "example": "prgr_human", "homepage": "http://www.receptors.org/nucleardb/", "keywords": [ "classification" ], "mappings": { "biocontext": "NUCLEARBD", "integbio": "nbdc00599", "miriam": "nuclearbd", "n2t": "nuclearbd", "prefixcommons": "nucleardb" }, "name": "NucleaRDB", "pattern": "^\\w+\\_\\w+$", "preferred_prefix": "nucleardb", "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/nucleardb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkr960", "pmc": "PMC3245090", "pubmed": "22064856", "title": "NucleaRDB: information system for nuclear receptors", "year": 2011 } ], "synonyms": [ "nuclearbd" ], "uri_format": "http://www.receptors.org/nucleardb/proteins/$1" }, "nucleotide": { "description": "The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.", "example": "880798137", "has_canonical": "insdc", "homepage": "https://www.ncbi.nlm.nih.gov/", "mappings": { "integbio": "nbdc00600", "miriam": "nucleotide" }, "name": "Nucleotide", "pattern": "^[a-zA-Z0-9_\\.]+$", "preferred_prefix": "nucleotide", "uri_format": "https://www.ncbi.nlm.nih.gov/nuccore/$1" }, "nxr": { "description": "National stock center for X. laevis and X. tropicalis and training center for advanced technologies (e.g. husbandry, cell biology, imaging, genetics, transgenesis, genomics). [from RRID]", "example": "0024", "homepage": "http://www.mbl.edu/xenopus/", "keywords": [ "laevis", "tropicalis", "xenopus" ], "mappings": { "rrid": "NXR" }, "name": "National Xenopus Resource", "pattern": "^\\d+$", "preferred_prefix": "nxr", "uri_format": "https://scicrunch.org/resolver/RRID:NXR_$1" }, "nztcs": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "email": "sumirp77@gmail.com", "github": "SumirHPandit", "name": "Sumir Pandit", "orcid": "0000-0002-1216-4761" } ], "description": "identifier for species classified under the New Zealand Threat Classification System", "example": "11061", "homepage": "https://nztcs.org.nz/", "keywords": [ "taxon", "taxonomy" ], "license": "CC-BY-4.0", "mappings": { "wikidata": "P9889" }, "name": "New Zealand Threat Classification System", "pattern": "^[1-9]\\d{3,7}$", "preferred_prefix": "nztcs", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1083" ], "uri_format": "https://nztcs.org.nz/nztcs-species/$1" }, "oa": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The W3C Web Annotation Working Group is chartered to develop a set of specifications for an interoperable, sharable, distributed Web Annotation architecture.", "download_owl": "http://aber-owl.net/media/ontologies/OA/4/oa.owl", "example": "sourceDateStart", "homepage": "http://www.w3.org/ns/oa", "keywords": [ "ontology", "quality" ], "mappings": { "aberowl": "OA", "biocontext": "oa", "bioportal": "OA", "lov": "oa", "zazuko": "oa" }, "name": "Web Annotation Ontology", "preferred_prefix": "oa", "uri_format": "http://www.w3.org/ns/oa#$1" }, "oae": { "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", "name": "Yongqunh He", "orcid": "0000-0001-9189-9661" }, "description": "The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc.", "download_owl": "http://purl.obolibrary.org/obo/oae.owl", "example": "0002959", "homepage": "https://github.com/OAE-ontology/OAE/", "keywords": [ "adverse reaction", "biomedical science", "drug", "obo", "ontology", "vaccine" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "OAE", "biocontext": "OAE", "bioportal": "OAE", "fairsharing": "FAIRsharing.tw4q8x", "obofoundry": "oae", "ols": "oae", "ontobee": "OAE" }, "name": "Ontology of Adverse Events", "pattern": "^\\d{7}$", "preferred_prefix": "OAE", "publications": [ { "doi": "10.1186/2041-1480-5-29", "pmc": "PMC4120740", "pubmed": "25093068", "title": "OAE: The Ontology of Adverse Events", "year": 2014 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/OAE_$1", "repository": "https://github.com/OAE-ontology/OAE", "uri_format": "http://purl.obolibrary.org/obo/OAE_$1", "version": "1.2.47" }, "oarcs": { "contact": { "email": "mjyoder@illinois.edu", "github": "mjy", "name": "Matt Yoder", "orcid": "0000-0002-5640-5491" }, "description": "OArCS is an ontology describing the Arthropod ciruclatory system.", "download_owl": "http://purl.obolibrary.org/obo/oarcs.owl", "example": "0000029", "homepage": "https://github.com/aszool/oarcs", "keywords": [ "anatomy", "angiology", "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "OARCS", "biocontext": "OARCS", "bioportal": "OARCS", "fairsharing": "FAIRsharing.yqn857", "obofoundry": "oarcs", "ols": "oarcs", "ontobee": "OARCS" }, "name": "Ontology of Arthropod Circulatory Systems", "pattern": "^\\d{7}$", "preferred_prefix": "OARCS", "publications": [ { "doi": "10.1093/sysbio/syw108", "pubmed": "28123116", "title": "The First Organ-Based Ontology for Arthropods (Ontology of Arthropod Circulatory Systems - OArCS) and its Integration into a Novel Formalization Scheme for Morphological Descriptions", "year": 2017 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/OARCS_$1", "repository": "https://github.com/aszool/oarcs", "uri_format": "http://purl.obolibrary.org/obo/OARCS_$1", "version": "2019-04-18" }, "oba": { "appears_in": [ "fovt" ], "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "description": "A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO.", "download_json": "http://purl.obolibrary.org/obo/oba.json", "download_obo": "http://purl.obolibrary.org/obo/oba.obo", "download_owl": "http://purl.obolibrary.org/obo/oba.owl", "example": "0000001", "example_extras": [ "VT0003769" ], "homepage": "https://github.com/obophenotype/bio-attribute-ontology", "keywords": [ "biology", "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "OBA", "agroportal": "OBA", "biocontext": "OBA", "bioportal": "OBA", "fairsharing": "FAIRsharing.mp0rwf", "obofoundry": "oba", "ols": "oba", "ontobee": "OBA" }, "name": "Ontology of Biological Attributes", "pattern": "^(VT)?\\d{7}$", "preferred_prefix": "OBA", "publications": [ { "doi": "10.1007/s00335-023-09992-1", "pubmed": "37076585", "title": "The Ontology of Biological Attributes (OBA)-computational traits for the life sciences", "year": 2023 }, { "doi": "10.1101/2023.01.26.525742", "pmc": "PMC9900877", "pubmed": "36747660", "title": "The Ontology of Biological Attributes (OBA) - Computational Traits for the Life Sciences", "year": 2023 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/OBA_$1", "repository": "https://github.com/obophenotype/bio-attribute-ontology", "uri_format": "http://purl.obolibrary.org/obo/OBA_$1", "version": "2025-03-28" }, "oban": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "It is an ontology model used to describe associations between biomedical entities in triple format based on W3C specification. OBAN is a generic association representation model that loosely couples a subject and object (e.g. disease and its associated phenotypes supported by the source of evidence for that association) via a construction of class OBAN:association. [from GitHub]", "download_owl": "https://raw.githubusercontent.com/EBISPOT/OBAN/master/ontology/oban_core.owl", "download_rdf": "https://raw.githubusercontent.com/EBISPOT/OBAN/master/ontology/oban_core.ttl", "example": "provenance", "homepage": "https://github.com/EBISPOT/OBAN", "keywords": [ "ontology" ], "mappings": { "biocontext": "OBAN", "biolink": "OBAN" }, "name": "Open Biomedical Annotations", "pattern": "^\\w+$", "preferred_prefix": "oban", "repository": "https://github.com/EBISPOT/OBAN", "uri_format": "http://purl.org/oban/$1" }, "obci": { "contact": { "email": "dan5@georgetown.edu", "github": "nataled", "name": "Darren A. Natale", "orcid": "0000-0001-5809-9523" }, "contributor": { "email": "dan5@georgetown.edu", "github": "nataled", "name": "Darren A. Natale", "orcid": "0000-0001-5809-9523" }, "description": "The Ontology for Biomarkers of Clinical Interest (OBCI) formally defines biomarkers for diseases, phenotypes, and effects.", "download_owl": "https://proteininformationresource.org/staff/nataled/OBCI/obci.owl", "example": "000000001", "github_request_issue": 1174, "homepage": "https://github.com/clinical-biomarkers/OBCI", "keywords": [ "ontology" ], "name": "Ontology for Biomarkers of Clinical Interest", "pattern": "^\\d+$", "preferred_prefix": "obci", "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "http://purl.obolibrary.org/obo/OBCI_$1" }, "obcs": { "banana": "OBCS", "contact": { "email": "jiezhen@med.umich.edu", "github": "zhengj2007", "name": "Jie Zheng", "orcid": "0000-0002-2999-0103" }, "description": "OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI)", "download_owl": "http://purl.obolibrary.org/obo/obcs.owl", "example": "0000121", "homepage": "https://github.com/obcs/obcs", "keywords": [ "biology", "biomedical science", "medical informatics", "medicine", "obo", "ontology", "statistics", "vaccine" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "OBCS", "biocontext": "OBCS", "bioportal": "OBCS", "fairsharing": "FAIRsharing.5p12xh", "miriam": "obcs", "obofoundry": "obcs", "ols": "obcs", "ontobee": "OBCS" }, "name": "Ontology of Biological and Clinical Statistics", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "OBCS", "publications": [ { "doi": "10.1186/s13326-016-0100-2", "pmc": "PMC5024438", "pubmed": "27627881", "title": "The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis", "year": 2016 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/OBCS_$1", "repository": "https://github.com/obcs/obcs", "uri_format": "http://purl.obolibrary.org/obo/OBCS_$1", "version": "2023-12-08" }, "obi": { "appears_in": [ "agro", "foodon", "gallont", "hso", "labo", "maxo", "mco", "one", "ons", "proco", "rbo", "scdo" ], "banana": "OBI", "banana_peel": "_", "contact": { "email": "bpeters@lji.org", "github": "bpeters42", "name": "Bjoern Peters", "orcid": "0000-0002-8457-6693" }, "description": "The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO).", "download_obo": "https://github.com/obi-ontology/obi/raw/master/views/obi.obo", "download_owl": "http://purl.obolibrary.org/obo/obi.owl", "example": "0400109", "homepage": "http://obi-ontology.org", "keywords": [ "assay", "biomedical science", "data transformation", "device", "functional genomics", "life science", "obo", "ontology", "protocol", "reagent", "report", "study design" ], "license": "CC-BY-4.0", "logo": "https://svn.code.sf.net/p/obi/code/trunk/web/htdocs/images/obi-lotext.png", "mappings": { "aberowl": "OBI", "biocontext": "OBI", "bioportal": "OBI", "fairsharing": "FAIRsharing.284e1z", "go": "OBI", "miriam": "obi", "n2t": "obi", "obofoundry": "obi", "ols": "obi", "ontobee": "OBI", "prefixcommons": "obi" }, "name": "Ontology for Biomedical Investigations", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "OBI", "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/obi:$1" } ], "publications": [ { "doi": "10.1371/journal.pone.0154556", "pmc": "PMC4851331", "pubmed": "27128319", "title": "The Ontology for Biomedical Investigations", "year": 2016 }, { "doi": "10.1093/database/bau132", "pmc": "PMC4309925", "pubmed": "25632945", "title": "Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach", "year": 2015 }, { "doi": "10.1186/2041-1480-4-s1-s6", "pmc": "PMC3633001", "pubmed": "23734660", "title": "Query enhancement through the practical application of ontology: the IEDB and OBI", "year": 2013 }, { "doi": "10.4056/sigs.1994602", "pmc": "PMC3235517", "pubmed": "22180825", "title": "Minimum Information about a Genotyping Experiment (MIGEN)", "year": 2011 }, { "doi": "10.1186/2041-1480-1-s1-s7", "pmc": "PMC2903726", "pubmed": "20626927", "title": "Modeling biomedical experimental processes with OBI", "year": 2010 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/OBI_$1", "repository": "https://github.com/obi-ontology/obi", "uri_format": "http://purl.obolibrary.org/obo/OBI_$1", "version": "2025-03-06" }, "obib": { "contact": { "email": "jmwhorton@uams.edu", "github": "jmwhorton", "name": "Justin Whorton", "orcid": "0009-0003-4268-6207" }, "description": "The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology.", "download_owl": "http://purl.obolibrary.org/obo/obib.owl", "example": "0000389", "homepage": "https://github.com/biobanking/biobanking", "keywords": [ "biobank", "health science", "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "OBIB", "biocontext": "OBIB", "bioportal": "OBIB", "fairsharing": "FAIRsharing.bxc508", "obofoundry": "obib", "ols": "obib", "ontobee": "OBIB" }, "name": "Ontology for Biobanking", "pattern": "^\\d{7}$", "preferred_prefix": "OBIB", "publications": [ { "doi": "10.1186/s13326-016-0068-y", "pmc": "PMC4855778", "pubmed": "27148435", "title": "OBIB-a novel ontology for biobanking", "year": 2016 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/OBIB_$1", "repository": "https://github.com/biobanking/biobanking", "uri_format": "http://purl.obolibrary.org/obo/OBIB_$1", "version": "2023-04-05" }, "obo": { "contact": { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" }, "description": "The OBO namespace is the top-level namespace used by Open Biological and Biomedical Ontology (OBO) Foundry ontologies.", "example": "uberon", "example_extras": [ "go", "uberon.owl" ], "homepage": "http://www.obofoundry.org/", "keywords": [ "biology", "health", "ontology and terminology" ], "mappings": { "biocontext": "OBO", "fairsharing": "FAIRsharing.847069", "integbio": "nbdc00305", "lov": "obo" }, "name": "Open Biological and Biomedical Ontologies", "preferred_prefix": "obo", "publications": [ { "doi": "10.1038/nbt1346", "pmc": "PMC2814061", "pubmed": "17989687", "title": "The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration", "year": 2007 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/$1", "references": [ "https://github.com/biopragmatics/bioregistry/pull/913", "https://github.com/biopragmatics/bioregistry/issues/910" ], "repository": "https://github.com/OBOFoundry/OBOFoundry.github.io", "twitter": "OBOFoundry", "uri_format": "http://purl.obolibrary.org/obo/$1" }, "oboe": { "contact": { "email": "brycemecum@gmail.com", "github": "amoeba", "name": "Bryce Mecum", "orcid": "0000-0002-0381-3766" }, "contributor": { "github": "StroemPhi", "name": "Philip Strömert", "orcid": "0000-0002-1595-3213" }, "description": "The Extensible Observation Ontology (OBOE) is a formal ontology for capturing the semantics of scientific observation and measurement. The ontology supports researchers to add detailed semantic annotations to scientific data, thereby clarifying the inherent meaning of scientific observations.", "download_owl": "https://raw.githubusercontent.com/NCEAS/oboe/refs/heads/master/oboe.owl", "example": "Characteristic", "github_request_issue": 1276, "homepage": "https://github.com/NCEAS/oboe", "keywords": [ "biodiversity", "ecology", "environmental science", "observations", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "OBOE", "agroportal": "OBOE", "bioportal": "OBOE", "ecoportal": "OBOE", "fairsharing": "FAIRsharing.5970hq" }, "name": "The Extensible Observation Ontology", "preferred_prefix": "oboe", "publications": [ { "doi": "10.1016/j.ecoinf.2007.05.004", "pmc": "PMC8612252", "pubmed": "34817235", "title": "An ontology for describing and synthesizing ecological observation data", "year": 2007 } ], "repository": "https://github.com/NCEAS/oboe", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#$1" }, "oboinowl": { "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties", "download_obo": "http://www.geneontology.org/formats/oboInOwl.obo", "download_owl": "http://www.geneontology.org/formats/oboInOwl.owl", "example": "hasDbXref", "example_extras": [ "auto_generated_by", "hasBroadSynonym", "hasExactSynonym", "hasNarrowSynonym" ], "homepage": "https://github.com/geneontology/go-ontology/tree/master/contrib", "keywords": [ "life science", "ontology" ], "mappings": { "biocontext": "oboInOwl", "biolink": "oboformat", "fairsharing": "FAIRsharing.aa0eat", "ols": "oboinowl" }, "name": "OBO in OWL", "pattern": "^[\\w-]+$", "preferred_prefix": "oboInOwl", "references": [ "https://github.com/biopragmatics/bioregistry/pull/973", "https://github.com/geneontology/go-site/issues/2157" ], "repository": "https://github.com/geneontology/go-ontology", "synonyms": [ "oboformat", "oio" ], "uri_format": "http://www.geneontology.org/formats/oboInOwl#$1" }, "obv": { "description": "The Austrian Library Network (OBV) is the largest network of scientific and administrative libraries in Austria with 70 participants, representing more than 90 individual institutions - including the Austrian National Library, university libraries, the colleges of education, individual ministries, numerous technical colleges and other important collections.", "example": "AC00963334", "homepage": "https://www.obvsg.at/", "mappings": { "bartoc": "20430", "miriam": "obv" }, "name": "Austrian Library Network", "pattern": "^AC[0-9]{8}$", "preferred_prefix": "obv", "uri_format": "https://permalink.obvsg.at/$1" }, "occ": { "description": "The OpenCitations Corpus is open repository of scholarly citation data made available under a Creative Commons public domain dedication (CC0), which provides accurate bibliographic references harvested from the scholarly literature that others may freely build upon, enhance and reuse for any purpose, without restriction under copyright or database law.", "example": "br/1", "homepage": "https://w3id.org/oc/corpus", "mappings": { "miriam": "occ", "n2t": "occ" }, "name": "OpenCitations Corpus", "pattern": "^[a-z][a-z]/[0-9]+$", "preferred_prefix": "occ", "uri_format": "https://w3id.org/oc/corpus/$1" }, "occo": { "contact": { "email": "zhengj2007@gmail.com", "github": "zhengj2007", "name": "Jie Zheng", "orcid": "0000-0002-2999-0103" }, "description": "An ontology representing occupations. It is designed to facilitate harmonization of existing occupation standards, such as the US Bureau of Labor Statistics Standard Occupational Classification (US SOC), the International Standard Classification of Occupations (ISCO), the UK National Statistics Standard Occupational Classification (UK SOC), and the European Skills, Competences, Qualifications and Occupations (ESCO) of the European Union.", "download_owl": "http://purl.obolibrary.org/obo/occo.owl", "example": "00000001", "homepage": "https://github.com/Occupation-Ontology/OccO", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "OCCO", "bioportal": "OCCO", "obofoundry": "occo", "ontobee": "OCCO" }, "name": "Occupation Ontology", "pattern": "^\\d+$", "preferred_prefix": "OCCO", "rdf_uri_format": "http://purl.obolibrary.org/obo/OCCO_$1", "repository": "https://github.com/Occupation-Ontology/OccO", "uri_format": "http://purl.obolibrary.org/obo/OCCO_$1" }, "oci": { "description": "Each OCI (Open Citation Identifier) has a simple structure: oci:-, where “oci:” is the identifier prefix, and is used to identify a citation as a first-class data entity - see https://doi.org/10.6084/m9.figshare.7127816.v2 for additional information. In each OCI, the first is the identifier for the citing bibliographic resource, while the second is the identifier for the cited bibliographic resource.", "example": "01027931310-01022252312", "homepage": "http://opencitations.net", "mappings": { "biocontext": "OCI", "miriam": "oci", "n2t": "oci" }, "name": "Open Citation Identifier", "pattern": "^0[1-9]+0[0-9]+-0[1-9]+0[0-9]+$", "preferred_prefix": "oci", "uri_format": "https://w3id.org/oc/oci/$1" }, "ocid": { "banana": "ocid", "description": "'ocid' stands for \"Ontology Concept Identifiers\" and are 12 digit long integers covering IDs in topical ontologies from anatomy up to toxicology.", "example": "190000021540", "homepage": "https://ontochem.com/", "mappings": { "miriam": "ocid" }, "name": "Ontology Concept Identifiers", "namespace_in_lui": true, "pattern": "^[0-9]{12}$", "preferred_prefix": "ocid", "uri_format": "https://ocid.ontochem.com/prefname?ocid=$1" }, "oclc": { "description": "The global library cooperative OCLC maintains WorldCat. WorldCat is the world's largest network of library content and services. WorldCat libraries are dedicated to providing access to their resources on the Web, where most people start their search for information.", "example": "634515043", "homepage": "https://www.oclc.org/en/about.html", "mappings": { "biocontext": "OCLC", "miriam": "oclc", "n2t": "oclc" }, "name": "Online Computer Library Center WorldCat", "pattern": "^[0-9]+$", "preferred_prefix": "oclc", "uri_format": "https://www.worldcat.org/oclc/$1" }, "odam": { "description": "Experimental data table management software to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines, allowing the dataset to be explored and then extracted in whole or in part as needed.", "example": "frim1", "homepage": "https://metabolome.cgfb.u-bordeaux.fr/", "mappings": { "miriam": "odam" }, "name": "Open Data for Access and Mining", "pattern": "^[A-Za-z0-9]+$", "preferred_prefix": "odam", "uri_format": "http://pmb-bordeaux.fr/getdata/json/$1/datapackage?links=1" }, "odamexplorer": { "description": "ODAM (Open Data for Access and Mining) is an Experimental data table management software (EDTMS) to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines.\n\nODAM allows datasets to be explored and then extracted in whole or in part as needed.\n\nFor more information/explanation, see ODAM User's Guide : https://inrae.github.io/ODAM/", "example": "frim1", "homepage": "https://eng-bfp.bordeaux-aquitaine.hub.inrae.fr/", "mappings": { "miriam": "odam.explorer" }, "name": "ODAM Data explorer", "pattern": "^[A-Za-z][A-Za-z0-9]+$", "preferred_prefix": "odamexplorer", "uri_format": "https://pmb-bordeaux.fr/dataexplorer/?ds=$1" }, "odc.sci": { "contact": { "email": "jgrethe@ucsd.edu", "name": "Jeffrey Grethe", "orcid": "0000-0001-5212-7052" }, "description": "The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven repository to store, share, and publish spinal cord injury research data.", "example": "602", "homepage": "https://odc-sci.org", "keywords": [ "biomedical science", "neurobiology", "neurology", "neuroscience" ], "mappings": { "fairsharing": "FAIRsharing.M6Ruz3", "miriam": "odc.sci", "re3data": "r3d100014071" }, "name": "Open Data Commons for Spinal Cord Injury", "pattern": "^[0-9]*$", "preferred_prefix": "odc.sci", "publications": [ { "doi": "10.1089/neu.2019.6674", "pmc": "PMC7071068", "pubmed": "31608767", "title": "FAIR SCI Ahead: The Evolution of the Open Data Commons for Pre-Clinical Spinal Cord Injury Research", "year": 2019 }, { "doi": "10.1016/j.expneurol.2017.05.012", "pmc": "PMC6448396", "pubmed": "28576567", "title": "Developing a data sharing community for spinal cord injury research", "year": 2017 }, { "doi": "10.1038/ncomms9581", "pmc": "PMC4634208", "pubmed": "26466022", "title": "Topological data analysis for discovery in preclinical spinal cord injury and traumatic brain injury", "year": 2015 }, { "doi": "10.1038/nn.3838", "pmc": "PMC4728080", "pubmed": "25349910", "title": "Big data from small data: data-sharing in the 'long tail' of neuroscience", "year": 2014 }, { "doi": "10.1089/neu.2014.3399", "pmc": "PMC4186058", "pubmed": "25077610", "title": "Development of a database for translational spinal cord injury research", "year": 2014 }, { "doi": "10.1371/journal.pone.0059712", "pmc": "PMC3609747", "pubmed": "23544088", "title": "Derivation of multivariate syndromic outcome metrics for consistent testing across multiple models of cervical spinal cord injury in rats", "year": 2013 }, { "doi": "10.1007/s12975-011-0121-1", "pmc": "PMC3236294", "pubmed": "22207883", "title": "Syndromics: a bioinformatics approach for neurotrauma research", "year": 2011 }, { "doi": "S0014-4886(17)30137-1", "title": "Developing a data sharing community for spinal cord injury research." } ], "uri_format": "https://odc-sci.org/data/$1" }, "odc.tbi": { "description": "The Open Data Commons for Traumatic Brain Injury is a cloud-based community-driven repository to store, share, and publish traumatic brain injury research data.", "example": "408", "homepage": "https://odc-tbi.org", "mappings": { "miriam": "odc.tbi" }, "name": "Open Data Commons for Traumatic Brain Injury", "pattern": "^[0-9]*$", "preferred_prefix": "odc.tbi", "uri_format": "https://odc-tbi.org/data/$1" }, "odor": { "description": "OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors", "example": "74", "homepage": "http://senselab.med.yale.edu/OdorDB", "mappings": { "biocontext": "ODOR", "miriam": "odor", "n2t": "odor" }, "name": "Odor Molecules DataBase", "pattern": "^\\d+$", "preferred_prefix": "odor", "uri_format": "http://senselab.med.yale.edu/OdorDB/Data/$1/?db=5" }, "odrl": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The ODRL Vocabulary and Expression defines a set of concepts and terms (the vocabulary) and encoding mechanism (the expression) for permissions and obligations statements describing digital content usage based on the ODRL Information Model.", "download_rdf": "https://www.w3.org/ns/odrl/2/ODRL22.rdf", "example": "assetConcepts", "homepage": "http://www.w3.org/ns/odrl/2", "keywords": [ "metadata" ], "mappings": { "lov": "odrl" }, "name": "Open Digital Rights Language Ontology", "preferred_prefix": "odrl", "uri_format": "http://www.w3.org/ns/odrl/2/$1" }, "oecd.template": { "comment": "The identifiers have two numbers separated by a dot. The first one corresponds to the template number which can be found on the homepage. The second number referes to the row within the corresponding spreadsheet.", "contributor": { "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "The Organisation for Economic Co-operation and Development (OECD) Harmonised Templates (OHTs) are standard data formats for reporting information used for the risk assessment of chemicals, mainly studies done on chemicals to determine their properties or effects on human health and the environment, but also for storing data on use and exposure.", "example": "74.186", "github_request_issue": 997, "homepage": "https://www.oecd.org/ehs/templates/", "name": "OECD Harmonised Templates", "pattern": "^\\d+\\.\\d+$", "preferred_prefix": "oecd.template", "references": [ "https://github.com/biopragmatics/bioregistry/issues/991" ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } }, "ogg": { "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", "name": "Yongqun Oliver He", "orcid": "0000-0001-9189-9661" }, "description": "OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets.", "download_owl": "http://purl.obolibrary.org/obo/ogg.owl", "example": "3000887619", "homepage": "https://bitbucket.org/hegroup/ogg", "keywords": [ "biology", "gene", "gene name", "genome", "life science", "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "OGG", "biocontext": "OGG", "bioportal": "OGG", "fairsharing": "FAIRsharing.zmx7nn", "obofoundry": "ogg", "ols": "ogg", "ontobee": "OGG" }, "name": "The Ontology of Genes and Genomes", "pattern": "^\\d+$", "preferred_prefix": "OGG", "rdf_uri_format": "http://purl.obolibrary.org/obo/OGG_$1", "repository": "https://bitbucket.org/hegroup/ogg", "uri_format": "http://purl.obolibrary.org/obo/OGG_$1", "version": "1.0.59" }, "ogi": { "contact": { "email": "linikujp@gmail.com", "github": "linikujp", "name": "Asiyah Yu Lin", "orcid": "0000-0002-5379-5359" }, "deprecated": true, "description": "OGI formalized the genomic element by defining an upper class 'genetic interval'.\n\nThe definition of 'genetic interval' is \"the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic Acid Base Residue) on a chromosome or RNA molecule which must have a liner primary sequence sturcture.\" \n\nRelated paper:\n\n1. Yu Lin, Norihiro Sakamoto (2009) “Genome, Gene, Interval and Ontology” Interdisciplinary Ontology Vol.2 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34 (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology)\nYu Lin, Hiroshi Tarui, Peter Simons (2009) “From Ontology for Genetic Interval(OGI) to Sequence Assembly – Ontology apply to next generation sequencing” Proceeding of the Semantic Web Applications and Tools for Life Science Workshop, Amsterdam, Nov.20th, 2009. (http://ceur-ws.org/Vol-559/Poster2.pdf)\nYu Lin, Peter Simons (2010) “DNA sequence from below: A Nominalist Approach” Interdisciplinary Ontology Vol.3 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2010. (http://philpapers.org/rec/LINDSF)\n\n\n", "download_owl": "http://purl.obolibrary.org/obo/ogi.owl", "example": "0000019", "homepage": "https://code.google.com/archive/p/ontology-for-genetic-interval/", "keywords": [ "obo", "ontology" ], "mappings": { "aberowl": "OGI", "biocontext": "OGI", "bioportal": "OGI", "obofoundry": "ogi", "ols": "ogi", "ontobee": "OGI" }, "name": "Ontology for genetic interval", "pattern": "^\\d{7}$", "preferred_prefix": "OGI", "rdf_uri_format": "http://purl.obolibrary.org/obo/OGI_$1", "synonyms": [ "OGI.owl" ], "uri_format": "http://purl.obolibrary.org/obo/OGI_$1", "version": "2.0" }, "ogms": { "appears_in": [ "labo", "scdo" ], "contact": { "email": "baeverma@jcvi.org", "github": "BAevermann", "name": "Brian Aevermann", "orcid": "0000-0003-1346-1327" }, "description": "The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats.\n\nOGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology.", "download_obo": "http://purl.obolibrary.org/obo/ogms.obo", "download_owl": "http://purl.obolibrary.org/obo/ogms.owl", "example": "0000031", "homepage": "https://github.com/OGMS/ogms", "keywords": [ "biomedical science", "cancer", "diagnosis", "disease", "disease phenotype", "medicine", "obo", "ontology" ], "license": "CC-BY-4.0", "logo": "https://avatars2.githubusercontent.com/u/12973154?s=200&v=4", "mappings": { "aberowl": "OGMS", "bartoc": "216", "biocontext": "OGMS", "bioportal": "OGMS", "fairsharing": "FAIRsharing.rvz0m9", "obofoundry": "ogms", "ols": "ogms", "ontobee": "OGMS" }, "name": "Ontology for General Medical Science", "pattern": "^\\d{7}$", "preferred_prefix": "OGMS", "publications": [ { "pubmed": "25991121", "title": "Biomarkers in the ontology for general medical science", "year": 2015 }, { "doi": "10.1186/2041-1480-4-42", "pmc": "PMC4028878", "pubmed": "24314207", "title": "The neurological disease ontology", "year": 2013 }, { "pmc": "PMC3041577", "pubmed": "21347182", "title": "Toward an ontological treatment of disease and diagnosis", "year": 2009 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/OGMS_$1", "repository": "https://github.com/OGMS/ogms", "synonyms": [ "ogms/OMRE" ], "uri_format": "http://purl.obolibrary.org/obo/OGMS_$1", "version": "2021-08-19" }, "ogsf": { "contact": { "email": "linikujp@gmail.com", "github": "linikujp", "name": "Asiyah Yu Lin", "orcid": "0000-0002-5379-5359" }, "deprecated": true, "description": "An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process.", "download_owl": "http://purl.obolibrary.org/obo/ogsf.owl", "example": "0000025", "homepage": "https://github.com/linikujp/OGSF", "keywords": [ "adverse reaction", "biomedical science", "disease", "epidemiology", "genetic disorder", "genetics", "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "OGSF", "biocontext": "OGSF", "bioportal": "OGSF", "fairsharing": "FAIRsharing.egv2cz", "obofoundry": "ogsf", "ols": "ogsf", "ontobee": "OGSF" }, "name": "Ontology of Genetic Susceptibility Factor", "pattern": "^\\d{7}$", "preferred_prefix": "OGSF", "publications": [ { "doi": "10.1186/2041-1480-5-19", "pmc": "PMC4068904", "pubmed": "24963371", "title": "The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events", "year": 2014 }, { "pubmed": "20847592", "title": "Ontology driven modeling for the knowledge of genetic susceptibility to disease", "year": 2009 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/OGSF_$1", "repository": "https://github.com/linikujp/OGSF", "uri_format": "http://purl.obolibrary.org/obo/OGSF_$1", "version": "2.0" }, "ohd": { "contact": { "email": "wdduncan@gmail.com", "github": "wdduncan", "name": "Bill Duncan", "orcid": "0000-0001-9625-1899" }, "description": "The Oral Health and Disease Ontology is used for representing the diagnosis and treatment of dental maladies.", "download_owl": "http://purl.obolibrary.org/obo/ohd.owl", "example": "0000006", "homepage": "https://purl.obolibrary.org/obo/ohd/home", "keywords": [ "dentistry", "medicine", "obo", "ontology", "oral surgery" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "OHD", "biocontext": "OHD", "bioportal": "OHD", "fairsharing": "FAIRsharing.bg7bb6", "obofoundry": "ohd", "ols": "ohd", "ontobee": "OHD" }, "name": "Oral Health and Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "OHD", "publications": [ { "doi": "10.1186/s13326-020-00222-0", "pmc": "PMC7439527", "pubmed": "32819435", "title": "Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology", "year": 2020 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/OHD_$1", "repository": "https://github.com/oral-health-and-disease-ontologies/ohd-ontology", "uri_format": "http://purl.obolibrary.org/obo/OHD_$1", "version": "2024-06-21" }, "ohmi": { "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", "name": "Yongqun Oliver He", "orcid": "0000-0001-9189-9661" }, "description": "OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions.", "download_owl": "http://purl.obolibrary.org/obo/ohmi.owl", "example": "0000460", "homepage": "https://github.com/ohmi-ontology/ohmi", "keywords": [ "host", "life science", "microbiome", "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "OHMI", "biocontext": "OHMI", "bioportal": "OHMI", "fairsharing": "FAIRsharing.cz9cnp", "obofoundry": "ohmi", "ols": "ohmi", "ontobee": "OHMI" }, "name": "Ontology of Host-Microbiome Interactions", "pattern": "^\\d{7}$", "preferred_prefix": "OHMI", "rdf_uri_format": "http://purl.obolibrary.org/obo/OHMI_$1", "repository": "https://github.com/ohmi-ontology/ohmi", "uri_format": "http://purl.obolibrary.org/obo/OHMI_$1", "version": "2019-09-17" }, "ohpi": { "contact": { "email": "edong@umich.edu", "github": "e4ong1031", "name": "Edison Ong", "orcid": "0000-0002-5159-414X" }, "description": "OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration).", "download_owl": "http://purl.obolibrary.org/obo/ohpi.owl", "example": "9001411", "homepage": "https://github.com/OHPI/ohpi", "keywords": [ "bioinformatics", "biomedical science", "host", "infection", "obo", "ontology", "pathogen" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "OHPI", "bioportal": "OHPI", "fairsharing": "FAIRsharing.vxpUJ6", "obofoundry": "ohpi", "ols": "ohpi", "ontobee": "OHPI" }, "name": "Ontology of Host Pathogen Interactions", "pattern": "^\\d+$", "preferred_prefix": "OHPI", "publications": [ { "doi": "10.1093/nar/gky999", "pmc": "PMC6324020", "pubmed": "30365026", "title": "Victors: a web-based knowledge base of virulence factors in human and animal pathogens", "year": 2019 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/OHPI_$1", "repository": "https://github.com/OHPI/ohpi", "uri_format": "http://purl.obolibrary.org/obo/OHPI_$1", "version": "2019-09-30" }, "oid": { "contributor_extras": [ { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } ], "description": "OIDs provide a persistent identification of objects based on a hierarchical structure of Registration Authorities (RA), where each parent has an object identifier and allocates object identifiers to child nodes.", "example": "2.16.840", "example_extras": [ "2", "2.16", "2.16.840.1", "2.16.840.1.113883", "2.16.840.1.113883.6", "2.16.840.1.113883.6.88" ], "homepage": "http://www.oid-info.com/introduction.htm", "mappings": { "miriam": "oid", "n2t": "oid" }, "name": "ISO Object Identifier", "pattern": "^[\\d.]+$", "preferred_prefix": "oid", "providers": [ { "code": "oid_www", "description": "OID w/ WWW", "homepage": "http://www.oid-info.com", "name": "OID w/ WWW", "uri_format": "http://www.oid-info.com/get/$1" }, { "code": "orange", "description": "Mirror of OID site from Orange", "homepage": "https://oid-rep.orange-labs.fr", "name": "Mirror of OID site from Orange", "uri_format": "https://oid-rep.orange-labs.fr/get/$1" } ], "references": [ "https://en.wikipedia.org/wiki/Object_identifier" ], "uri_format": "http://oid-info.com/get/$1" }, "olatdv": { "contact": { "email": "frederic.bastian@unil.ch", "github": "fbastian", "name": "Frédéric Bastian", "orcid": "0000-0002-9415-5104" }, "deprecated": true, "description": "Life cycle stages for Medaka", "download_obo": "http://purl.obolibrary.org/obo/olatdv.obo", "download_owl": "http://purl.obolibrary.org/obo/olatdv.owl", "example": "0000210", "homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv", "keywords": [ "aquaculture", "developmental biology", "life cycle stage", "life science", "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "OLATDV", "biocontext": "OLATDV", "bioportal": "OLATDV", "fairsharing": "FAIRsharing.c86z66", "obofoundry": "olatdv", "ols": "olatdv", "ontobee": "OlatDv" }, "name": "Medaka Developmental Stages", "pattern": "^\\d{7}$", "preferred_prefix": "OlatDv", "rdf_uri_format": "http://purl.obolibrary.org/obo/OlatDv_$1", "repository": "https://github.com/obophenotype/developmental-stage-ontologies", "uri_format": "http://purl.obolibrary.org/obo/OlatDv_$1" }, "om": { "contact": { "email": "hajo.rijgersberg@wur.nl", "name": "Hajo Rijgersberg" }, "description": "The Ontology of units of Measure (OM) 2.0 models concepts and relations important to scientific research. It has a strong focus on units, quantities, measures, and dimensions.", "download_owl": "http://aber-owl.net/media/ontologies/OM/33/om.owl", "download_rdf": "https://raw.githubusercontent.com/HajoRijgersberg/OM/master/om-2.0.rdf", "example": "Dimension", "homepage": "https://github.com/HajoRijgersberg/OM", "keywords": [ "ontology" ], "mappings": { "aberowl": "OM", "agroportal": "OM", "bioportal": "OM", "ols": "om", "ontobee": "OM" }, "name": "Ontology of units of Measure", "preferred_prefix": "om", "repository": "https://github.com/HajoRijgersberg/OM", "uri_format": "http://www.ontology-of-units-of-measure.org/resource/om-2/$1", "version": "2.0.59" }, "oma.grp": { "description": "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs.", "example": "LCSCCPN", "homepage": "https://omabrowser.org/cgi-bin/gateway.pl", "mappings": { "biocontext": "OMA.GRP", "miriam": "oma.grp", "n2t": "oma.grp" }, "name": "OMA Group", "pattern": "^[A-Z]+$", "preferred_prefix": "oma.grp", "uri_format": "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1" }, "oma.hog": { "banana": "HOG", "description": "Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix) database. Hierarchical orthologous groups are sets of genes that have started diverging from a single common ancestor gene at a certain taxonomic level of reference. ", "example": "0459895", "homepage": "https://omabrowser.org", "mappings": { "miriam": "oma.hog" }, "name": "OMA HOGs", "namespace_in_lui": true, "pattern": "^[0-9]{7}(\\.[0-9a-z.]+)?(_[0-9]+)?$", "preferred_prefix": "oma.hog", "uri_format": "https://omabrowser.org/oma/hog/HOG:$1" }, "oma.protein": { "description": "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records.", "example": "HUMAN16963", "homepage": "https://omabrowser.org/oma/home/", "mappings": { "biocontext": "OMA.PROTEIN", "miriam": "oma.protein", "n2t": "oma.protein", "togoid": "OmaProtein" }, "name": "OMA Protein", "pattern": "^[A-Z0-9]{5}\\d+$", "preferred_prefix": "oma.protein", "uri_format": "https://omabrowser.org/oma/vps/$1" }, "omia": { "contact": { "email": "imke.tammen@sydney.edu.au", "github": "ImkeTammen", "name": "Imke Tammen", "orcid": "0000-0002-5520-6597" }, "contributor_extras": [ { "email": "imke.tammen@sydney.edu.au", "github": "ImkeTammen", "name": "Imke Tammen", "orcid": "0000-0002-5520-6597" } ], "description": "Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and associated genes and variants in more than 500 vertebrate animal species (other than human, mouse, rats, zebrafish and western clawed frog, which have their own resources). The 'omia' prefix is used for phenes, either across species (omia:001000) or in a specific species (omia:001000-9615)", "example": "001000", "example_extras": [ "001000-9615" ], "homepage": "https://omia.org", "keywords": [ "classification", "disorders", "gene", "model organism database", "traits" ], "mappings": { "biocontext": "OMIA", "integbio": "nbdc00153", "miriam": "omia", "n2t": "omia", "prefixcommons": "omia" }, "name": "Online Mendelian Inheritance in Animals", "pattern": "^\\d{6}(-\\d+)?$", "preferred_prefix": "omia", "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/omia:$1" } ], "publications": [ { "doi": "10.1007/s00335-024-10059-y", "pubmed": "39143381", "title": "Online Mendelian Inheritance in Animals (OMIA): a genetic resource for vertebrate animals", "year": 2024 } ], "synonyms": [ "OMIA" ], "uri_format": "https://omia.org/phene/omia:$1" }, "omia.variant": { "contact": { "email": "imke.tammen@sydney.edu.au", "github": "ImkeTammen", "name": "Imke Tammen", "orcid": "0000-0002-5520-6597" }, "contributor_extras": [ { "email": "imke.tammen@sydney.edu.au", "github": "ImkeTammen", "name": "Imke Tammen", "orcid": "0000-0002-5520-6597" } ], "description": "Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and associated genes and variants in more than 500 vertebrate animal species (other than human, mouse, rats, zebrafish and western clawed frog, which have their own resources). The 'omia.variant' prefix is used for genetic variants associated with phenes listed in OMIA", "example": "1710", "example_extras": [ "620" ], "homepage": "https://omia.org", "keywords": [ "disorders", "model organism database", "traits" ], "mappings": { "biocontext": "OMIA", "integbio": "nbdc00153" }, "name": "OMIA variants", "pattern": "^\\d+$", "preferred_prefix": "omia.variant", "publications": [ { "doi": "10.1007/s00335-024-10059-y", "pubmed": "39143381", "title": "Online Mendelian Inheritance in Animals (OMIA): a genetic resource for vertebrate animals", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://omia.org/variant/omia.variant:$1" }, "omiabis": { "appears_in": [ "labo" ], "contact": { "email": "mbrochhausen@gmail.com", "name": "Mathias Brochhausen", "orcid": "0000-0003-1834-3856" }, "deprecated": true, "description": "An ontological version of MIABIS (Minimum Information About BIobank data Sharing)", "download_owl": "http://purl.obolibrary.org/obo/omiabis.owl", "example": "0001079", "homepage": "https://github.com/OMIABIS/omiabis-dev", "keywords": [ "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "OMIABIS", "biocontext": "OMIABIS", "bioportal": "OMIABIS", "obofoundry": "omiabis", "ols": "omiabis", "ontobee": "OMIABIS" }, "name": "Ontologized MIABIS", "pattern": "^\\d{7}$", "preferred_prefix": "OMIABIS", "rdf_uri_format": "http://purl.obolibrary.org/obo/OMIABIS_$1", "repository": "https://github.com/OMIABIS/omiabis-dev", "uri_format": "http://purl.obolibrary.org/obo/OMIABIS_$1", "version": "2014-05-28" }, "omid": { "description": "Every entity in OpenCitations Meta (https://opencitations.net/meta) is assigned persistent internal identifier called OpenCitations Meta Identifier (OMID). The OMID has structure [[entity_type_abbreviation]]/[[supplier_prefix]][[sequential_number]]. For example, the first journal article ever processed has OMID br/0601 (the full URI is https://w3id.org/oc/meta/br/0601), where br is the abbreviation of bibliographic resource, and 060 corresponds to the supplier prefix, helpful in recognising at a glance the index it belongs to (i.e., OpenCitations Meta). Finally, 1 indicates that this is the index's first bibliographic resource ever minted.", "example": "br/0601", "homepage": "http://opencitations.net/", "mappings": { "miriam": "omid" }, "name": "OpenCitations Meta Identifier", "pattern": "^[a-z][a-z]/06[1-9]*0[1-9][0-9]*$", "preferred_prefix": "omid", "uri_format": "https://w3id.org/oc/meta/$1" }, "omim": { "contact": { "email": "ahamosh@jhmi.edu", "github": "ahamosh", "name": "Ada Hamosh", "orcid": "0000-0002-1780-5230" }, "description": "Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders.", "example": "603903", "homepage": "https://omim.org/", "keywords": [ "biomedical science", "disease", "disease process modeling", "gene", "gene expression", "genetic disorder", "genotype", "ontology", "phenotype" ], "license": "https://www.omim.org/help/agreement", "mappings": { "aberowl": "OMIM", "biocontext": "OMIM", "bioportal": "OMIM", "edam": "1153", "fairsharing": "FAIRsharing.b084yh", "go": "OMIM", "hl7": "2.16.840.1.113883.6.174", "integbio": "nbdc00154", "miriam": "mim", "n2t": "mim", "ncbi": "MIM", "prefixcommons": "omim", "uniprot": "DB-0062", "wikidata": "P492" }, "name": "Online Mendelian Inheritance in Man", "pattern": "^\\d+$", "preferred_prefix": "omim", "providers": [ { "code": "CURATOR_REVIEW", "description": "OMIM mirror at John Hopkins", "homepage": "http://mirror.omim.org/", "name": "OMIM mirror at John Hopkins", "uri_format": "http://mirror.omim.org/entry/$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/omim:$1" }, { "code": "legacy", "description": "This is the actual endpoint for OMIM entries", "homepage": "https://www.omim.org", "name": "OMIM", "uri_format": "https://www.omim.org/entry/$1" }, { "code": "miriam_legacy", "description": "Legacy URLs for identifiers.org", "homepage": "http://identifiers.org", "name": "MIRIAM Legacy", "uri_format": "http://identifiers.org/omim/$1" }, { "code": "ncbi.omim", "description": "An NCBI endpoint for OMIM entries", "homepage": "http://www.ncbi.nlm.nih.gov/omim", "name": "NCBI", "uri_format": "http://www.ncbi.nlm.nih.gov/omim/$1" }, { "code": "purl", "description": "An extra purl that was registred, but probably won't be used.", "homepage": "https://www.omim.org", "name": "OMIM PURL (not in use)", "uri_format": "https://purl.org/mim/MIM:$1" }, { "code": "purl2", "description": "An extra purl that was registred, but probably won't be used.", "homepage": "https://www.omim.org", "name": "OMIM PURL (not in use)", "uri_format": "https://omim.org/OMIM:$1" } ], "publications": [ { "doi": "10.1093/nar/gky1151", "pubmed": "30445645" }, { "doi": "10.1093/nar/gku1205", "pmc": "PMC4383985", "pubmed": "25428349", "title": "OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders", "year": 2014 }, { "doi": "10.1093/nar/gki033", "pmc": "PMC539987", "pubmed": "15608251", "title": "Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders", "year": 2005 } ], "references": [ "https://github.com/biopragmatics/bioregistry/issues/497" ], "synonyms": [ "OMIM", "mim" ], "uri_format": "https://omim.org/MIM:$1" }, "omim.ps": { "banana": "PS", "contact": { "email": "ahamosh@jhmi.edu", "github": "ahamosh", "name": "Ada Hamosh", "orcid": "0000-0002-1780-5230" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "github": "sierra-moxon", "name": "Sierra Moxon", "orcid": "0000-0002-8719-7760" } ], "description": "A Phenotypic Series is a tabular view of genetic heterogeneity of similar phenotypes across the genome.", "example": "214100", "homepage": "https://www.omim.org/phenotypicSeriesTitles/all", "license": "https://www.omim.org/help/agreement", "mappings": { "biolink": "OMIM.PS" }, "name": "OMIM Phenotypic Series", "part_of": "omim", "pattern": "^\\d+$", "preferred_prefix": "omim.ps", "providers": [ { "code": "legacy", "description": "This is the actual endpoint for OMIM phenotypic series entries", "homepage": "https://www.omim.org", "name": "OMIM", "uri_format": "https://omim.org/phenotypicSeries/PS$1" } ], "synonyms": [ "MIMPS", "OMIMPS", "PS", "mim.ps" ], "uri_format": "https://omim.org/MIM:PS$1" }, "omit": { "appears_in": [ "mco" ], "contact": { "email": "huang@southalabama.edu", "github": "Huang-OMIT", "name": "Jingshan Huang", "orcid": "0000-0003-2408-2883" }, "description": "The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes).", "download_obo": "https://raw.githubusercontent.com/OmniSearch/omit/master/src/ontology/omit.obo", "download_owl": "http://purl.obolibrary.org/obo/omit.owl", "example": "0000069", "homepage": "http://omit.cis.usouthal.edu/", "keywords": [ "annotation", "biology", "cell", "computational biological predictions", "gene", "gene prediction", "life science", "micro rna", "molecular entity", "molecular interaction", "obo", "ontology", "protein", "regulation of gene expression" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "OMIT", "biocontext": "OMIT", "bioportal": "OMIT", "fairsharing": "FAIRsharing.mf91p5", "miriam": "omit", "n2t": "omit", "obofoundry": "omit", "ols": "omit", "ontobee": "OMIT" }, "name": "Ontology for MicroRNA Target", "pattern": "^\\d{7}$", "preferred_prefix": "OMIT", "publications": [ { "doi": "10.1186/s13326-016-0064-2", "pmc": "PMC4863347", "pubmed": "27175225", "title": "OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data", "year": 2016 }, { "doi": "10.1371/journal.pone.0100855", "pmc": "PMC4099014", "pubmed": "25025130", "title": "OMIT: dynamic, semi-automated ontology development for the microRNA domain", "year": 2014 }, { "doi": "10.1007/s11095-011-0573-8", "pubmed": "21879385", "title": "OMIT: a domain-specific knowledge base for microRNA target prediction", "year": 2011 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/OMIT_$1", "repository": "https://github.com/OmniSearch/omit", "synonyms": [ "OMIT" ], "uri_format": "http://purl.obolibrary.org/obo/OMIT_$1", "version": "dev" }, "omo": { "appears_in": [ "cl", "pcl", "uberon" ], "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "description": "An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO).", "download_owl": "http://purl.obolibrary.org/obo/omo.owl", "example": "0003003", "homepage": "https://github.com/information-artifact-ontology/ontology-metadata", "keywords": [ "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "OMO", "bioportal": "OMO", "obofoundry": "omo", "ols": "omo", "ontobee": "OMO" }, "name": "OBO Metadata Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "OMO", "rdf_uri_format": "http://purl.obolibrary.org/obo/OMO_$1", "repository": "https://github.com/information-artifact-ontology/ontology-metadata", "uri_format": "http://purl.obolibrary.org/obo/OMO_$1", "version": "2024-11-13" }, "omon": { "contributor": { "email": "oga.t@northeastern.edu", "github": "tomo-oga", "name": "Tomohiro Oga", "orcid": "0009-0001-6787-3995" }, "description": "The new national clinical trials registry of the Netherlands", "example": "53367", "github_request_issue": 1157, "homepage": "https://onderzoekmetmensen.nl/en", "logo": "https://onderzoekmetmensen.nl/themes/custom/trialregister/logo.svg", "name": "Overview of Medical Research in the Netherlands", "pattern": "^\\d{5}$", "preferred_prefix": "omon", "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://onderzoekmetmensen.nl/en/trial/$1" }, "omop": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" } ], "description": "The OMOP Common Data Model allows for the systematic analysis of disparate observational databases. The concept behind this approach is to transform data contained within those databases into a common format (data model) as well as a common representation (terminologies, vocabularies, coding schemes), and then perform systematic analyses using a library of standard analytic routines that have been written based on the common format.", "example": "1", "homepage": "https://www.ohdsi.org/data-standardization/the-common-data-model/", "name": "Observational Medical Outcomes Partnership", "pattern": "^\\d+$", "preferred_prefix": "omop", "providers": [ { "code": "ohdsi.api", "description": "Programmatic access to OMOP terms", "homepage": "http://api.ohdsi.org", "name": "OHDSI API", "uri_format": "http://api.ohdsi.org/WebAPI/vocabulary/concept/$1" }, { "code": "ohdsi.data", "description": " https://faircookbook.elixir-europe.org/content/recipes/applied-examples/ehden-ohdsi.html suggests https://data.ohdsi.org/concept/ as another uri expansion but it does not resolve.", "homepage": "https://data.ohdsi.org/concept", "name": "OHDSI Data Endpoint", "uri_format": "https://data.ohdsi.org/concept/$1" } ], "references": [ "https://github.com/callahantiff/OMOP2OBO", "https://github.com/biopragmatics/bioregistry/issues/599", "https://github.com/biopragmatics/bioregistry/pull/600" ], "synonyms": [ "OMOP" ], "uri_format": "https://athena.ohdsi.org/search-terms/terms/$1" }, "omp": { "appears_in": [ "mco" ], "contact": { "email": "jimhu@tamu.edu", "github": "jimhu-tamu", "name": "James C. Hu", "orcid": "0000-0001-9016-2684" }, "description": "An ontology of phenotypes covering microbes", "download_obo": "http://purl.obolibrary.org/obo/omp.obo", "download_owl": "http://purl.obolibrary.org/obo/omp.owl", "example": "0005067", "homepage": "http://microbialphenotypes.org", "keywords": [ "chemical biology", "microbe-host interaction phenotype", "microbial ecology", "microbiology", "obo", "omics", "omics data analysis", "ontology", "phenomics", "phenotype" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "OMP", "biocontext": "OMP", "bioportal": "OMP", "fairsharing": "FAIRsharing.cc3f2x", "obofoundry": "omp", "ols": "omp", "ontobee": "OMP" }, "name": "Ontology of Microbial Phenotypes", "pattern": "^\\d{7}$", "preferred_prefix": "OMP", "publications": [ { "doi": "10.1186/s12866-014-0294-3", "pmc": "PMC4287307", "pubmed": "25433798", "title": "An ontology for microbial phenotypes", "year": 2014 }, { "doi": "10.1186/s13326-019-0205-5", "title": "Phenotype annotation with the ontology of microbial phenotypes (OMP)", "year": 2019 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/OMP_$1", "repository": "https://github.com/microbialphenotypes/OMP-ontology", "uri_format": "http://purl.obolibrary.org/obo/OMP_$1", "version": "2024-03-25" }, "omrse": { "appears_in": [ "labo" ], "contact": { "email": "hoganwr@gmail.com", "github": "hoganwr", "name": "Bill Hogan", "orcid": "0000-0002-9881-1017" }, "description": "The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations.", "download_json": "http://purl.obolibrary.org/obo/omrse.json", "download_obo": "https://github.com/ufbmi/OMRSE/raw/master/omrse-full.obo", "download_owl": "http://purl.obolibrary.org/obo/omrse.owl", "example": "00000022", "homepage": "https://github.com/mcwdsi/OMRSE/wiki/OMRSE-Overview", "keywords": [ "biomedical science", "demographics", "health science", "hospital", "obo", "ontology", "patient care", "social science" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "OMRSE", "biocontext": "OMRSE", "bioportal": "OMRSE", "fairsharing": "FAIRsharing.z0p37e", "obofoundry": "omrse", "ols": "omrse", "ontobee": "OMRSE" }, "name": "Ontology for Modeling and Representation of Social Entities", "pattern": "^\\d{8}$", "preferred_prefix": "OMRSE", "publications": [ { "doi": "10.1186/s13326-016-0087-8", "pmc": "PMC4942889", "pubmed": "27406187", "title": "The ontology of medically related social entities: recent developments", "year": 2016 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/OMRSE_$1", "repository": "https://github.com/mcwdsi/OMRSE", "uri_format": "http://purl.obolibrary.org/obo/OMRSE_$1", "version": "2025-03-26" }, "omx.dataset": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "OncoMX is a knowledgebase for exploring cancer biomarkers in the context of related cancer and healthy data. This resource is for datasets within OncoMX.", "example": "000059", "homepage": "https://data.oncomx.org", "name": "OncoMX Dataset", "pattern": "^\\d+$", "preferred_prefix": "omx.dataset", "uri_format": "https://data.oncomx.org/OMX_$1" }, "oncotree": { "appears_in": [ "efo" ], "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research.", "example": "BLL", "homepage": "http://oncotree.mskcc.org", "keywords": [ "cancer", "clinical decision support systems", "oncology" ], "name": "OncoTree", "preferred_prefix": "oncotree", "uri_format": "http://oncotree.mskcc.org/api/tumorTypes/search/code/$1" }, "one": { "contact": { "email": "chenyangnutrition@gmail.com", "github": "cyang0128", "name": "Chen Yang", "orcid": "0000-0001-9202-5309" }, "depends_on": [ "foodon", "obi", "ons" ], "description": "An ontology to standardize research output of nutritional epidemiologic studies.", "download_owl": "http://purl.obolibrary.org/obo/one.owl", "example": "0001021", "homepage": "https://github.com/cyang0128/Nutritional-epidemiologic-ontologies", "keywords": [ "diet", "epidemiology", "metabolomics", "nutritional science", "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "ONE", "bioportal": "ONE", "fairsharing": "FAIRsharing.USxx0K", "obofoundry": "one", "ols": "one", "ontobee": "ONE" }, "name": "Ontology for Nutritional Epidemiology", "pattern": "^\\d{7}$", "preferred_prefix": "ONE", "publications": [ { "doi": "10.3390/nu11061300", "pmc": "PMC6628051", "pubmed": "31181762", "title": "An Ontology to Standardize Research Output of Nutritional Epidemiology: From Paper-Based Standards to Linked Content", "year": 2019 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/ONE_$1", "repository": "https://github.com/cyang0128/Nutritional-epidemiologic-ontologies", "uri_format": "http://purl.obolibrary.org/obo/ONE_$1" }, "ons": { "appears_in": [ "one" ], "contact": { "email": "francesco.vitali@ibba.cnr.it", "github": "FrancescoVit", "name": "Francesco Vitali", "orcid": "0000-0001-9125-4337" }, "depends_on": [ "bfo", "chebi", "envo", "foodon", "ncbitaxon", "obi", "ro", "uberon" ], "description": "An ontology for description of concepts in the nutritional studies domain.", "download_owl": "http://purl.obolibrary.org/obo/ons.owl", "example": "0000060", "homepage": "https://github.com/enpadasi/Ontology-for-Nutritional-Studies", "keywords": [ "biomedical science", "nutritional science", "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "ONS", "agroportal": "ONS", "bioportal": "ONS", "fairsharing": "FAIRsharing.rfec93", "obofoundry": "ons", "ols": "ons", "ontobee": "ONS" }, "name": "Ontology for Nutritional Studies", "pattern": "^\\d{7}$", "preferred_prefix": "ONS", "publications": [ { "doi": "10.1186/s12263-018-0601-y", "pmc": "PMC5928560", "pubmed": "29736190", "title": "ONS: an ontology for a standardized description of interventions and observational studies in nutrition", "year": 2018 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/ONS_$1", "repository": "https://github.com/enpadasi/Ontology-for-Nutritional-Studies", "uri_format": "http://purl.obolibrary.org/obo/ONS_$1", "version": "2024-07-03" }, "ontie": { "contact": { "email": "bpeters@lji.org", "github": "bpeters42", "name": "Bjoern Peters", "orcid": "0000-0002-8457-6693" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Ontology of Immune Epitopes (ONTIE) is an effort to represent terms in the immunology domain in a formal ontology with the specific goal of representing experiments that identify and characterize immune epitopes.", "download_owl": "https://raw.githubusercontent.com/IEDB/ONTIE/master/ontie.owl", "example": "0000001", "homepage": "https://ontology.iedb.org/", "keywords": [ "immunology", "infection", "life science", "major histocompatibility complex", "ontology" ], "mappings": { "fairsharing": "FAIRsharing.kx2md1" }, "name": "Ontology for Immune Epitopes", "pattern": "^\\d{7}$", "preferred_prefix": "ontie", "repository": "https://github.com/IEDB/ONTIE", "uri_format": "https://ontology.iedb.org/ontology/ONTIE_$1" }, "ontoavida": { "contact": { "email": "fortuna@ebd.csic.es", "github": "miguelfortuna", "name": "Miguel A. Fortuna", "orcid": "0000-0002-8374-1941" }, "depends_on": [ "fbcv", "gsso", "ncit", "ro", "stato" ], "description": "The Ontology for Avida (OntoAvida) project aims to develop an integrated vocabulary for the description of the most widely used computational approach for performing experimental evolution using digital organisms (i.e., self-replicating computer programs that evolve within a user-defined computational environment).\n\nThe lack of a clearly defined vocabulary makes biologists feel reluctant to embrace the field of digital evolution. This unique ontology has the potential to change this picture overnight.\n\nOntoAvida was initially developed by https://fortunalab.org, the computational biology lab at the Doñana Biological Station (a research institute of the Spanish National Research Council based at Seville, Spain). Contributors to OntoAvida are expected to include members of the Digital Evolution Laboratory (https://devolab.org/) at Michigan State University (USA).\n\nMore information can be found at https://obofoundry.org/ontology/ontoavida.html", "download_obo": "http://purl.obolibrary.org/obo/ontoavida.obo", "download_owl": "http://purl.obolibrary.org/obo/ontoavida.owl", "example": "00000001", "homepage": "https://gitlab.com/fortunalab/ontoavida", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "ONTOAVIDA", "bioportal": "ONTOAVIDA", "obofoundry": "ontoavida", "ols": "ontoavida", "ontobee": "ONTOAVIDA" }, "name": "Ontology for Avida digital evolution platform", "pattern": "^\\d{8}$", "preferred_prefix": "ONTOAVIDA", "publications": [ { "doi": "10.1038/s41597-023-02514-3", "title": "Ontology for the Avida digital evolution platform" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/ONTOAVIDA_$1", "repository": "https://gitlab.com/fortunalab/ontoavida", "uri_format": "http://purl.obolibrary.org/obo/ONTOAVIDA_$1", "version": "2022-03-15" }, "ontoneo": { "contact": { "email": "fernanda.farinelli@gmail.com", "github": "FernandaFarinelli", "name": "Fernanda Farinelli", "orcid": "0000-0003-2338-8872" }, "description": "The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby.", "download_owl": "http://purl.obolibrary.org/obo/ontoneo.owl", "example": "00000098", "homepage": "http://ontoneo.com", "keywords": [ "electronic health record", "obo", "obstetrics", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "ONTONEO", "biocontext": "ONTONEO", "bioportal": "ONTONEO", "fairsharing": "FAIRsharing.5a4y1y", "obofoundry": "ontoneo", "ols": "ontoneo", "ontobee": "ONTONEO" }, "name": "Obstetric and Neonatal Ontology", "pattern": "^\\d{8}$", "preferred_prefix": "ONTONEO", "publications": [ { "doi": "10.1002/asi.23900", "title": "Ontologies for the representation of electronic medical records: The obstetric and neonatal ontology", "year": 2017 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/ONTONEO_$1", "repository": "https://github.com/ontoneo-project/Ontoneo", "uri_format": "http://purl.obolibrary.org/obo/ONTONEO_$1", "version": "2025-03-14" }, "ontorxn": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "OntoRXN is an ontology for the description of reaction networks as undirected graphs characterized by energies.", "download_owl": "https://gitlab.com/dgarayr/ontorxn/-/raw/prod/OntoRXN.owl", "example": "hasCalculation", "github_request_issue": 1311, "homepage": "https://gitlab.com/dgarayr/ontorxn", "keywords": [ "ontology" ], "license": "CC-BY-4.0", "name": "OntoRXN", "preferred_prefix": "ontorxn", "publications": [ { "doi": "10.1186/s13321-022-00610-x", "pmc": "PMC9153116", "pubmed": "35637523", "title": "Chemical reaction network knowledge graphs: the OntoRXN ontology", "year": 2022 } ] }, "oostt": { "contact": { "email": "mbrochhausen@gmail.com", "github": "mbrochhausen", "name": "Mathias Brochhausen", "orcid": "0000-0003-1834-3856" }, "description": "The Ontology of Organizational Structures of Trauma centers and Trauma systems (OOSTT) is a representation of the components of trauma centers and trauma systems coded in Web Ontology Language (OWL2).", "download_owl": "http://purl.obolibrary.org/obo/oostt.owl", "example": "00000099", "homepage": "https://github.com/OOSTT/OOSTT", "keywords": [ "obo", "ontology", "traumatology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "OOSTT", "biocontext": "OOSTT", "bioportal": "OOSTT", "fairsharing": "FAIRsharing.b4sa0w", "obofoundry": "oostt", "ols": "oostt", "ontobee": "OOSTT" }, "name": "Ontology of Organizational Structures of Trauma centers and Trauma systems", "pattern": "^\\d{8}$", "preferred_prefix": "OOSTT", "rdf_uri_format": "http://purl.obolibrary.org/obo/OOSTT_$1", "repository": "https://github.com/OOSTT/OOSTT", "uri_format": "http://purl.obolibrary.org/obo/OOSTT_$1", "version": "2025-01-24" }, "opb": { "banana": "OPB", "banana_peel": "_", "contact": { "email": "maxneal@gmail.com", "name": "Maxwell L. Neal", "orcid": "0000-0002-2390-6572" }, "contributor_extras": [ { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" } ], "description": "The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms.", "download_owl": "http://aber-owl.net/media/ontologies/OPB/13/opb.owl", "example": "00573", "homepage": "http://bioportal.bioontology.org/ontologies/OPB", "keywords": [ "concentration", "kinetic model", "life science", "mathematical model", "ontology", "physics", "structure" ], "mappings": { "aberowl": "OPB", "biocontext": "OPB", "bioportal": "OPB", "fairsharing": "FAIRsharing.qcceez", "miriam": "opb", "n2t": "opb", "prefixcommons": "opb" }, "name": "Ontology of Physics for Biology", "pattern": "^\\d+$", "preferred_prefix": "opb", "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/opb:$1" } ], "publications": [ { "doi": "10.1186/2041-1480-4-41", "pmc": "PMC3904761", "pubmed": "24295137", "title": "Ontology of physics for biology: representing physical dependencies as a basis for biological processes", "year": 2013 }, { "doi": "10.1371/journal.pone.0028708", "pmc": "PMC3246444", "pubmed": "22216106", "title": "Physical properties of biological entities: an introduction to the ontology of physics for biology", "year": 2011 } ], "uri_format": "https://bioportal.bioontology.org/ontologies/OPB/?p=classes&conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_$1" }, "openalex": { "contact": { "email": "hpiwowar@gmail.com", "github": "hpiwowar", "name": "Heather Piwowar", "orcid": "0000-0003-1613-5981" }, "contributor": { "github": "dhimmel", "name": "Daniel Himmelstein", "orcid": "0000-0002-3012-7446" }, "description": "OpenAlex is a fully open catalog of the global research system that describes scholarly entities and how those entities are connected to each other.", "example": "W2741809807", "github_request_issue": 280, "homepage": "https://openalex.org/", "keywords": [ "knowledge graph", "wikidata" ], "name": "OpenAlex", "pattern": "^[WAICV]\\d{2,}$", "preferred_prefix": "openalex", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://openalex.org/$1" }, "openwemi": { "contact": { "email": "kcoyle@kcoyle.net", "github": "kcoyle", "name": "Karen Coyle", "orcid": "0000-0002-1085-7089" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "openWEMI is a minimally constrained vocabulary for describing created resources using the concepts of Work, Expression, Manifestation, Item.", "example": "Endeavor", "homepage": "https://dcmi.github.io/openwemi/", "license": "CC0-1.0", "name": "openWEMI Vocabulary", "pattern": "^\\w+$", "preferred_prefix": "openwemi", "references": [ "https://journal.code4lib.org/articles/16491", "http://archive.ifla.org/VII/s13/frbr/frbr_2008.pdf" ], "repository": "https://github.com/dcmi/openwemi", "uri_format": "https://dcmi.github.io/openwemi/ns#$1" }, "opl": { "banana": "OPL", "contact": { "email": "zhengj2007@gmail.com", "github": "zhengj2007", "name": "Jie Zheng", "orcid": "0000-0002-2999-0103" }, "description": "The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc.", "download_owl": "http://purl.obolibrary.org/obo/opl.owl", "example": "0000319", "homepage": "https://github.com/OPL-ontology/OPL", "keywords": [ "anatomy", "developmental biology", "host", "life cycle", "life cycle stage", "life science", "obo", "ontology", "parasite" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "OPL", "biocontext": "OPL", "bioportal": "OPL", "fairsharing": "FAIRsharing.ez2nhb", "miriam": "opl", "obofoundry": "opl", "ols": "opl", "ontobee": "OPL" }, "name": "Ontology for Parasite LifeCycle", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "OPL", "publications": [ { "doi": "10.1186/2041-1480-3-5", "pmc": "PMC3488002", "pubmed": "22621763", "title": "The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms", "year": 2012 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/OPL_$1", "repository": "https://github.com/OPL-ontology/OPL", "uri_format": "http://purl.obolibrary.org/obo/OPL_$1", "version": "2023-08-28" }, "opm": { "description": "The Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization.", "example": "1h68", "homepage": "http://opm.phar.umich.edu/", "keywords": [ "computer science", "data management" ], "mappings": { "biocontext": "OPM", "fairsharing": "FAIRsharing.7c683b", "miriam": "opm", "n2t": "opm" }, "name": "Orientations of Proteins in Membranes Database", "pattern": "^[0-9][A-Za-z0-9]{3}$", "preferred_prefix": "opm", "uri_format": "http://opm.phar.umich.edu/protein.php?pdbid=$1" }, "opmi": { "appears_in": [ "labo", "scdo" ], "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", "name": "Yongqun Oliver He", "orcid": "0000-0001-9189-9661" }, "description": "OPMI is a biomedical ontology in the area of precision medicine and its related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles.", "download_owl": "http://purl.obolibrary.org/obo/opmi.owl", "example": "0000101", "homepage": "https://github.com/OPMI/opmi", "keywords": [ "clinical studies", "disease", "obo", "omics", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "OPMI", "bioportal": "OPMI", "fairsharing": "FAIRsharing.d2d84f", "obofoundry": "opmi", "ols": "opmi", "ontobee": "OPMI" }, "name": "Ontology of Precision Medicine and Investigation", "pattern": "^\\d{7}$", "preferred_prefix": "OPMI", "rdf_uri_format": "http://purl.obolibrary.org/obo/OPMI_$1", "repository": "https://github.com/OPMI/opmi", "uri_format": "http://purl.obolibrary.org/obo/OPMI_$1", "version": "1.0.166" }, "orangebook": { "comment": "The web pages on the digital edition can be constructed with some programmatic logic, but not directly", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The first number is the chapter then the remainder are subsections.", "example": "10.2.1.1.3", "github_request_issue": 1311, "homepage": "https://media.iupac.org/publications/analytical_compendium/", "name": "IUPAC Compendium of Analytical Nomenclature (Orange Book)", "preferred_prefix": "orangebook", "references": [ "https://iupac.org/what-we-do/books/orangebook/" ] }, "orcid": { "contact": { "email": "w.simpson@orcid.org", "github": "wjrsimpson", "name": "Will Simpson", "orcid": "0000-0003-4654-1403" }, "description": "ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers. ORCID records hold non-sensitive information such as name, email, organization name, and research activities.", "example": "0000-0003-4423-4370", "homepage": "https://orcid.org", "keywords": [ "person", "subject agnostic" ], "mappings": { "bartoc": "2021", "biocontext": "ORCID", "biolink": "ORCID", "fairsharing": "FAIRsharing.nx58jg", "go": "orcid", "miriam": "orcid", "n2t": "orcid", "wikidata": "P496" }, "mastodon": "ORCID_Org@scicomm.xyz", "name": "Open Researcher and Contributor", "pattern": "^\\d{4}-\\d{4}-\\d{4}-\\d{3}(\\d|X)$", "preferred_prefix": "orcid", "providers": [ { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", "homepage": "https://scholia.toolforge.org/", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/orcid/$1" } ], "publications": [ { "doi": "10.23640/07243.16687207.v1", "title": "From Vision to Value: ORCID's 2022–2025 Strategic Plan", "year": 2021 }, { "doi": "10.23640/07243.12009255.v3", "title": "ORCID's 2025 Vision", "year": 2020 } ], "rdf_uri_format": "https://orcid.org/$1", "repository": "https://github.com/ORCID", "synonyms": [ "ORCID", "ORCiD" ], "twitter": "ORCID_Org", "uri_format": "https://orcid.org/$1" }, "ordb": { "description": "The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs). It includes a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs).", "example": "8497", "homepage": "http://senselab.med.yale.edu/OrDB/", "keywords": [ "gene", "life science", "protein" ], "mappings": { "biocontext": "ORDB", "fairsharing": "FAIRsharing.6375zh", "miriam": "ordb", "n2t": "ordb", "pathguide": "65", "prefixcommons": "ordb" }, "name": "Olfactory Receptor Database", "pattern": "^\\d+$", "preferred_prefix": "ordb", "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/ordb:$1" } ], "publications": [ { "doi": "10.1093/database/baw132", "pmc": "PMC5045865", "pubmed": "27694208", "title": "ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions", "year": 2016 }, { "doi": "10.1093/nar/30.1.354", "pmc": "PMC99065", "pubmed": "11752336", "title": "Olfactory Receptor Database: a metadata-driven automated population from sources of gene and protein sequences", "year": 2002 }, { "doi": "10.1093/nar/28.1.341", "pmc": "PMC102443", "pubmed": "10592268", "title": "Olfactory receptor database: a sensory chemoreceptor resource", "year": 2000 } ], "uri_format": "http://senselab.med.yale.edu/ORDB/Data/$1" }, "oridb.sacch": { "description": "OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae.", "example": "1", "homepage": "http://cerevisiae.oridb.org/index.php", "mappings": { "biocontext": "ORIDB.SACCH", "miriam": "oridb.sacch", "n2t": "oridb.sacch" }, "name": "OriDB Saccharomyces", "pattern": "^\\d+$", "preferred_prefix": "oridb.sacch", "uri_format": "http://cerevisiae.oridb.org/details.php?id=$1" }, "oridb.schizo": { "description": "OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Schizosaccharomyces pombe.", "example": "1", "homepage": "http://pombe.oridb.org/index.php", "mappings": { "biocontext": "ORIDB.SCHIZO", "miriam": "oridb.schizo", "n2t": "oridb.schizo" }, "name": "OriDB Schizosaccharomyces", "pattern": "^\\d+$", "preferred_prefix": "oridb.schizo", "uri_format": "http://pombe.oridb.org/details.php?id=$1" }, "ornaseq": { "contact": { "email": "safisher@upenn.edu", "github": "safisher", "name": "Stephen Fisher", "orcid": "0000-0001-8034-7685" }, "description": "An application ontology designed to annotate next-generation sequencing experiments performed on RNA.", "download_obo": "http://purl.obolibrary.org/obo/ornaseq.obo", "download_owl": "http://purl.obolibrary.org/obo/ornaseq.owl", "example": "0000010", "homepage": "http://kim.bio.upenn.edu/software/ornaseq.shtml", "keywords": [ "obo", "ontology", "rna sequencing", "single cell", "single cell rna-seq", "transcriptomics" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "ORNASEQ", "bioportal": "ORNASEQ", "fairsharing": "FAIRsharing.e6f303", "obofoundry": "ornaseq", "ols": "ornaseq", "ontobee": "ORNASEQ" }, "name": "Ontology of RNA Sequencing", "pattern": "^\\d{7}$", "preferred_prefix": "ORNASEQ", "rdf_uri_format": "http://purl.obolibrary.org/obo/ORNASEQ_$1", "repository": "https://github.com/safisher/ornaseq", "uri_format": "http://purl.obolibrary.org/obo/ORNASEQ_$1", "version": "2019-07-08" }, "orphanet": { "contact": { "email": "bliemsl@xs4all.nl", "name": "Spencer L. Liem", "orcid": "0000-0002-1575-9365" }, "description": "Orphanet is a reference portal for information on rare diseases and orphan drugs. It’s aim is to help improve the diagnosis, care and treatment of patients with rare diseases.", "download_owl": "http://www.orphadata.org/data/ORDO/ordo_orphanet.owl", "example": "85163", "homepage": "http://www.orpha.net/consor/", "keywords": [ "disease", "drug", "human", "life science", "ontology", "ontology and terminology" ], "license": "CC-BY-4.0", "mappings": { "biocontext": "Orphanet", "biolink": "orphanet", "fairsharing": "FAIRsharing.6bd5k6", "integbio": "nbdc01422", "miriam": "orphanet", "n2t": "orphanet", "prefixcommons": "orphanet", "uniprot": "DB-0068", "wikidata": "P1550" }, "name": "Orphanet", "pattern": "^\\d+$", "preferred_prefix": "orphanet", "providers": [ { "code": "CURATOR_REVIEW", "description": "Bio2RDF", "homepage": "http://bio2rdf.org/", "name": "Bio2RDF", "uri_format": "http://bio2rdf.org/orphanet:$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/orphanet:$1" } ], "publications": [ { "pubmed": "19058507", "title": "[Orphanet and the Dutch Steering Committee Orphan Drugs. A European and Dutch databank of information on rare diseases]", "year": 2008 } ], "synonyms": [ "ORPHA" ], "twitter": "orphanet", "uri_format": "http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=$1" }, "orphanet.ordo": { "banana": "Orphanet", "banana_peel": "_", "contact": { "email": "ordo.orphanet@inserm.fr", "name": "Ana Rath", "orcid": "0000-0003-4308-6337" }, "description": "The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases.\nIt integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10).", "download_owl": "http://www.orphadata.org/data/ORDO/ordo_orphanet.owl", "example": "C023", "example_extras": [ "478" ], "homepage": "https://www.ebi.ac.uk/ols4/ontologies/ordo", "keywords": [ "biomedical science", "diagnosis", "disease", "gene", "health science", "ontology", "phenotype", "rare disease" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "ordo", "biocontext": "ORPHANET.ORDO", "biolink": "ORPHA", "bioportal": "ORDO", "cellosaurus": "ORDO", "fairsharing": "FAIRsharing.pbbnwa", "miriam": "orphanet.ordo", "n2t": "orphanet.ordo", "ols": "ordo" }, "name": "Orphanet Rare Disease Ontology", "pattern": "^C?\\d+$", "preferred_prefix": "orphanet.ordo", "providers": [ { "code": "legacy", "description": "This link is no longer live", "homepage": "https://www.orpha.net", "name": "Legacy Orphanet Expert", "uri_format": "https://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=en&Expert=$1" } ], "publications": [ { "pubmed": "22874158", "title": "Rare diseases knowledge management: the contribution of proximity measurements in OntoOrpha and OMIM", "year": 2012 } ], "synonyms": [ "ordo" ], "uri_format": "http://www.orpha.net/ORDO/Orphanet_$1", "version": "4.6" }, "orth": { "contact": { "email": "jfernand@um.es", "github": "jesualdotomasfernandezbreis", "name": "Jesualdo Tomás Fernández-Breis", "orcid": "0000-0002-7558-2880" }, "description": "The need of a common ontology for describing orthology information in biological research communities has led to the creation of the Orthology Ontology (ORTH). ORTH ontology is designed to describe sequence homology data available in multiple orthology databases on the Web (e.g.: OMA, OrthoDB, HieranoiDB, and etc.). By sequence homology data, we mostly mean gene region, gene and protein centric orthology, paralogy, and xenology information. Depending on the database, the homology information is structured in different ways. ORTH ontology accommodates these disparate data structures namely Hierarchical Orthologous Group (HOG), cluster of homologous sequences and homologous-pairwise relations between sequences. In addition to the specific ORTH terms, this specification includes terms of the imported ontologies (e.g. Semanticscience Integrated Ontology, SIO) which are pertinents to represent the information from various orthology databases in a homogeneous way.", "download_owl": "https://github.com/qfo/OrthologyOntology/raw/master/orthOntology_RC_v2_A.owl", "example": "HomologyRelation", "homepage": "https://github.com/qfo/OrthologyOntology", "keywords": [ "comparative genomics", "gene", "homologous", "ontology", "orthologous", "paralogous", "protein", "sequence" ], "mappings": { "aberowl": "ORTH", "bioportal": "ORTH", "fairsharing": "FAIRsharing.4877h0", "ols": "orth" }, "name": "Orthology Ontology", "preferred_prefix": "orth", "publications": [ { "doi": "10.1186/s13326-016-0077-x", "pmc": "PMC4893294", "pubmed": "27259657", "title": "The Orthology Ontology: development and applications", "year": 2016 } ], "repository": "https://github.com/qfo/OrthologyOntology", "uri_format": "http://purl.org/net/orth#$1", "version": "2.0" }, "orthodb": { "contact": { "email": "evgeny.zdobnov@unige.ch", "name": "Evgeny M Zdobnov", "orcid": "0000-0002-5178-1498" }, "description": "OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups", "example": "Q9P0K8", "homepage": "https://www.orthodb.org", "keywords": [ "dna", "eukaryotic", "life science", "protein" ], "mappings": { "biocontext": "ORTHODB", "fairsharing": "FAIRsharing.x989d5", "miriam": "orthodb", "n2t": "orthodb", "prefixcommons": "orthodb", "uniprot": "DB-0143" }, "name": "OrthoDB", "pattern": "^\\w+$", "preferred_prefix": "orthodb", "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/orthodb:$1" } ], "provides": "uniprot", "publications": [ { "doi": "10.1093/nar/gky1053", "pmc": "PMC6323947", "pubmed": "30395283", "title": "OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs", "year": 2019 }, { "doi": "10.1093/nar/gku1220", "pmc": "PMC4383991", "pubmed": "25428351", "title": "OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software", "year": 2014 }, { "doi": "10.1093/nar/gkq930", "pmc": "PMC3013786", "pubmed": "20972218", "title": "OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011", "year": 2010 } ], "uri_format": "http://cegg.unige.ch/orthodb/results?searchtext=$1" }, "oryzabase.gene": { "description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information.", "example": "117", "homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/", "mappings": { "biocontext": "ORYZABASE.GENE", "miriam": "oryzabase.gene", "n2t": "oryzabase.gene" }, "name": "Oryzabase Gene", "pattern": "^\\d+$", "preferred_prefix": "oryzabase.gene", "uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1" }, "oryzabase.mutant": { "description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information.", "example": "21393", "homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/", "mappings": { "biocontext": "ORYZABASE.MUTANT", "miriam": "oryzabase.mutant", "n2t": "oryzabase.mutant" }, "name": "Oryzabase Mutant", "pattern": "^\\d+$", "preferred_prefix": "oryzabase.mutant", "uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$1" }, "oryzabase.reference": { "description": "The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan.", "example": "42840", "homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/", "mappings": { "miriam": "oryzabase.reference", "n2t": "oryzabase.reference" }, "name": "Oryzabase Reference", "pattern": "^\\d+$", "preferred_prefix": "oryzabase.reference", "uri_format": "https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/$1" }, "oryzabase.stage": { "description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references development stage information.", "example": "34", "homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/", "mappings": { "biocontext": "ORYZABASE.STAGE", "miriam": "oryzabase.stage", "n2t": "oryzabase.stage" }, "name": "Oryzabase Stage", "pattern": "^\\d+$", "preferred_prefix": "oryzabase.stage", "uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$1" }, "oryzabase.strain": { "description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references wild strain information.", "example": "1", "homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/", "mappings": { "biocontext": "ORYZABASE.STRAIN", "miriam": "oryzabase.strain", "n2t": "oryzabase.strain" }, "name": "Oryzabase Strain", "pattern": "^\\d+$", "preferred_prefix": "oryzabase.strain", "uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1" }, "osf": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "ID in osf.io", "example": "2u4tf", "homepage": "https://osf.io", "keywords": [ "author", "paper", "person", "researcher", "work" ], "mappings": { "wikidata": "P7238" }, "name": "Open Science Framework ID", "pattern": "^[a-z0-9]{5}$", "preferred_prefix": "osf", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1171" ], "uri_format": "https://osf.io/$1" }, "oslc": { "contact": { "email": "jamsden@us.ibm.com", "name": "Jim Amsden" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Core Vocabulary defines the OSLC Core RDF vocabulary terms and resources, that have broad applicability across various domains.", "example": "Property", "homepage": "http://open-services.net/ns/core", "keywords": [ "plm" ], "mappings": { "lov": "oslc" }, "name": "OASIS Open Services for Lifecycle Collaboration Core Vocabulary", "preferred_prefix": "oslc", "uri_format": "http://open-services.net/ns/core#$1" }, "osti.article": { "comment": "Corresponding GitHub linked to software registrations is located at https://github.com/doecode. All related contact information can be found here https://www.osti.gov/contact", "contributor": { "email": "Lindsey.Anderson@pnnl.gov", "github": "lnanderson", "name": "Lindsey Anderson", "orcid": "0000-0002-8741-7823" }, "description": "The U.S. Department of Energy (DOE) Office of Scientific and Technical Information (OSTI) is the main metadata archive for permanent storage of registered [DOE DOI products](https://www.osti.gov/pids/doi-services/doe-data-id-service) (datasets, code, articles, patents, multimedia, etc.). When a DOI is minted a unique OSTI identifier for each record [{osti_id}](https://www.osti.gov/api/v1/docs#endpoints-singlerecord) is provided as the suffix in the DOI schema ([{site-specific-prefix}/{user-supplied-doi-infix}/{osti_id}](https://www.osti.gov/pids/doi-services)) and can be alternatively used as the main product identifier endpoint when [searching OSTI.GOV](https://www.osti.gov/search-tools) registry archive (see example below). OSTI.GOV is the primary registry and search tool for all Department of Energy (DOE) funded science, technology, and engineering research and development (R&D) results and the organizational hub for information about the DOE Office of Scientific and Technical Information (OSTI. **Data Product Type Example:** - https://www.osti.gov/biblio/1668761 - https://www.osti.gov/search/semantic:1668761 - https://www.osti.gov/dataexplorer/biblio/dataset/1668761 - https://www.osti.gov/api/v1/records/1668761 - https://doi.org/10.11578/1668761 **Other Core Product Registry Examples:** - Journal Articles: https://www.osti.gov/pages/biblio - Datasets: https://www.osti.gov/dataexplorer/biblio/dataset/ - Software: https://www.osti.gov/doecode/biblio/ - Patents: https://www.osti.gov/doepatents/biblio/ - Multimedia: https://www.osti.gov/sciencecinema/biblio/", "example": "1668761", "github_request_issue": 1050, "homepage": "https://www.osti.gov/", "keywords": [ "article", "articles", "publication", "publications" ], "license": "https://www.osti.gov/disclaim", "mappings": { "wikidata": "P3894" }, "name": "Office of Scientific and Technical Information (OSTI)", "pattern": "^\\d+$", "preferred_prefix": "osti.article", "references": [ "https://www.energy.gov/doe-public-access-plan" ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.osti.gov/biblio/$1" }, "otl": { "contact": { "email": "guiderdoni@cirad.fr", "name": "Emmanuel Guiderdoni", "orcid": "0000-0003-2760-2864" }, "description": "Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information.", "example": "AADB12", "homepage": "http://oryzatagline.cirad.fr/", "keywords": [ "dna", "life science" ], "mappings": { "biocontext": "OTL", "fairsharing": "FAIRsharing.61c2x6", "miriam": "otl", "n2t": "otl", "prefixcommons": "otl" }, "name": "Oryza Tag Line", "pattern": "^A[A-Z]+\\d+$", "preferred_prefix": "otl", "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/otl:$1" } ], "publications": [ { "doi": "10.1093/nar/gkm762", "pmc": "PMC2238859", "pubmed": "17947330", "title": "Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library", "year": 2007 }, { "doi": "17947330", "title": "Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library." } ], "uri_format": "http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1" }, "otol": { "contributor": { "email": "meghan.balk@gmail.com", "github": "megbalk", "name": "Meghan Balk", "orcid": "0000-0003-2699-3066" }, "description": "Identifier for an entity in open tree of life", "example": "3905431", "github_request_issue": 470, "homepage": "https://tree.opentreeoflife.org", "mappings": { "wikidata": "P9157" }, "name": "Open Tree of Life", "pattern": "^[1-9]\\d*$", "preferred_prefix": "otol", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://tree.opentreeoflife.org/taxonomy/browse?id=$1" }, "ovae": { "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", "name": "Yongqunh He", "orcid": "0000-0001-9189-9661" }, "description": "OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE).", "download_owl": "http://purl.obolibrary.org/obo/ovae.owl", "example": "0000609", "homepage": "http://www.violinet.org/ovae/", "keywords": [ "adverse reaction", "biomedical science", "obo", "ontology", "vaccine" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "OVAE", "biocontext": "OVAE", "bioportal": "OVAE", "fairsharing": "FAIRsharing.w4x6n4", "obofoundry": "ovae", "ols": "ovae", "ontobee": "OVAE" }, "name": "Ontology of Vaccine Adverse Events", "pattern": "^\\d{7}$", "preferred_prefix": "OVAE", "publications": [ { "doi": "10.1186/2041-1480-4-40", "pmc": "PMC4177204", "pubmed": "24279920", "title": "The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines", "year": 2013 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/OVAE_$1", "repository": "https://github.com/OVAE-Ontology/ovae", "uri_format": "http://purl.obolibrary.org/obo/OVAE_$1", "version": "1.0.34" }, "owl": { "contact": { "email": "rmrich5@gmail.com", "name": "Rafael Richards", "orcid": "0000-0001-5699-0515" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Overview of the Web Ontology Language (OWL) which provides an introduction to OWL by informally describing the features of each of the sublanguages. ", "download_owl": "https://triplydb.com/w3c/owl/download.trig.gz", "example": "Ontology", "homepage": "https://www.w3.org/TR/owl-features/", "keywords": [ "computer science", "informatics", "ontology", "ontology and terminology", "subject agnostic", "w3c rec" ], "mappings": { "biocontext": "owl", "fairsharing": "FAIRsharing.atygwy", "integbio": "nbdc00307", "lov": "owl", "ols": "owl", "zazuko": "owl" }, "name": "Web Ontology Language", "preferred_prefix": "owl", "uri_format": "http://www.w3.org/2002/07/owl#$1", "version": "$Date: 2009/11/15 10:54:12 $" }, "owlstar": { "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This proposed vocabulary allows edges in Property Graphs (e.g Neo4j, RDF*) to be augmented with edge properties that specify ontological semantics, including (but not limited) to OWL-DL interpretations. [from GitHub]", "download_rdf": "https://github.com/linkml/owlstar/raw/master/owlstar.ttl", "example": "AllSomeInterpretation", "homepage": "https://linkml.io/owlstar/", "license": "CC0-1.0", "mappings": { "biolink": "os" }, "name": "Ontological Interpretations for Web Property Graphs", "pattern": "^\\w+$", "preferred_prefix": "owlstar", "repository": "https://github.com/linkml/owlstar", "uri_format": "http://w3id.org/owlstar/$1" }, "p3db.protein": { "description": "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references plant proteins that contain phosphorylation sites.", "example": "70", "homepage": "http://www.p3db.org/", "keywords": [ "protein", "small molecule" ], "mappings": { "biocontext": "P3DB.PROTEIN", "miriam": "p3db.protein", "n2t": "p3db.protein", "prefixcommons": "p3db" }, "name": "P3DB Protein", "pattern": "^\\d+$", "preferred_prefix": "p3db.protein", "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/p3db:$1" } ], "uri_format": "http://www.p3db.org/protein.php?id=$1&ref=0" }, "p3db.site": { "description": "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins.", "example": "65", "homepage": "http://www.p3db.org/", "mappings": { "biocontext": "P3DB.SITE", "miriam": "p3db.site", "n2t": "p3db.site" }, "name": "P3DB Site", "pattern": "^\\d+$", "preferred_prefix": "p3db.site", "uri_format": "http://www.p3db.org/phosphosite.php?id=$1&ref=0" }, "packagist": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A repository of software packages written in PHP.", "example": "florianv/swap", "homepage": "https://packagist.org", "name": "Packagist", "preferred_prefix": "packagist", "uri_format": "https://packagist.org/packages/$1" }, "pactr": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Pan African Clinical Trials Registry (PACTR) is a regional register of clinical trials conducted in Africa. The registry is an African initiative serving the needs of Africans. It provides an open-access platform where clinical trials can be registered free of charge. The PACTR aims to increase clinical trial registration in Africa by developing awareness of the need to register trials and supporting trialists during registration. (from homepage)", "example": "PACTR202304525632216", "homepage": "https://pactr.samrc.ac.za/", "logo": "https://pactr.samrc.ac.za/images/Banner_Split.jpg", "name": "Pan African Clinical Trials Registry", "pattern": "^PACTR\\d+$", "preferred_prefix": "pactr", "references": [ "https://pactr.samrc.ac.za/TrialDisplay.aspx?TrialID=25488" ] }, "paleodb": { "description": "The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data.", "example": "83088", "homepage": "http://paleodb.org/", "keywords": [ "taxonomy" ], "mappings": { "biocontext": "PALEODB", "miriam": "paleodb", "n2t": "paleodb", "prefixcommons": "paleodb" }, "name": "Paleobiology Database", "pattern": "^\\d+$", "preferred_prefix": "paleodb", "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/paleodb:$1" } ], "uri_format": "http://fossilworks.org/?a=taxonInfo&taxon_no=$1" }, "pandit": { "description": "PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains.", "example": "PF00004", "homepage": "http://www.ebi.ac.uk/goldman-srv/pandit", "keywords": [ "dna", "protein", "structure" ], "mappings": { "integbio": "nbdc00607", "prefixcommons": "pandit", "re3data": "r3d100011232" }, "name": "Protein and Associated NucleotideDomains with Inferred Trees", "preferred_prefix": "pandit", "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/pandit:$1" } ], "provides": "pfam", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi?action=browse&fam=$1" }, "panorama": { "contact": { "email": "brendanx@uw.edu", "name": "Brendan MacLean", "orcid": "0000-0002-9575-0255" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Panorama is a freely-available, open-source repository server application for targeted mass spectrometry assays that integrates into a Skyline mass spec workflow. It makes links to the Proteomics Exchange when possible.", "example": "FxnI151FMs", "homepage": "https://panoramaweb.org", "keywords": [ "life science", "metabolomics", "proteomics" ], "mappings": { "fairsharing": "FAIRsharing.uBpQ1q" }, "name": "Panorama Public", "preferred_prefix": "panorama", "publications": [ { "doi": "10.1074/mcp.ra117.000543", "pmc": "PMC5986241", "pubmed": "29487113", "title": "Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline", "year": 2018 }, { "doi": "10.1021/pr5006636", "pmc": "PMC4156235", "pubmed": "25102069", "title": "Panorama: a targeted proteomics knowledge base", "year": 2014 }, { "doi": "10.1074/mcp.RA117.000543", "title": "Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline." } ], "uri_format": "https://panoramaweb.org/$1.url" }, "panther.family": { "contact": { "email": "pdthomas@usc.edu", "name": "Paul D Thomas", "orcid": "0000-0002-9074-3507" }, "description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. This collection references groups of genes that have been organised as families.", "example": "PTHR12345", "homepage": "http://www.pantherdb.org/", "keywords": [ "classification", "gene", "ontology", "pathway", "protein" ], "mappings": { "biocontext": "PANTHER.FAMILY", "biolink": "PANTHER.FAMILY", "go": "PANTHER", "miriam": "panther.family", "n2t": "panther.family", "prefixcommons": "panther", "uniprot": "DB-0069" }, "name": "PANTHER Family", "part_of": "panther", "pattern": "^PTHR\\d{5}(\\:SF\\d{1,3})?$", "preferred_prefix": "panther.family", "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/panther:$1" } ], "publications": [ { "doi": "10.1093/nar/gky1038", "pmc": "PMC6323939", "pubmed": "30407594", "title": "PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools", "year": 2019 }, { "doi": "10.1101/gr.772403", "pmc": "PMC403709", "pubmed": "12952881", "title": "PANTHER: a library of protein families and subfamilies indexed by function", "year": 2003 } ], "uri_format": "http://www.pantherdb.org/panther/family.do?clsAccession=$1" }, "panther.node": { "description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. PANTHER tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes.", "example": "PTN000000026", "homepage": "http://pantree.org/", "mappings": { "biocontext": "PANTHER.NODE", "miriam": "panther.node", "n2t": "panther.node" }, "name": "PANTHER Node", "part_of": "panther", "pattern": "^PTN\\d{9}$", "preferred_prefix": "panther.node", "uri_format": "http://www.pantree.org/node/annotationNode.jsp?id=$1" }, "panther.pathway": { "description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway collection references pathway information, primarily for signaling pathways, each with subfamilies and protein sequences mapped to individual pathway components.", "example": "P00024", "homepage": "http://www.pantherdb.org/", "mappings": { "biocontext": "PANTHER.PATHWAY", "edam": "1161", "miriam": "panther.pathway", "n2t": "panther.pathway" }, "name": "PANTHER Pathway", "part_of": "panther", "pattern": "^P\\d{5}$", "preferred_prefix": "panther.pathway", "uri_format": "http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$1" }, "panther.pthcmp": { "description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway\ncomponents may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation.", "example": "P00266", "homepage": "http://www.pantherdb.org/", "mappings": { "biocontext": "PANTHER.PTHCMP", "miriam": "panther.pthcmp", "n2t": "panther.pthcmp" }, "name": "PANTHER Pathway Component", "part_of": "panther", "pattern": "^(G|P|U|C|S)\\d{5}$", "preferred_prefix": "panther.pthcmp", "uri_format": "http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$1" }, "pao": { "contact": { "email": "jaiswalp@science.oregonstate.edu", "github": "jaiswalp", "name": "Pankaj Jaiswal", "orcid": "0000-0002-1005-8383" }, "deprecated": true, "homepage": "http://www.plantontology.org", "keywords": [ "obo", "ontology" ], "mappings": { "biocontext": "PAO", "obofoundry": "pao" }, "name": "Plant Anatomy Ontology", "preferred_prefix": "PAO", "rdf_uri_format": "http://purl.obolibrary.org/obo/PAO_$1", "uri_format": "http://purl.obolibrary.org/obo/PAO_$1" }, "pass2": { "deprecated": true, "description": "The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity.", "example": "46977", "homepage": "http://caps.ncbs.res.in/pass2", "keywords": [ "classification", "dna", "genome", "structure" ], "mappings": { "biocontext": "PASS2", "integbio": "nbdc02108", "miriam": "pass2", "n2t": "pass2", "prefixcommons": "pass2" }, "name": "Protein Alignment organised as Structural Superfamily", "pattern": "^\\d+$", "preferred_prefix": "pass2", "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/pass2:$1" } ], "uri_format": "http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=$1" }, "pathbank": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana.", "example": "SMP0000219", "homepage": "https://pathbank.org", "keywords": [ "animal genetics", "bioinformatics", "biology", "cell biology", "cheminformatics", "database management", "drug metabolism", "endocrinology", "genetics", "human genetics", "medical informatics", "metabolomics", "microbiology", "molecular biology", "molecular microbiology", "plant genetics", "proteomics", "systems biology", "transcriptomics" ], "license": "ODbL-1.0", "mappings": { "fairsharing": "FAIRsharing.3xwMon", "togoid": "Pathbank" }, "name": "PathBank", "pattern": "^(SMP|PW)\\d+$", "preferred_prefix": "pathbank", "uri_format": "https://pathbank.org/view/$1" }, "pathguide": { "contact": { "email": "gary.bader@utoronto.ca", "github": "gbader", "name": "Gary Bader", "orcid": "0000-0003-0185-8861" }, "description": "Pathguide contains information about 325 biological related resources and molecular interaction related resources.", "example": "49", "homepage": "http://pathguide.org", "keywords": [ "gene", "interaction", "pathway", "protein", "small molecule" ], "mappings": { "integbio": "nbdc00608", "prefixcommons": "pathguide" }, "name": "Pathguide", "pattern": "^\\d+$", "preferred_prefix": "pathguide", "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/pathguide:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.pathguide.org/fullrecord.php?organisms=all&availability=all&standards=all&order=alphabetic&DBID=$1" }, "pathoplant": { "description": "PathoPlant® is a database on plant-pathogen interactions and components of signal transduction pathways related to plant pathogenesis. PathoPlant® also harbors gene expression data from Arabidopsis thaliana microarray experiments to enable searching for specific genes regulated upon pathogen infection or elicitor treatment.", "example": "MO000027", "homepage": "http://www.pathoplant.de", "keywords": [ "gene expression", "interaction", "pathway", "protein", "small molecule" ], "mappings": { "pathguide": "333", "prefixcommons": "pathoplant" }, "name": "PathoPlant®", "preferred_prefix": "pathoplant", "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/pathoplant:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.pathoplant.de/detail.php?accNo=$1" }, "pathwaycommons": { "contact": { "email": "chris@sanderlab.org", "github": "sanderlab", "name": "Chris Sander", "orcid": "0000-0001-6059-6270" }, "description": "Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language.", "example": "485991", "homepage": "http://www.pathwaycommons.org/pc/", "keywords": [ "pathway" ], "mappings": { "biocontext": "PATHWAYCOMMONS", "miriam": "pathwaycommons", "n2t": "pathwaycommons", "prefixcommons": "pathwaycommons", "re3data": "r3d100012731", "uniprot": "DB-0253" }, "name": "Pathway Commons", "pattern": "^\\d+$", "preferred_prefix": "pathwaycommons", "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/pathwaycommons:$1" } ], "publications": [ { "doi": "10.1093/nar/gkz946/5606621", "pubmed": "31647099" }, { "doi": "10.1093/nar/gkq1039", "pmc": "PMC3013659", "pubmed": "21071392", "title": "Pathway Commons, a web resource for biological pathway data", "year": 2010 } ], "uri_format": "http://www.pathwaycommons.org/pc/record2.do?id=$1" }, "pato": { "appears_in": [ "agro", "aism", "cdno", "cl", "colao", "ecocore", "ecto", "fovt", "gallont", "lepao", "mco", "ms", "pcl", "pco", "phipo", "planp", "proco", "rbo", "uberon", "xpo", "zp" ], "banana": "PATO", "contact": { "email": "g.gkoutos@gmail.com", "github": "gkoutos", "name": "George Gkoutos", "orcid": "0000-0002-2061-091X" }, "description": "PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation.", "download_json": "http://purl.obolibrary.org/obo/pato.json", "download_obo": "http://purl.obolibrary.org/obo/pato.obo", "download_owl": "http://purl.obolibrary.org/obo/pato.owl", "example": "0001998", "homepage": "https://github.com/pato-ontology/pato/", "keywords": [ "biodiversity", "biology", "obo", "ontology", "phenotype", "quality" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "PATO", "agroportal": "PATO", "biocontext": "PATO", "bioportal": "PATO", "fairsharing": "FAIRsharing.ezwdhz", "go": "PATO", "miriam": "pato", "n2t": "pato", "obofoundry": "pato", "ols": "pato", "ontobee": "PATO", "prefixcommons": "pato" }, "name": "Phenotype And Trait Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "PATO", "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/pato:$1" }, { "code": "purl", "description": "Legacy PURLs found in OAE", "homepage": "http://purl.org/obo/owl/", "name": "Legacy PURL", "uri_format": "http://purl.org/obo/owl/PATO#PATO_$1" } ], "publications": [ { "doi": "10.1093/bib/bbx035", "pmc": "PMC6169674", "pubmed": "28387809", "title": "The anatomy of phenotype ontologies: principles, properties and applications", "year": 2018 }, { "doi": "10.1186/gb-2010-11-1-r2", "pmc": "PMC2847714", "pubmed": "20064205", "title": "Integrating phenotype ontologies across multiple species", "year": 2010 }, { "doi": "10.1186/gb-2004-6-1-r8", "pmc": "PMC549069", "pubmed": "15642100", "title": "Using ontologies to describe mouse phenotypes", "year": 2004 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/PATO_$1", "repository": "https://github.com/pato-ontology/pato", "uri_format": "http://purl.obolibrary.org/obo/PATO_$1", "version": "2025-02-01" }, "pav": { "contact": { "email": "stian@soiland-reyes.com", "name": "Stian Soiland-Reyes", "orcid": "0000-0001-9842-9718" }, "contributor": { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" }, "contributor_extras": [ { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } ], "description": "PAV is a lightweight ontology for tracking provenance, authorship, and versioning. It specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources.", "download_owl": "http://aber-owl.net/media/ontologies/PAV/3/pav.owl", "example": "authoredBy", "github_request_issue": 186, "homepage": "https://pav-ontology.github.io/pav/", "keywords": [ "citation", "data management", "ontology", "quality", "resource metadata", "subject agnostic" ], "mappings": { "aberowl": "PAV", "biocontext": "pav", "biolink": "pav", "bioportal": "PAV", "fairsharing": "FAIRsharing.nbfwwv", "lov": "pav" }, "name": "Provenance, Authoring, and Versioning Vocabulary", "pattern": "^[a-z][a-zA-Z]+$", "preferred_prefix": "pav", "publications": [ { "doi": "10.1186/2041-1480-4-37", "pmc": "PMC4177195", "pubmed": "24267948", "title": "PAV ontology: provenance, authoring and versioning", "year": 2013 } ], "repository": "http://pav-ontology.github.io/pav/", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://purl.org/pav/$1" }, "paxdb.organism": { "description": "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species.", "example": "9606", "homepage": "http://pax-db.org/", "mappings": { "biocontext": "PAXDB.ORGANISM", "miriam": "paxdb.organism", "n2t": "paxdb.organism" }, "name": "PaxDb Organism", "pattern": "^\\d+$", "preferred_prefix": "paxdb.organism", "uri_format": "http://pax-db.org/#!species/$1" }, "paxdb.protein": { "description": "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels.", "example": "977869", "homepage": "http://pax-db.org/", "mappings": { "biocontext": "PAXDB.PROTEIN", "miriam": "paxdb.protein", "n2t": "paxdb.protein" }, "name": "PaxDb Protein", "pattern": "^\\d+$", "preferred_prefix": "paxdb.protein", "uri_format": "http://pax-db.org/#!protein/$1" }, "pazar": { "contact": { "email": "wyeth@cmmt.ubc.ca", "name": "Wyeth W. Wasserman", "orcid": "0000-0001-6098-6412" }, "deprecated": true, "description": "The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors.", "example": "TF0001053", "homepage": "http://www.pazar.info/", "keywords": [ "dna", "life science", "regulation", "rna" ], "mappings": { "biocontext": "PAZAR", "fairsharing": "FAIRsharing.33yggg", "integbio": "nbdc00611", "miriam": "pazar", "n2t": "pazar", "pathguide": "521", "prefixcommons": "pazar" }, "name": "Pazar Transcription Factor", "pattern": "^TF\\w+$", "preferred_prefix": "pazar", "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/pazar:$1" } ], "publications": [ { "doi": "10.1093/nar/gkn783", "pmc": "PMC2686574", "pubmed": "18971253", "title": "The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences", "year": 2008 }, { "doi": "10.1186/gb-2007-8-10-r207", "pmc": "PMC2246282", "pubmed": "17916232", "title": "PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation", "year": 2007 } ], "uri_format": "http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$1" }, "pba": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A controlled vocabulary to support the study of transcription in the primate brain", "download_obo": "https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-pba.obo", "example": "128011350", "homepage": "https://www.blueprintnhpatlas.org/", "keywords": [ "ontology" ], "name": "Primate Brain Atlas", "pattern": "^\\d+$", "preferred_prefix": "PBA", "uri_format": "https://biopragmatics.github.io/providers/pba/$1" }, "pcl": { "contact": { "email": "davidos@ebi.ac.uk", "github": "dosumis", "name": "David Osumi-Sutherland", "orcid": "0000-0002-7073-9172" }, "depends_on": [ "bfo", "chebi", "cl", "go", "nbo", "ncbitaxon", "omo", "pato", "pr", "ro", "so", "uberon" ], "description": "Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties.", "download_json": "http://purl.obolibrary.org/obo/pcl.json", "download_obo": "http://purl.obolibrary.org/obo/pcl.obo", "download_owl": "http://purl.obolibrary.org/obo/pcl.owl", "example": "0011124", "homepage": "https://github.com/obophenotype/provisional_cell_ontology", "keywords": [ "anatomy", "annotation", "cell", "cell biology", "life science", "obo", "omics", "ontology", "phenomics", "sequencing", "single-cell multimodal omics", "transcriptomics" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "PCL", "bioportal": "PCL", "fairsharing": "FAIRsharing.bfcfd0", "obofoundry": "pcl", "ols": "pcl", "ontobee": "PCL" }, "name": "Provisional Cell Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "PCL", "publications": [ { "doi": "10.1101/2021.10.10.463703", "title": "Brain Data Standards - A method for building data-driven cell-type ontologies", "year": 2021 }, { "doi": "10.1038/s41597-022-01886-2", "title": "Brain Data Standards - A method for building data-driven cell-type ontologies", "year": 2023 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/PCL_$1", "repository": "https://github.com/obophenotype/provisional_cell_ontology", "uri_format": "http://purl.obolibrary.org/obo/PCL_$1", "version": "2025-01-08" }, "pco": { "appears_in": [ "ecocore", "envo" ], "contact": { "email": "rlwalls2008@gmail.com", "github": "ramonawalls", "name": "Ramona Walls", "orcid": "0000-0001-8815-0078" }, "depends_on": [ "bfo", "caro", "envo", "go", "iao", "ncbitaxon", "pato", "ro" ], "description": "The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology.", "download_obo": "http://purl.obolibrary.org/obo/pco.obo", "download_owl": "http://purl.obolibrary.org/obo/pco.owl", "example": "0000021", "homepage": "https://github.com/PopulationAndCommunityOntology/pco", "keywords": [ "biodiversity", "community care", "ecology", "evolution", "obo", "ontology", "population genetics", "social and behavioural science" ], "license": "CC0-1.0", "mappings": { "aberowl": "PCO", "agroportal": "PCO", "biocontext": "PCO", "bioportal": "PCO", "ecoportal": "PCO", "fairsharing": "FAIRsharing.vq28qp", "obofoundry": "pco", "ols": "pco", "ontobee": "PCO" }, "name": "Population and Community Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "PCO", "publications": [ { "doi": "10.1371/journal.pone.0089606", "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/PCO_$1", "repository": "https://github.com/PopulationAndCommunityOntology/pco", "uri_format": "http://purl.obolibrary.org/obo/PCO_$1", "version": "2021-05-03" }, "pd_st": { "contact": { "email": "henrich@embl.de", "github": "ThorstenHen", "name": "Thorsten Henrich", "orcid": "0000-0002-1548-3290" }, "deprecated": true, "homepage": "http://4dx.embl.de/platy", "keywords": [ "obo", "ontology" ], "mappings": { "biocontext": "PD_ST", "obofoundry": "pd_st" }, "name": "Platynereis stage ontology", "preferred_prefix": "PD_ST", "rdf_uri_format": "http://purl.obolibrary.org/obo/PD_ST_$1", "uri_format": "http://purl.obolibrary.org/obo/PD_ST_$1" }, "pdb": { "contact": { "email": "harukin@protein.osaka-u.ac.jp", "name": "Haruki Nakamura", "orcid": "0000-0001-6690-5863" }, "description": "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.", "example": "2gc4", "example_extras": [ "157d", "9ii2" ], "homepage": "https://www.wwpdb.org/", "keywords": [ "bioinformatics", "epidemiology", "protein", "proteomics", "structural biology", "structure", "virology" ], "mappings": { "biocontext": "PDB", "edam": "1127", "fairsharing": "FAIRsharing.rs2815", "go": "PDB", "integbio": "nbdc00613", "miriam": "pdb", "n2t": "pdb", "ncbi": "PDB", "pathguide": "398", "prefixcommons": "pdbj", "re3data": "r3d100010910", "togoid": "Pdb", "uniprot": "DB-0172", "wikidata": "P638" }, "name": "PDB Structure", "pattern": "^[0-9][A-Za-z0-9]{3}$", "preferred_prefix": "pdb", "providers": [ { "code": "CURATOR_REVIEW", "description": "Proteopedia", "homepage": "http://www.proteopedia.org/", "name": "Proteopedia", "uri_format": "http://proteopedia.org/wiki/index.php/$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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Warr", "year": 2011 }, { "doi": "10.1093/database/baq021", "pmc": "PMC2997606", "pubmed": "20798081", "title": "PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan", "year": 2010 }, { "pubmed": "12099029", "title": "[Development of PDBj: Advanced database for protein structures]", "year": 2002 } ], "rdf_uri_format": "https://rdf.wwpdb.org/pdb/$1", "synonyms": [ "RCSB_PDB", "pdbe", "pdbj", "wwpdb" ], "twitter": "PDBj_en", "uri_format": "https://www.wwpdb.org/pdb?id=$1" }, "pdb-ccd": { "comment": "might be same as pdb.ligand, not sure though", "contact": { "email": "berman@rcsb.rutgers.edu", "name": "Helen Berman", "orcid": "0000-0002-3337-0660" }, "contributor_extras": [ { "email": "bmeldal@ebi.ac.uk", "github": "bmeldal-eg", "name": "Birgit Meldal", "orcid": "0000-0003-4062-6158" } ], "description": "The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. 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PEPhub uses Portable Encapsulated Projects (PEP) biological metadata standard to store, edit, and access PEPs in one place.", "example": "geo", "example_extras": [ "bedbase/gse198944", "databio/encode_batch_1", "geo/gse185244" ], "github_request_issue": 1194, "homepage": "https://pephub.databio.org/", "name": "PEPhub", "pattern": "^[A-Za-z0-9_\\-]+(/[A-Za-z0-9_\\-]+)?$", "preferred_prefix": "pephub", "publications": [ { "doi": "10.1093/gigascience/giae033", "pmc": "PMC11238423", "pubmed": "38991851", "title": "PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://pephub.databio.org/$1" }, "peptideatlas": { "contact": { "email": "edeutsch@systemsbiology.org", "github": "edeutsch", "name": "Eric W. 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Each PASS entry provides direct access to the data files submitted to PeptideAtlas.", "example": "PASS01237", "homepage": "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/PASS_Summary", "mappings": { "miriam": "peptideatlas.dataset", "n2t": "peptideatlas.dataset" }, "name": "PeptideAtlas Dataset", "pattern": "^PASS\\d{5}$", "preferred_prefix": "peptideatlas.dataset", "uri_format": "http://www.peptideatlas.org/PASS/$1" }, "perkinelmer": { "description": "Cell line collections (Providers)", "example": "SCC111", "homepage": "https://www.perkinelmer.com/", "mappings": { "cellosaurus": "PerkinElmer" }, "name": "PerkinElmer cell line collection", "preferred_prefix": "perkinelmer", "uri_format": "https://www.perkinelmer.com/searchresult?searchName=$1" }, "peroxibase": { "contact": { "email": "dunand@lrsv.ups-tlse.fr", "name": "Christophe Dunand", "orcid": "0000-0003-1637-4042" }, "description": "Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences.", "example": "5282", "homepage": "http://peroxibase.toulouse.inra.fr/", "keywords": [ "enzyme", "life science", "protein", "regulation" ], "mappings": { "biocontext": "PEROXIBASE", "fairsharing": "FAIRsharing.z1czxj", "integbio": "nbdc01869", "miriam": "peroxibase", "n2t": "peroxibase", "prefixcommons": "peroxibase", "uniprot": "DB-0072" }, "name": "Peroxibase", "pattern": "^\\d+$", "preferred_prefix": "peroxibase", "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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"10.1093/nar/gkae997", "pubmed": "39540428", "title": "The Pfam protein families database: embracing AI/ML", "year": 2024 }, { "doi": "10.1093/nar/gkaa913", "pmc": "PMC7779014", "pubmed": "33125078", "title": "Pfam: The protein families database in 2021", "year": 2021 }, { "doi": "10.1093/nar/gky995", "pmc": "PMC6324024", "pubmed": "30357350", "title": "The Pfam protein families database in 2019", "year": 2019 }, { "doi": "10.1093/nar/gkv1344", "pmc": "PMC4702930", "pubmed": "26673716", "title": "The Pfam protein families database: towards a more sustainable future", "year": 2015 }, { "doi": "10.1093/nar/gkt1223", "pmc": "PMC3965110", "pubmed": "24288371", "title": "Pfam: the protein families database", "year": 2013 }, { "doi": "10.1093/nar/gkr1065", "pmc": "PMC3245129", "pubmed": "22127870", "title": "The Pfam protein families database", "year": 2011 }, { "doi": "10.1093/nar/gkp985", "pmc": "PMC2808889", "pubmed": "19920124", "title": "The Pfam protein families database", "year": 2009 }, { "doi": "10.1093/nar/gkm960", "pmc": "PMC2238907", "pubmed": "18039703", "title": "The Pfam protein families database", "year": 2007 }, { "doi": "10.1093/nar/gkj149", "pmc": "PMC1347511", "pubmed": "16381856", "title": "Pfam: clans, web tools and services", "year": 2006 }, { "doi": "10.1093/nar/gkh121", "pmc": "PMC308855", "pubmed": "14681378", "title": "The Pfam protein families database", "year": 2004 }, { "doi": "10.1093/nar/30.1.276", "pmc": "PMC99071", "pubmed": "11752314", "title": "The Pfam protein families database", "year": 2002 }, { "doi": "10.1093/nar/28.1.263", "pmc": "PMC102420", "pubmed": "10592242", "title": "The Pfam protein families database", "year": 2000 } ], "references": [ "https://twitter.com/PfamDB/status/1555149527228813314" ], "synonyms": [ "PF" ], "twitter": "Xfam_EBI", "uri_format": "https://www.ebi.ac.uk/interpro/entry/pfam/$1" }, "pfam.clan": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": 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"keywords": [ "data management", "subject agnostic" ], "mappings": { "fairsharing": "FAIRsharing.wqsxtg", "re3data": "r3d100012385" }, "name": "Proteoform Atlas", "pattern": "^\\d+$", "preferred_prefix": "pfr", "synonyms": [ "TDR" ], "uri_format": "http://repository.topdownproteomics.org/proteoforms/$1" }, "pgdso": { "contact": { "email": "po-discuss@plantontology.org", "name": "Plant Ontology Administrators" }, "deprecated": true, "homepage": "http://www.plantontology.org", "keywords": [ "obo", "ontology" ], "mappings": { "biocontext": "PGDSO", "obofoundry": "pgdso" }, "name": "Plant Growth and Development Stage", "preferred_prefix": "PGDSO", "rdf_uri_format": "http://purl.obolibrary.org/obo/PGDSO_$1", "uri_format": "http://purl.obolibrary.org/obo/PGDSO_$1" }, "pgs": { "description": "The Polygenic Score (PGS) Catalog is an open database of PGS and the relevant metadata required for accurate application and evaluation.", "example": "PGS000018", "homepage": "http://pgscatalog.org", 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The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.", "example": "PA131", "homepage": "http://www.pharmgkb.org/", "keywords": [ "gene", "ontology", "pharmacogenomics" ], "license": "CC-BY-SA-4.0", "mappings": { "biocontext": "PHARMGKB.GENE", "biolink": "PHARMGKB.GENE", "bioportal": "PHARMGKB", "go": "PharmGKB", "miriam": "pharmgkb.gene", "n2t": "pharmgkb.gene", "prefixcommons": "pharmgkb.gene", "uniprot": "DB-0074", "wikidata": "P7001" }, "name": "PharmGKB Gene", "pattern": "^PA\\w+$", "preferred_prefix": "pharmgkb.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/pharmgkb.gene:$1" } ], "publications": [ { "doi": "10.2217/bmm.11.94", "pmc": "PMC3339046", "pubmed": "22103613", "title": "From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource", "year": 2011 }, { "doi": "10.1385/1-59259-957-5:179", "pubmed": "16100408", "title": "PharmGKB: the pharmacogenetics and pharmacogenomics knowledge base", "year": 2005 } ], "uri_format": "http://www.pharmgkb.org/gene/$1" }, "pharmgkb.pathways": { "contact": { "email": "teri.klein@stanford.edu", "github": "TeriKlein", "name": "Teri E Klein", "orcid": "0000-0001-5527-6475" }, "description": "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. \nPharmGKB Pathways are drug centric, gene based, interactive pathways which focus on candidate genes and gene groups and associated genotype and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies.", "example": "PA146123006", "homepage": "http://www.pharmgkb.org/", "keywords": [ "pathway", "pharmacogenomics" ], "license": "CC-BY-SA-4.0", "mappings": { "biocontext": "PHARMGKB.PATHWAYS", "biolink": "PHARMGKB.PATHWAYS", "edam": "2650", "miriam": "pharmgkb.pathways", "n2t": "pharmgkb.pathways", "prefixcommons": "pharmgkb.pathways", "wikidata": "P7001" }, "name": "PharmGKB", "pattern": "^PA\\d+$", "preferred_prefix": "pharmgkb.pathways", "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/pharmgkb.pathways:$1" } ], "publications": [ { "doi": "10.2217/bmm.11.94", "pmc": "PMC3339046", "pubmed": "22103613", "title": "From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource", "year": 2011 }, { "doi": "10.1038/sj.tpj.6500035", "pubmed": "11908751", "title": "Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base", "year": 2001 } ], "uri_format": "http://www.pharmgkb.org/pathway/$1" }, "pharmgkb.variant": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "SNPs and other variants that can be mapped to dbSNP.", "example": "PA166156302", "github_request_issue": 1368, "homepage": "https://www.pharmgkb.org", "license": "CC-BY-SA-4.0", "mappings": { "biolink": "PHARMGKB.VARIANT" }, "name": "PharmGKB Variant", "pattern": "^PA\\d+$", "preferred_prefix": "pharmgkb.variant", "uri_format": "https://www.pharmgkb.org/variant/$1" }, "pharmvar": { "contact": { "email": "agaedigk@cmh.edu", "name": "Andrea Gaedigk", "orcid": "0000-0001-6968-1893" }, "description": "The Pharmacogene Variation (PharmVar) Consortium is the new home for PGx gene nomenclature serving as a centralized ‘Next-Generation’ Pharmacogene Variation data repository. The major focus of PharmVar is to catalogue allelic variation of genes impacting drug metabolism, disposition and response and provide a unifying designation system (nomenclature) for the global pharmacogenetic/genomic community. Efforts are synchronized between PharmVar, the Pharmacogenomic KnowledgeBase, and the Clinical Pharmacogenetic Implementation Consortium.", "example": "CYP2A6", "homepage": "https://www.pharmvar.org", "keywords": [ "gene", "pharmacogenomics", "variant" ], "mappings": { "prefixcommons": "pharmvar" }, "name": "Pharmacogene Variation Consortium", "preferred_prefix": "pharmvar", "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/pharmvar:$1" } ], "provides": "hgnc.symbol", "publications": [ { "doi": "10.1002/cpt.910", "pmc": "PMC5836850", "pubmed": "29134625", "title": "The Pharmacogene Variation (PharmVar) Consortium: Incorporation of the Human Cytochrome P450 (CYP) Allele Nomenclature Database", "year": 2017 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.pharmvar.org/gene/$1" }, "phenolexplorer": { "description": "Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis.", "example": "75", "homepage": "http://www.phenol-explorer.eu/foods/", "mappings": { "biocontext": "PHENOLEXPLORER", "miriam": "phenolexplorer", "n2t": "phenolexplorer", "re3data": "r3d100012197" }, "name": "Phenol-Explorer", "pattern": "^\\d+$", "preferred_prefix": "phenolexplorer", "uri_format": "http://phenol-explorer.eu/foods/$1" }, "phenx": { "contact": { "email": "yingqin@rti.org", "name": "PhenX Admin" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A web-based catalog of recommended measurement protocols selected by experts to include in studies with human participants.", "download_owl": "http://aber-owl.net/media/ontologies/PHENX/16/phenx.owl", "example": "130502", "github_request_issue": 503, "homepage": "https://www.phenxtoolkit.org/", "keywords": [ "biomedical science", "disease", "environmental science", "exposure", "life science", "ontology", "phenotype" ], "mappings": { "aberowl": "PHENX", "bioportal": "PHENX", "fairsharing": "FAIRsharing.y5jcwa", "integbio": "nbdc02244" }, "name": "PhenX Toolkit", "pattern": "^\\d+$", "preferred_prefix": "phenx", "publications": [ { "doi": "10.1038/gim.2016.199", "pmc": "PMC5507752", "pubmed": "28079902", "title": "PhenX measures for phenotyping rare genetic conditions", "year": 2017 }, { "doi": "10.1093/aje/kwr193", "pmc": "PMC3141081", "pubmed": "21749974", "title": "The PhenX Toolkit: get the most from your measures", "year": 2011 }, { "doi": "10.1097/mol.0b013e3283377395", "pmc": "PMC8038872", "pubmed": "20154612", "title": "PhenX: a toolkit for interdisciplinary genetics research", "year": 2010 } ], "synonyms": [ "phenxtoolkit" ], "uri_format": "https://www.phenxtoolkit.org/protocols/view/$1" }, "phipo": { "contact": { "email": "alayne.cuzick@rothamsted.ac.uk", "github": "CuzickA", "name": "Alayne Cuzick", "orcid": "0000-0001-8941-3984" }, "depends_on": [ "pato" ], "description": "Ontology of species-neutral phenotypes observed in pathogen-host interactions.", "download_obo": "http://purl.obolibrary.org/obo/phipo.obo", "download_owl": "http://purl.obolibrary.org/obo/phipo.owl", "example": "0000001", "homepage": "https://github.com/PHI-base/phipo", "keywords": [ "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "PHIPO", "bioportal": "PHIPO", "obofoundry": "phipo", "ols": "phipo", "ontobee": "PHIPO" }, "name": "Pathogen Host Interaction Phenotype Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "PHIPO", "publications": [ { "doi": "10.1093/nar/gkab1037", "pmc": "PMC8728202", "pubmed": "34788826", "title": "PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions", "year": 2022 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/PHIPO_$1", "repository": "https://github.com/PHI-base/phipo", "uri_format": "http://purl.obolibrary.org/obo/PHIPO_$1", "version": "2024-08-29" }, "phosphopoint.kinase": { "description": "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information.", "example": "AURKA", "homepage": "http://kinase.bioinformatics.tw/", "mappings": { "biocontext": "PHOSPHOPOINT.KINASE", "miriam": "phosphopoint.kinase", "n2t": "phosphopoint.kinase" }, "name": "PhosphoPoint Kinase", "pattern": "^\\w+$", "preferred_prefix": "phosphopoint.kinase", "uri_format": "http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$1&drawing=0&sorting=0&kinome=1" }, "phosphopoint.protein": { "deprecated": true, "description": "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references phosphoprotein information.", "example": "AURKA", "homepage": "http://kinase.bioinformatics.tw/", "mappings": { "biocontext": "PHOSPHOPOINT.PROTEIN", "miriam": "phosphopoint.protein", "n2t": "phosphopoint.protein" }, "name": "PhosphoPoint Phosphoprotein", "pattern": "^\\w+$", "preferred_prefix": "phosphopoint.protein", "uri_format": "http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$1&drawing=0&sorting=0&kinome=0" }, "phosphosite.curation": { "contributor": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to curation records that collect information extracted from specific publications.", "example": "34665743", "github_request_issue": 1136, "homepage": "https://www.phosphosite.org", "name": "PhosphoSite Curation", "pattern": "^\\d+$", "preferred_prefix": "phosphosite.curation", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.phosphosite.org/curatedInfoAction.action?record=$1" }, "phosphosite.protein": { "description": "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database.", "example": "12300", "homepage": "http://www.phosphosite.org/homeAction.do", "mappings": { "biocontext": "PHOSPHOSITE.PROTEIN", "miriam": "phosphosite.protein", "n2t": "phosphosite.protein" }, "name": "PhosphoSite Protein", "pattern": "^\\d{5}$", "preferred_prefix": "phosphosite.protein", "uri_format": "http://www.phosphosite.org/proteinAction.do?id=$1" }, "phosphosite.residue": { "description": "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to residue-level information, providing a information about a single modification position in a specific protein sequence.", "example": "2842", "homepage": "http://www.phosphosite.org/homeAction.do", "mappings": { "biocontext": "PHOSPHOSITE.RESIDUE", "miriam": "phosphosite.residue", "n2t": "phosphosite.residue" }, "name": "PhosphoSite Residue", "pattern": "^\\d+$", "preferred_prefix": "phosphosite.residue", "uri_format": "http://www.phosphosite.org/siteAction.do?id=$1" }, "phosphosite.sitegroup": { "comment": "Potentially could use a URI format like https://www.phosphosite.org/siteGroupAction.action?protOrg=1156&id=$1, but it's not obvious what the protOrg does.", "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "Site groups are orthologous positions in human, mouse, rat, etc. where phosphorylations or other PTMs occur.", "example": "447860", "github_request_issue": 432, "homepage": "https://www.phosphosite.org", "keywords": [ "biochemistry", "grouping", "post-translational modification" ], "name": "PhosphoSite Site Group", "pattern": "^\\d+$", "preferred_prefix": "phosphosite.sitegroup", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } }, "phrr": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Philippine Health Research Registry (PHRR), managed by the Philippine Council for Health Research and Development, is a tool for good governance to promote transparency and accountability in health research. PHRR is a publicly accessible database on newly approved health researches. It includes clinical trials and non-clinical studies conducted in the Philippines. The registry is compliant with the World Health Organization (WHO) standard for clinical trials registry. [from website]", "example": "4195", "homepage": "https://registry.healthresearch.ph", "name": "Philippine Health Research Registry", "preferred_prefix": "phrr", "uri_format": "https://registry.healthresearch.ph/index.php/registry?view=research&layout=details&cid=$1" }, "phylomedb": { "contact": { "email": "toni.gabaldon@crg.eu", "github": "tgabaldon", "name": "Toni Gabaldón", "orcid": "0000-0003-0019-1735" }, "description": "PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins.", "example": "Phy000CLXM_RAT", "homepage": "http://phylomedb.org/", "keywords": [ "genome", "life science", "phylogenetics", "phylogenomics", "phylogeny", "protein", "taxonomy" ], "mappings": { "biocontext": "PHYLOMEDB", "fairsharing": "FAIRsharing.7hxxc4", "integbio": "nbdc01764", "miriam": "phylomedb", "n2t": "phylomedb", "prefixcommons": "phylomedb", "uniprot": "DB-0144" }, "name": "PhylomeDB", "pattern": "^\\w+$", "preferred_prefix": "phylomedb", "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/phylomedb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkab966", "pmc": "PMC8728271", "pubmed": "34718760", "title": "PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies", "year": 2022 }, { "doi": "10.1093/nar/gkt1177", "pmc": "PMC3964985", "pubmed": "24275491", "title": "PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome", "year": 2013 }, { "doi": "10.1093/nar/gkq1109", "pmc": "PMC3013701", "pubmed": "21075798", "title": "PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions", "year": 2010 }, { "doi": "10.1093/nar/gkm899", "pmc": "PMC2238872", "pubmed": "17962297", "title": "PhylomeDB: a database for genome-wide collections of gene phylogenies", "year": 2007 } ], "twitter": "phylomedb", "uri_format": "http://phylomedb.org/?seqid=$1" }, "phytozome.locus": { "description": "Phytozome is a project to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. This collection references locus information.", "example": "Glyma0021s00410", "homepage": "http://www.phytozome.net/", "mappings": { "biocontext": "PHYTOZOME.LOCUS", "miriam": "phytozome.locus", "n2t": "phytozome.locus", "ncbi": "Phytozome" }, "name": "Plant Genome Network", "pattern": "^[A-Za-z0-9]+$", "preferred_prefix": "phytozome.locus", "synonyms": [ "JGI Phytozome" ], "uri_format": "http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$1" }, "pibase": { "description": "PIBASE is a collection of all protein structural interfaces extracted from the Protein Data Bank and PQS structure databases. Both chain-chain and domain-domain (SCOP and CATH definitions) interfaces are detected.", "example": "21692", "homepage": "http://salilab.org/pibase", "keywords": [ "protein", "structure" ], "mappings": { "pathguide": "183", "prefixcommons": "pibase" }, "name": "Database of structurally defined protein interfaces", "preferred_prefix": "pibase", "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/pibase:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://modbase.compbio.ucsf.edu/pibase-cgi/get_details.pl?object_type=complexes&bdp_id=$1" }, "pictar": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "example": "hsa-let-7a", "homepage": "https://pictar.mdc-berlin.de/", "name": "PicTar", "preferred_prefix": "pictar", "synonyms": [ "pictar-vert" ] }, "pid.pathway": { "contact": { "email": "schaefec@mail.nih.gov", "name": "Carl F. Schaefer", "orcid": "0000-0002-5941-3390" }, "deprecated": true, "description": "The Pathway Interaction Database is a highly-structured, curated collection of information about known human biomolecular interactions and key cellular processes assembled into signaling pathways. This datatype provides access to pathway information.", "example": "eff796f3-6195-11e5-8ac5-06603eb7f303", "homepage": "https://www.ndexbio.org/index.html#/networkset/8a2d7ee9-1513-11e9-bb6a-0ac135e8bacf", "keywords": [ "gene", "life science", "pathway", "protein", "small molecule" ], "mappings": { "biocontext": "PID.PATHWAY", "edam": "2344", "fairsharing": "FAIRsharing.ncgh1j", "miriam": "pid.pathway", "n2t": "pid.pathway", "pathguide": "119", "prefixcommons": "pid" }, "name": "NCI Pathway Interaction Database: Pathway", "pattern": "^\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b$", "preferred_prefix": "pid.pathway", "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/pid:$1" } ], "publications": [ { "doi": "10.1093/nar/gkn653", "pmc": "PMC2686461", "pubmed": "18832364", "title": "PID: the Pathway Interaction Database", "year": 2008 } ], "synonyms": [ "pid" ], "uri_format": "http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1" }, "pigqtldb": { "description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references pig QTLs.", "example": "14", "homepage": "https://www.animalgenome.org/QTLdb", "keywords": [ "dna", "genome" ], "mappings": { "biocontext": "PIGQTLDB", "miriam": "pigqtldb", "n2t": "pigqtldb", "prefixcommons": "pigqtldb" }, "name": "Animal Genome Pig QTL", "part_of": "qtldb", "pattern": "^\\d+$", "preferred_prefix": "pigqtldb", "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/pigqtldb:$1" } ], "uri_format": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1" }, "pii": { "appears_in": [ "pubmed" ], "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A combination of an ISBN and local unique identifier for articles and other published works. Please see the [Wikipedia page](https://en.wikipedia.org/wiki/Publisher_Item_Identifier) for a detailed explanation. Some PIIs are used as the local identifiers in DOIs, such as https://doi.org/10.1136/S0003-4967(24)38620-0.", "example": "S0960-9822(11)01319-4", "example_extras": [ "B0-123-12345-1/12345-1" ], "github_request_issue": 1447, "homepage": "https://en.wikipedia.org/wiki/Publisher_Item_Identifier", "name": "Publisher Item Identifier", "pattern": "^((S\\d{4}-\\d{4}\\(\\d{2}\\)\\d{5})|(B\\d-\\d{3}-\\d{5}-\\d/\\d{5}))-[\\d|X]$", "preferred_prefix": "pii" }, "pina": { "contact": { "email": "wujm@bjmu.edu.cn", "name": "Jianmin Wu", "orcid": "0000-0002-8876-128X" }, "description": "Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms.", "example": "Q13485", "homepage": "http://cbg.garvan.unsw.edu.au/pina/", "keywords": [ "data visualization", "life science" ], "mappings": { "biocontext": "PINA", "fairsharing": "FAIRsharing.7q4gsz", "miriam": "pina", "n2t": "pina", "pathguide": "348" }, "name": "Protein Interaction Network Analysis", "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])$", "preferred_prefix": "pina", "provides": "uniprot", "publications": [ { "doi": "10.1093/nar/gkaa1075", "pmc": "PMC7779002", "pubmed": "33231689", "title": "PINA 3.0: mining cancer interactome", "year": 2021 }, { "doi": "10.1093/nar/gkr967", "pmc": "PMC3244997", "pubmed": "22067443", "title": "PINA v2.0: mining interactome modules", "year": 2011 }, { "doi": "10.1038/nmeth.1282", "pubmed": "19079255", "title": "Integrated network analysis platform for protein-protein interactions", "year": 2008 } ], "uri_format": "http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?showExtend=null&ac=$1" }, "piroplasma": { "description": "PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", "example": "TA14985", "homepage": "http://piroplasmadb.org/", "mappings": { "biocontext": "PIROPLASMA", "miriam": "piroplasma", "n2t": "piroplasma" }, "name": "PiroplasmaDB", "pattern": "^TA\\d+$", "preferred_prefix": "piroplasma", "uri_format": "http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1" }, "pirsf": { "contact": { "email": "wuc@udel.edu", "name": "Cathy H. Wu", "orcid": "0000-0001-6379-8601" }, "description": "The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.", "example": "PIRSF000100", "homepage": "https://pir.georgetown.edu/", "keywords": [ "life science", "protein", "proteomics", "structure" ], "mappings": { "biocontext": "PIRSF", "edam": "1136", "fairsharing": "FAIRsharing.vssch2", "go": "PIRSF", "miriam": "pirsf", "n2t": "pirsf", "prefixcommons": "pirsf", "uniprot": "DB-0079" }, "name": "PIR Superfamily Classification System", "pattern": "^PIRSF\\d{6}$", "preferred_prefix": "pirsf", "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/pirsf:$1" } ], "publications": [ { "doi": "10.1093/nar/gkh097", "pmc": "PMC308831", "pubmed": "14681371", "title": "PIRSF: family classification system at the Protein Information Resource", "year": 2004 } ], "uri_format": "https://pir.georgetown.edu/cgi-bin/ipcSF?id=$1" }, "pkdb": { "contact": { "email": "konigmatt@googlemail.com", "name": "Matthias König", "orcid": "0000-0003-1725-179X" }, "description": "PK-DB an open database for pharmacokinetics information from clinical trials as well as pre-clinical research. The focus of PK-DB is to provide high-quality pharmacokinetics data enriched with the required meta-information for computational modeling and data integration. ", "example": "PKDB00198", "homepage": "https://www.hu-berlin.de/?set_language=en&cl=en", "keywords": [ "clinical studies", "clinical veterinary medicine", "life science", "personalized medicine", "pharmacogenomics", "pharmacology", "preclinical studies" ], "mappings": { "fairsharing": "FAIRsharing.AYegqK", "miriam": "pkdb" }, "name": "PK-DB", "pattern": "^PKDB[0-9]{5}$", "preferred_prefix": "pkdb", "publications": [ { "doi": "10.1093/nar/gkaa990", "pmc": "PMC7779054", "pubmed": "33151297", "title": "PK-DB: pharmacokinetics database for individualized and stratified computational modeling", "year": 2021 } ], "repository": "https://github.com/matthiaskoenig/pkdb/issues", "uri_format": "https://pk-db.com/data/$1" }, "plana": { "appears_in": [ "planp" ], "contact": { "email": "smr@stowers.org", "github": "srobb1", "name": "Sofia Robb", "orcid": "0000-0002-3528-5267" }, "depends_on": [ "ro", "uberon" ], "description": "PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea.", "download_obo": "http://purl.obolibrary.org/obo/plana.obo", "download_owl": "http://purl.obolibrary.org/obo/plana.owl", "example": "0000001", "homepage": "https://github.com/obophenotype/planaria-ontology", "keywords": [ "anatomy", "developmental biology", "life science", "obo", "ontology", "organ", "organelle", "tissue" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "PLANA", "biocontext": "PLANA", "bioportal": "PLANA", "fairsharing": "FAIRsharing.g1qrqs", "obofoundry": "plana", "ols": "plana", "ontobee": "PLANA" }, "name": "Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "PLANA", "publications": [ { "doi": "10.1242/dev.196097", "pmc": "PMC8353266", "pubmed": "34318308", "title": "Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms", "year": 2021 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/PLANA_$1", "repository": "https://github.com/obophenotype/planaria-ontology", "uri_format": "http://purl.obolibrary.org/obo/PLANA_$1", "version": "2023-03-13" }, "planp": { "contact": { "email": "smr@stowers.org", "github": "srobb1", "name": "Sofia Robb", "orcid": "0000-0002-3528-5267" }, "depends_on": [ "go", "pato", "plana", "ro" ], "description": "Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea.", "download_obo": "http://purl.obolibrary.org/obo/planp.obo", "download_owl": "http://purl.obolibrary.org/obo/planp.owl", "example": "0000001", "homepage": "https://github.com/obophenotype/planarian-phenotype-ontology", "keywords": [ "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "PLANP", "bioportal": "PLANP", "obofoundry": "planp", "ols": "planp", "ontobee": "PLANP" }, "name": "Planarian Phenotype Ontology", "pattern": "^\\d+$", "preferred_prefix": "PLANP", "rdf_uri_format": "http://purl.obolibrary.org/obo/PLANP_$1", "repository": "https://github.com/obophenotype/planarian-phenotype-ontology", "uri_format": "http://purl.obolibrary.org/obo/PLANP_$1", "version": "2020-03-28" }, "planttfdb": { "contact": { "email": "gaog@mail.cbi.pku.edu.cn", "github": "gao-ge", "name": "Ge Gao", "orcid": "0000-0001-6470-8815" }, "description": "The Plant TF database (PlantTFDB) systematically identifies transcription factors for plant species. It includes annotation for identified TFs, including information on expression, regulation, interaction, conserved elements, phenotype information. It also provides curated descriptions and cross-references to other life science databases, as well as identifying evolutionary relationship among identified factors.", "example": "Ath_AT1G01030.1", "homepage": "http://planttfdb.cbi.pku.edu.cn", "keywords": [ "dna", "gene", "life science", "protein", "regulation", "rna", "small molecule" ], "mappings": { "biocontext": "PLANTTFDB", "fairsharing": "FAIRsharing.ex3fqk", "miriam": "planttfdb", "n2t": "planttfdb", "pathguide": "497", "prefixcommons": "planttfdb", "re3data": "r3d100011301" }, "name": "Plant Transcription Factor Database", "pattern": "^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\\._\\-#]*)$", "preferred_prefix": "planttfdb", "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/planttfdb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkw982", "pmc": "PMC5210657", "pubmed": "27924042", "title": "PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants", "year": 2016 }, { "doi": "10.1093/molbev/msv058", "pmc": "PMC4476157", "pubmed": "25750178", "title": "An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors", "year": 2015 }, { "doi": "10.1093/nar/gkt1016", "pmc": "PMC3965000", "pubmed": "24174544", "title": "PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors", "year": 2013 } ], "uri_format": "http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$1" }, "plasmodb": { "contact": { "email": "oharb@upenn.edu", "github": "ramobrah", "name": "Omar S. Harb", "orcid": "0000-0003-4446-6200" }, "description": "AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", "example": "PF11_0344", "homepage": "http://plasmodb.org/plasmo/", "keywords": [ "genome", "genomics", "infectious disease medicine" ], "mappings": { "biocontext": "PLASMODB", "fairsharing": "FAIRsharing.g4n8sw", "go": "PlasmoDB", "integbio": "nbdc01783", "miriam": "plasmodb", "n2t": "plasmodb", "ncbi": "ApiDB_PlasmoDB", "pathguide": "514", "prefixcommons": "plasmodb", "re3data": "r3d100011569" }, "name": "PlasmoDB", "pattern": "^\\w+$", "preferred_prefix": "plasmodb", "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/plasmodb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkn814", "pmc": "PMC2686598", "pubmed": "18957442", "title": "PlasmoDB: a functional genomic database for malaria parasites", "year": 2008 } ], "synonyms": [ "ApiDB_PlasmoDB" ], "twitter": "VEuPathDB", "uri_format": "http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1" }, "plo": { "contact": { "email": "mb4@sanger.ac.uk", "name": "Matt Berriman" }, "deprecated": true, "homepage": "http://www.sanger.ac.uk/Users/mb4/PLO/", "keywords": [ "obo", "ontology" ], "mappings": { "biocontext": "PLO", "obofoundry": "plo" }, "name": "Plasmodium Life Cycle", "preferred_prefix": "PLO", "rdf_uri_format": "http://purl.obolibrary.org/obo/PLO_$1", "uri_format": "http://purl.obolibrary.org/obo/PLO_$1" }, "plos": { "contact": { "email": "subjectareas@plos.org", "name": "PLOS Taxonomy Team" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontologization of Public Library of Science (PLOS) journal keywords and topics. It's not clear how the IDs correspond to the actual pages. Appears in ADCAD.", "example": "1443", "github_request_issue": 1318, "homepage": "http://journals.plos.org", "keywords": [ "ontology", "publication", "subject agnostic" ], "mappings": { "aberowl": "PLOSTHES", "bioportal": "PLOSTHES", "fairsharing": "FAIRsharing.2ndf9r" }, "name": "PLOS Thesaurus", "pattern": "^\\d+$", "preferred_prefix": "plos", "synonyms": [ "PLOSTHES" ], "uri_format": "http://localhost/plosthes.2017-1#$1" }, "pmap.cutdb": { "contact": { "email": "adam@burnham.org", "name": "Adam Godzik", "orcid": "0000-0002-2425-852X" }, "deprecated": true, "description": "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites).", "example": "25782", "homepage": "http://cutdb.burnham.org", "keywords": [ "enzyme", "pathway", "protein" ], "mappings": { "biocontext": "PMAP.CUTDB", "miriam": "pmap.cutdb", "n2t": "pmap.cutdb", "prefixcommons": "pmap.cutdb" }, "name": "CutDB", "pattern": "^\\d+$", "preferred_prefix": "pmap.cutdb", "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/pmap.cutdb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkl813", "pmc": "PMC1669773", "pubmed": "17142225", "title": "CutDB: a proteolytic event database", "year": 2006 } ], "uri_format": "http://cutdb.burnham.org/relation/show/$1" }, "pmap.substratedb": { "contact": { "email": "eroshkin@burnham.org", "name": "Alexey M. Eroshkin", "orcid": "0000-0003-2023-4608" }, "description": "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates.", "example": "1915", "homepage": "http://substrate.burnham.org/", "keywords": [ "domain", "protein", "reaction" ], "mappings": { "biocontext": "PMAP.SUBSTRATEDB", "miriam": "pmap.substratedb", "n2t": "pmap.substratedb", "prefixcommons": "pmap.substratedb" }, "name": "SubstrateDB", "pattern": "^\\d+$", "preferred_prefix": "pmap.substratedb", "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/pmap.substratedb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkn683", "pmc": "PMC2686432", "pubmed": "18842634", "title": "PMAP: databases for analyzing proteolytic events and pathways", "year": 2008 } ], "uri_format": "http://substrate.burnham.org/protein/annotation/$1/html" }, "pmc": { "comment": "Note that the Europe PMC instance redirects canonical local unique identifiers from https://europepmc.org/articles/PMC3084216 to https://europepmc.org/article/PMC/3084216. However, this is an implementation detail and does not reflect the official format of a PMC identifier, which indeed does include `PMC` at the beginning of the local unique identifier", "contact": { "email": "beck@ncbi.nlm.nih.gov", "github": "jeffbeckncbi", "name": "Jeff Beck", "orcid": "0000-0002-1798-9797" }, "description": "PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature.", "example": "PMC3084216", "example_extras": [ "PMC7418728", "PMC7418728.1", "PMC7418728.2" ], "homepage": "http://europepmc.org/", "keywords": [ "bibliography", "centrally registered identifier", "knowledge and information systems" ], "mappings": { "biocontext": "PMCID", "biolink": "PMC", "cellosaurus": "PMCID", "fairsharing": "FAIRsharing.2b4316", "go": "PMCID", "miriam": "pmc", "n2t": "pmc", "prefixcommons": "pmc", "togoid": "Pmc", "wikidata": "P932" }, "name": "PubMed Central", "pattern": "^PMC\\d+(\\.\\d+)?$", "preferred_prefix": "pmc", "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/pmc:$1" }, { "code": "ncbi.pmc", "description": "PubMed Central", "homepage": "https://www.ncbi.nlm.nih.gov/pmc/", "name": "PubMed Central", "uri_format": "https://www.ncbi.nlm.nih.gov/pmc/articles/$1" } ], "publications": [ { "doi": "10.1093/nar/gkr1184", "pmc": "PMC3245031", "pubmed": "22140104", "title": "Database resources of the National Center for Biotechnology Information", "year": 2011 }, { "doi": "10.1093/nar/gkq1172", "pmc": "PMC3013733", "pubmed": "21097890", "title": "Database resources of the National Center for Biotechnology Information", "year": 2010 } ], "references": [ "https://github.com/biopragmatics/bioregistry/issues/965" ], "synonyms": [ "PMC", "PMCID" ], "uri_format": "http://europepmc.org/articles/$1" }, "pmdb": { "description": "The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques.", "example": "PM0012345", "homepage": "https://bioinformatics.cineca.it/PMDB/", "keywords": [ "protein", "structural biology", "structure" ], "mappings": { "biocontext": "PMDB", "fairsharing": "FAIRsharing.wkaakq", "miriam": "pmdb", "n2t": "pmdb", "prefixcommons": "pmdb" }, "name": "Protein Model Database", "pattern": "^PM\\d{7}$", "preferred_prefix": "pmdb", "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/protonet.cluster:$1" } ], "publications": [ { "doi": "10.1110/ps.062185706", "pmc": "PMC2242553", "pubmed": "16672244", "title": "Functional annotation prediction: all for one and one for all", "year": 2006 } ], "uri_format": "http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1" }, "protonet.proteincard": { "contact": { "email": "michall@cc.huji.ac.il", "github": "LinialLab", "name": "Michal Linial", "orcid": "0000-0002-9357-4526" }, "description": "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information.", "example": "16941567", "homepage": "http://www.protonet.cs.huji.ac.il/", "keywords": [ "protein" ], "mappings": { "biocontext": "PROTONET.PROTEINCARD", "miriam": "protonet.proteincard", "n2t": "protonet.proteincard", "prefixcommons": "protonet.proteincard" }, "name": "ProtoNet ProteinCard", "pattern": "^\\d+$", "preferred_prefix": "protonet.proteincard", "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/protonet.proteincard:$1" } ], "publications": [ { "doi": "10.1110/ps.062185706", "pmc": "PMC2242553", "pubmed": "16672244", "title": "Functional annotation prediction: all for one and one for all", "year": 2006 } ], "uri_format": "http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1" }, "prov": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The namespace name http://www.w3.org/ns/prov# is intended for use with the PROV family of documents that support the interchange of provenance on the web.", "download_owl": "http://aber-owl.net/media/ontologies/PROV/1/prov.owl", "example": "Activity", "homepage": "https://www.w3.org/ns/prov", "keywords": [ "ontology", "w3c rec" ], "mappings": { "aberowl": "PROV", "biocontext": "prov", "biolink": "prov", "lov": "prov", "ols": "prov", "zazuko": "prov" }, "name": "PROV Namespace", "preferred_prefix": "prov", "uri_format": "http://www.w3.org/ns/prov#$1" }, "pscdb": { "contact": { "email": "mota@i.nagoya-u.ac.jp", "name": "Motonori Ota", "orcid": "0000-0001-9090-668X" }, "description": "The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion.", "example": "051", "homepage": "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/index.html", "keywords": [ "life science" ], "mappings": { "biocontext": "PSCDB", "fairsharing": "FAIRsharing.3d4jx0", "integbio": "nbdc01636", "miriam": "pscdb", "n2t": "pscdb" }, "name": "Protein Structural Change Database", "pattern": "^\\d+$", "preferred_prefix": "pscdb", "publications": [ { "doi": "10.1093/nar/gkr966", "pmc": "PMC3245091", "pubmed": "22080505", "title": "PSCDB: a database for protein structural change upon ligand binding", "year": 2011 }, { "doi": "10.1016/j.jmb.2011.02.058", "pubmed": "21376729", "title": "Classification and annotation of the relationship between protein structural change and ligand binding", "year": 2011 } ], "uri_format": "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html" }, "psdo": { "contact": { "email": "zachll@umich.edu", "github": "zachll", "name": "Zach Landis-Lewis", "orcid": "0000-0002-9117-9338" }, "depends_on": [ "bfo", "iao", "ro", "stato" ], "description": "Performance Summary Display Ontology (PSDO) is an application ontology about motivating information in performance summaries and the visual and textual entities that are used to communicate about performance. Motivating information includes performance comparisons and changes that motivate improvement or sustainment, such as improvement towards a goal, loss of high performer status, or the presence of a performance gap. Visual and textual entities include charts, tables, and graphs that display performance information. PSDO's domain focus is healthcare organizations that use clinical quality dashboards and feedback interventions for healthcare professionals and teams. Performance information is commonly about the quality of care and health outcomes that have been derived from clinical data using performance measures (aka metrics, process indicators, quality measures, etc). PSDO uses Basic Formal Ontology as its upper level ontology. This work is supported by the NIH, National Library of Medicine (1K01LM012528-01, 1R01LM013894-01).\n\nLandis-Lewis Z, Stansbury C, Rincón J, Gross C. Performance Summary Display Ontology: Feedback intervention content, delivery, and interpreted information. International Conference on Biomedical Ontology 2022 (ICBO 2022). https://icbo-conference.github.io/icbo2022/papers/ICBO-2022_paper_2172.pdf", "download_owl": "http://purl.obolibrary.org/obo/psdo.owl", "example": "0000055", "homepage": "https://github.com/Display-Lab/psdo", "keywords": [ "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "PSDO", "bioportal": "PSDO", "obofoundry": "psdo", "ols": "psdo", "ontobee": "PSDO" }, "name": "Performance Summary Display Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "PSDO", "rdf_uri_format": "http://purl.obolibrary.org/obo/PSDO_$1", "repository": "https://github.com/Display-Lab/psdo", "uri_format": "http://purl.obolibrary.org/obo/PSDO_$1", "version": "1.0.1" }, "pseudogene": { "contact": { "email": "mark@gersteinlab.org", "name": "Mark Gerstein", "orcid": "0000-0002-9746-3719" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This site contains a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase.", "example": "PGOHUM00000289843", "homepage": "http://www.pseudogene.org", "keywords": [ "gene", "ontology" ], "mappings": { "bioportal": "pseudo", "integbio": "nbdc00178", "prefixcommons": "pseudogene" }, "name": "PseudoGene", "preferred_prefix": "pseudogene", "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/pseudogene:$1" } ], "synonyms": [ "pseudogene.org" ], "uri_format": "http://tables.pseudogene.org/[?species_name]/$1" }, "pseudomonas": { "description": "The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation.", "example": "PSEEN0001", "homepage": "http://www.pseudomonas.com/", "mappings": { "biocontext": "PSEUDOMONAS", "miriam": "pseudomonas", "n2t": "pseudomonas" }, "name": "Pseudomonas Genome Database", "pattern": "^P\\w+$", "preferred_prefix": "pseudomonas", "uri_format": "http://www.pseudomonas.com/feature/show/?locus_tag=$1" }, "psipar": { "banana": "PAR", "comment": "This resource is no longer loaded on XML and the sourceforge link from the HUPO website to the psi-par.obo artifact is dead.", "deprecated": true, "description": "Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms.", "example": "0116", "homepage": "https://www.psidev.info/psi-par", "mappings": { "biocontext": "PSIPAR", "miriam": "psipar", "n2t": "psipar" }, "name": "Protein Affinity Reagents", "pattern": "^\\d+$", "preferred_prefix": "psipar", "uri_format": "https://www.ebi.ac.uk/ontology-lookup/?termId=PAR:$1" }, "pso": { "contact": { "email": "cooperl@oregonstate.edu", "github": "cooperl09", "name": "Laurel Cooper", "orcid": "0000-0002-6379-8932" }, "depends_on": [ "ro" ], "description": "The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter.", "download_obo": "http://purl.obolibrary.org/obo/pso.obo", "download_owl": "http://purl.obolibrary.org/obo/pso.owl", "example": "0000013", "homepage": "https://github.com/Planteome/plant-stress-ontology", "keywords": [ "hospital", "medical informatics", "monitoring", "obo", "occupational medicine", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "PSO", "agroportal": "PSO", "bioportal": "PSO", "fairsharing": "FAIRsharing.dyj433", "obofoundry": "pso", "ols": "pso", "ontobee": "PSO" }, "name": "Plant Stress Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "PSO", "publications": [ { "doi": "10.1093/nar/gkx1152", "pmc": "PMC5753347", "pubmed": "29186578", "title": "The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics", "year": 2018 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/PSO_$1", "repository": "https://github.com/Planteome/plant-stress-ontology", "uri_format": "http://purl.obolibrary.org/obo/PSO_$1", "version": "2023-11-14" }, "pspub": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Documentation of the Phenoscape Curation Workflow", "homepage": "https://wiki.phenoscape.org/wiki/Curation_workflow", "name": "Phenoscape Publication", "preferred_prefix": "pspub" }, "psskb": { "contact": { "email": "kaysheva1@gmail.com", "name": "Anna L. Kaysheva", "orcid": "0000-0003-4472-2016" }, "contributor": { "email": "palayoor.n@northeastern.edu", "github": "nalikapalayoor", "name": "Nalika Palayoor", "orcid": "0009-0008-8406-631X" }, "description": "PSSKB allows researchers to model post translational modifications and amino acid substitutions in proteins, providing 3D structural representations. Identifiers represent protein motifs on which PSSKB provides data.", "example": "2VM6_A55_A135", "github_request_issue": 1398, "homepage": "https://psskb.org/", "name": "Protein Structure and Stability Knowledge Base", "pattern": "^[A-Za-z0-9_]+$", "preferred_prefix": "psskb", "publications": [ { "doi": "10.1002/jcc.70046", "pubmed": "39876062", "title": "PSSKB: A Web Application to Study Protein Structures", "year": 2025 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://psskb.org/motif/card/$1" }, "pubchem.bioassay": { "contact": { "email": "pruitt@ncbi.nlm.nih.gov", "name": "Kim Dixon Pruitt", "orcid": "0000-0001-7950-1374" }, "description": "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem bioassay archives active compounds and bioassay results.", "example": "1018", "homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay", "keywords": [ "small molecule" ], "mappings": { "biocontext": "PUBCHEM.BIOASSAY", "edam": "2638", "go": "PubChem_BioAssay", "integbio": "nbdc00640", "miriam": "pubchem.bioassay", "n2t": "pubchem.bioassay", "prefixcommons": "pubchem.bioassay" }, "name": "NCBI PubChem database of bioassay records", "part_of": "pubchem", "pattern": "^\\d+$", "preferred_prefix": "pubchem.bioassay", "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/pubchem.bioassay:$1" } ], "publications": [ { "doi": "10.1093/nar/gkl1031", "pmc": "PMC1781113", "pubmed": "17170002", "title": "Database resources of the National Center for Biotechnology Information", "year": 2006 } ], "synonyms": [ "pubchem.aid", "pubchem.assay" ], "twitter": "pubchem", "uri_format": "https://pubchem.ncbi.nlm.nih.gov/bioassay/$1" }, "pubchem.cell": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Cell Lines in PubChem", "example": "31", "homepage": "https://pubchem.ncbi.nlm.nih.gov", "keywords": [ "bioactivities", "cell lines", "chemistry" ], "name": "PubChem Cell Line", "part_of": "pubchem", "pattern": "^\\d+$", "preferred_prefix": "pubchem.cell", "twitter": "pubchem", "uri_format": "https://pubchem.ncbi.nlm.nih.gov/cell/$1" }, "pubchem.classification": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The PubChem Classification Browser allows you to browse the distribution of PubChem data among nodes in the hierarchy of interest, thereby providing an aggregate view of PubChem data. It also allows you to search for PubChem records annotated with the desired hierarchy/term, providing a powerful way to quickly find the subset of PubChem records.", "example": "87", "homepage": "https://pubchem.ncbi.nlm.nih.gov/classification/", "keywords": [ "chemistry" ], "name": "PubChem Classification", "part_of": "pubchem", "pattern": "^\\d+$", "preferred_prefix": "pubchem.classification", "twitter": "pubchem", "uri_format": "https://pubchem.ncbi.nlm.nih.gov/classification/#hid=$1" }, "pubchem.compound": { "contact": { "email": "bolton@ncbi.nlm.nih.gov", "name": "Evan E Bolton", "orcid": "0000-0002-5959-6190" }, "description": "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records.", "example": "100101", "homepage": "https://pubchem.ncbi.nlm.nih.gov/", "keywords": [ "chemical", "chemistry", "epidemiology", "metabolite", "structure", "virology" ], "mappings": { "biocontext": "PUBCHEM.COMPOUND", "biolink": "CID", "cellosaurus": "PubChem", "cheminf": "000140", "edam": "2639", "fairsharing": "FAIRsharing.qt3w7z", "go": "PubChem_Compound", "integbio": "nbdc02626", "miriam": "pubchem.compound", "n2t": "pubchem.compound", "pathguide": "361", "prefixcommons": "pubchem.compound", "re3data": "r3d100010129", "togoid": "PubchemCompound", "wikidata": "P662" }, "name": "PubChem CID", "part_of": "pubchem", "pattern": "^\\d+$", "preferred_prefix": "pubchem.compound", "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/pubchem.compound:$1" }, { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", "homepage": "https://scholia.toolforge.org/", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/pubchem/$1" } ], "publications": [ { "doi": "10.1093/nar/gkaa971", "pmc": "PMC7778930", "pubmed": "33151290", "title": "PubChem in 2021: new data content and improved web interfaces", "year": 2021 }, { "doi": "10.1093/nar/gky1033", "pmc": "PMC6324075", "pubmed": "30371825", "title": "PubChem 2019 update: improved access to chemical data", "year": 2019 }, { "doi": "10.1093/nar/gkw1118", "pmc": "PMC5210581", "pubmed": "27899599", "title": "PubChem BioAssay: 2017 update", "year": 2016 }, { "doi": "10.1093/nar/gkt978", "pmc": "PMC3965008", "pubmed": "24198245", "title": "PubChem BioAssay: 2014 update", "year": 2013 }, { "doi": "10.1093/nar/gkr1132", "pmc": "PMC3245056", "pubmed": "22140110", "title": "PubChem's BioAssay Database", "year": 2011 }, { "doi": "10.1016/j.drudis.2010.10.003", "pmc": "PMC3010383", "pubmed": "20970519", "title": "PubChem as a public resource for drug discovery", "year": 2010 }, { "doi": "10.1093/nar/gkp456", "pmc": "PMC2703903", "pubmed": "19498078", "title": "PubChem: a public information system for analyzing bioactivities of small molecules", "year": 2009 }, { "doi": "10.1093/nar/gkl1031", "pmc": "PMC1781113", "pubmed": "17170002", "title": "Database resources of the National Center for Biotechnology Information", "year": 2006 } ], "rdf_uri_format": "http://rdf.ncbi.nlm.nih.gov/pubchem/compound/CID$1", "synonyms": [ "CID", "DSSTox_CID", "PUBCHEM_CID", "PubChem_Compound_CID", "Pubchem", "pubchem_id" ], "twitter": "pubchem", "uri_format": "https://pubchem.ncbi.nlm.nih.gov/compound/$1" }, "pubchem.element": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "PubChem Element gives information on chemical elements like Hydrogen, with the local identifier corresponding to the atomic number.", "example": "1", "homepage": "https://pubchem.ncbi.nlm.nih.gov/periodic-table", "keywords": [ "chemistry" ], "name": "PubChem Element", "part_of": "pubchem", "pattern": "^\\d+$", "preferred_prefix": "pubchem.element", "twitter": "pubchem", "uri_format": "https://pubchem.ncbi.nlm.nih.gov/element/$1" }, "pubchem.substance": { "description": "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Substance archives chemical substance records.", "example": "100101", "homepage": "https://pubchem.ncbi.nlm.nih.gov/", "keywords": [ "protein", "small molecule", "structure" ], "mappings": { "biocontext": "PUBCHEM.SUBSTANCE", "cheminf": "000141", "go": "PubChem_Substance", "integbio": "nbdc00642", "miriam": "pubchem.substance", "n2t": "pubchem.substance", "prefixcommons": "pubchem.substance", "togoid": "PubchemSubstance", "wikidata": "P2153" }, "name": "PubChem Substance ID (SID)", "part_of": "pubchem", "pattern": "^\\d+$", "preferred_prefix": "pubchem.substance", "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/pubchem.substance:$1" } ], "publications": [ { "doi": "10.1093/nar/gkl1031", "pmc": "PMC1781113", "pubmed": "17170002", "title": "Database resources of the National Center for Biotechnology Information", "year": 2006 } ], "rdf_uri_format": "http://rdf.ncbi.nlm.nih.gov/pubchem/substance/SID$1", "synonyms": [ "DSSTox_Generic_SID" ], "twitter": "pubchem", "uri_format": "https://pubchem.ncbi.nlm.nih.gov/substance/$1" }, "publons.publication": { "description": "identifier for the defunct/merged Publons website; URL redirects to Web of Science's P8372 (WOSID)", "example": "18466622", "homepage": "https://publons.com", "mappings": { "wikidata": "P3431" }, "name": "Publons publication", "preferred_prefix": "publons.publication", "uri_format": "https://publons.com/publon/$1" }, "publons.researcher": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Database of researchers to track publications, citation metrics, peer reviews, and journal editing work.", "example": "1981638", "homepage": "https://publons.com/researcher", "mappings": { "biolink": "ResearchID", "wikidata": "P3829" }, "name": "Publons Researcher", "pattern": "^\\d+$", "preferred_prefix": "publons.researcher", "uri_format": "https://publons.com/researcher/$1" }, "pubmed": { "contact": { "email": "beck@ncbi.nlm.nih.gov", "github": "jeffbeckncbi", "name": "Jeff Beck", "orcid": "0000-0002-1798-9797" }, "description": "PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s.", "example": "16333295", "homepage": "https://www.ncbi.nlm.nih.gov/PubMed/", "keywords": [ "bibliography", "biomedical science", "citation", "publication" ], "mappings": { "biocontext": "PUBMED", "cellosaurus": "PubMed", "cheminf": "000302", "edam": "1187", "fairsharing": "FAIRsharing.2b9b61", "go": "PMID", "integbio": "nbdc00179", "miriam": "pubmed", "n2t": "pubmed", "prefixcommons": "pubmed", "togoid": "Pubmed", "wikidata": "P698" }, "name": "PubMed", "pattern": "^\\d+$", "preferred_prefix": "pubmed", "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/pubmed:$1" }, { "code": "epmc", "description": "Europe PMC", "homepage": "http://europepmc.org/", "name": "Europe PMC", "uri_format": "http://europepmc.org/abstract/MED/$1" }, { "code": "hubmed", "description": "HubMed", "homepage": "http://www.hubmed.org/", "name": "HubMed", "uri_format": "https://www.hubmed.org/?term=$1" }, { "code": "pubmed.new", "description": "New-style link for pubmed", "homepage": "https://pubmed.ncbi.nlm.nih.gov", "name": "PubMed (new)", "uri_format": "https://pubmed.ncbi.nlm.nih.gov/$1" }, { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", "homepage": "https://scholia.toolforge.org/", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/pubmed/$1" }, { "code": "uniprot.citation", "description": "UniProt mints PURLs for citations identifiers", "homepage": "https://uniprot.org/", "name": "UniProt", "uri_format": "http://purl.uniprot.org/citations/$1" }, { "code": "uniprot.pubmed", "description": "UniProt mints PURLs for PubMed identifiers", "homepage": "https://uniprot.org/", "name": "UniProt", "uri_format": "http://purl.uniprot.org/pubmed/$1" } ], "publications": [ { "doi": "10.1093/nar/gkj158", "pmc": "PMC1347520", "pubmed": "16381840", "title": "Database resources of the National Center for Biotechnology Information", "year": 2006 } ], "rdf_uri_format": "http://rdf.ncbi.nlm.nih.gov/pubchem/reference/$1", "synonyms": [ "MEDLINE", "PMID", "PubMed", "PubMed ID", "pmid" ], "uri_format": "https://pubmed.ncbi.nlm.nih.gov/$1/" }, "puro": { "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 the characterisation of the roles of agents – people, corporate bodies and computational agents in the publication process. These agents can be, e.g. authors, editors, reviewers, publishers or librarians.", "example": "RoleInTime", "homepage": "http://www.sparontologies.net/ontologies/pro", "keywords": [ "bibliography", "citation", "data model", "report", "subject agnostic" ], "mappings": { "fairsharing": "FAIRsharing.3e88d6" }, "name": "Publishing Roles Ontology", "preferred_prefix": "PuRO", "publications": [ { "doi": "10.1145/2362499.2362502", "title": "Scholarly publishing and linked data", "year": 2012 } ], "repository": "https://github.com/sparontologies/pro", "twitter": "sparontologies", "uri_format": "http://purl.org/spar/pro/$1" }, "pw": { "banana": "PW", "contact": { "email": "gthayman@mcw.edu", "github": "gthayman", "name": "G. Thomas Hayman", "orcid": "0000-0002-9553-7227" }, "description": "The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions.", "download_obo": "https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/pathway/pathway.obo", "download_owl": "http://purl.obolibrary.org/obo/pw.owl", "example": "0000423", "homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html", "keywords": [ "biological regulation", "disease", "drug", "drug metabolism", "enzymatic reaction", "human", "life science", "mathematical model", "molecular entity", "network model", "obo", "ontology", "pathway", "pathway model", "signaling" ], "license": "CC-BY-4.0", "logo": "http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif", "mappings": { "aberowl": "PW", "biocontext": "PW", "bioportal": "PW", "fairsharing": "FAIRsharing.f73xhd", "miriam": "pw", "n2t": "pw", "obofoundry": "pw", "ols": "pw", "ontobee": "PW", "prefixcommons": "pw", "wikidata": "P7333" }, "name": "Pathway ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "PW", "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/pw:$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.pw/PW:$1" } ], "publications": [ { "doi": "10.1186/s40246-014-0017-8", "pmc": "PMC4191248", "pubmed": "25265995", "title": "Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease", "year": 2014 }, { "doi": "10.1186/2041-1480-5-7", "pmc": "PMC3922094", "pubmed": "24499703", "title": "The pathway ontology - updates and applications", "year": 2014 }, { "doi": "10.1093/database/bar010", "pmc": "PMC3072770", "pubmed": "21478484", "title": "The Rat Genome Database pathway portal", "year": 2011 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/PW_$1", "repository": "https://github.com/rat-genome-database/PW-Pathway-Ontology", "twitter": "ratgenome", "uri_format": "http://purl.obolibrary.org/obo/PW_$1", "version": "7.89" }, "pwo": { "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 steps in the workflow associated with the publication of a document or other publication entity.", "example": "Workflow", "homepage": "http://www.sparontologies.net/ontologies/pwo", "keywords": [ "bibliography", "citation", "data model", "report", "spar", "subject agnostic" ], "mappings": { "fairsharing": "FAIRsharing.c4e46c", "lov": "pwo" }, "name": "Publishing Workflow Ontology", "preferred_prefix": "PWO", "publications": [ { "doi": "10.3233/sw-160230", "title": "The Publishing Workflow Ontology (PWO)", "year": 2017 } ], "repository": "https://github.com/sparontologies/pwo", "twitter": "sparontologies", "uri_format": "http://purl.org/spar/pwo/$1" }, "px": { "description": "The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination.", "example": "PXD000500", "homepage": "http://www.proteomexchange.org/", "mappings": { "biocontext": "PX", "miriam": "px", "n2t": "px" }, "name": "ProteomeXchange", "pattern": "^(R)?PXD\\d{6}$", "preferred_prefix": "px", "uri_format": "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$1" }, "pypi": { "description": "The Python Package Index (PyPI) is a repository for Python packages.", "example": "numpy", "homepage": "https://www.python.org/psf/", "mappings": { "miriam": "pypi" }, "name": "PyPI", "pattern": "^[a-zA-Z_][a-zA-Z0-9\\-_]+$", "preferred_prefix": "pypi", "uri_format": "https://pypi.org/project/$1" }, "qb": { "contact": { "email": "richard@cyganiak.de", "github": "cygri", "name": "Richard Cyganiak", "orcid": "0000-0001-9950-5209" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This vocabulary allows multi-dimensional data, such as statistics, to be published in RDF. It is based on the core information model from SDMX (and thus also DDI).", "download_rdf": "http://purl.org/linked-data/cube#", "example": "Observation", "homepage": "https://www.w3.org/TR/vocab-data-cube", "keywords": [ "methods", "w3c rec" ], "mappings": { "lov": "qb", "zazuko": "qb" }, "name": "The data cube vocabulary", "pattern": "^\\w+$", "preferred_prefix": "qb", "repository": "https://github.com/UKGovLD/publishing-statistical-data", "uri_format": "http://purl.org/linked-data/cube#$1" }, "qtldb": { "description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection is species-independent.", "example": "4685", "homepage": "https://www.animalgenome.org/QTLdb", "mappings": { "miriam": "qtldb" }, "name": "Animal Genome QTL", "pattern": "^\\d+$", "preferred_prefix": "qtldb", "uri_format": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1" }, "qudt": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types.", "download_owl": "http://aber-owl.net/media/ontologies/QUDT/4/qudt.owl", "download_rdf": "http://qudt.org/schema/qudt/", "example": "baseDimensionEnumeration", "homepage": "https://qudt.org", "keywords": [ "astrophysics and astronomy", "experimental measurement", "methods", "ontology", "unit" ], "mappings": { "aberowl": "QUDT", "bartoc": "18206", "biolink": "qud", "bioportal": "QUDT", "fairsharing": "FAIRsharing.d3pqw7", "lov": "qudt", "zazuko": "qudt" }, "name": "Quantities, Units, Dimensions, and Types Ontology", "preferred_prefix": "qudt", "providers": [ { "code": "v11", "description": "Version 1.1 provider", "homepage": "http://qudt.org", "name": "Version 1.1", "uri_format": "http://qudt.org/1.1/schema/qudt#$1" } ], "repository": "https://github.com/qudt/qudt-public-repo", "uri_format": "http://qudt.org/schema/qudt#$1" }, "radiomics": { "contact": { "email": "alberto.traverso@maastro.nl", "name": "Alberto Traverso", "orcid": "0000-0001-6183-4429" }, "description": "The Radiomics Ontology aims to cover the radiomics feature domain with a strong focus on first order, shape, textural radiomics features. In addition, in the original version. it includes classes about segmentation algorithms and imaging filters. Due to a recent collaboration with the IBSI (International Biomarkers Standardization Initiative), the ontology has been expanded (v 1.6) and it includes all the entities presented in the IBSI document. Therefore, a broad coverage of not only radiomics features, but also every entity (e.g. software properties, filter properties, features extraction parameters) involved into radiomics computation has been added. In the latest version (v2.0), the ontology URIs have been updated to reflect the codes avaialble in the IBSI latest manual. [bioportal]", "example": "LK99", "homepage": "http://www.radiomics.org/RO", "keywords": [ "ontology" ], "mappings": { "bioportal": "RO" }, "name": "Radiomics Ontology", "preferred_prefix": "radiomics", "uri_format": "http://www.radiomics.org/RO/$1" }, "radlex": { "contact": { "email": "radlex-feedback@lists.rsna.org", "name": "Radiological Society of North America" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A comprehensive set of radiology terms for use in radiology reporting, decision support, data mining, data registries, education and research.\n\nRadLex provides the foundation for vital data resources used in radiology:\n\n- The LOINC/RSNA Radiology Playbook\n- RadElement Common Data Elements\n-RadReport Radiology Reporting Templates\n\nThe development of RadLex has been supported by the National Institute of Biomedical Imaging and Bioengineering (NIBIB) and the cancer Biomedical Informatics Grid (caBIG) project.", "download_owl": "http://aber-owl.net/media/ontologies/RADLEX/37/radlex.owl", "example": "RID1", "homepage": "https://radlex.org", "keywords": [ "anatomy", "biomedical science", "clinical studies", "diagnosis", "medical imaging", "medical informatics", "ontology", "radiology" ], "license": "http://www.rsna.org/uploadedFiles/RSNA/Content/Informatics/RadLex_License_Agreement_and_Terms_of_Use_V2_Final.pdf", "mappings": { "aberowl": "RADLEX", "bartoc": "20689", "bioportal": "RADLEX", "fairsharing": "FAIRsharing.shm2f2", "hl7": "2.16.840.1.113883.6.256" }, "name": "RSNA Informatics RadLex", "pattern": "^RID\\d+$", "preferred_prefix": "radlex", "publications": [ { "doi": "10.1016/j.jvir.2009.04.031", "pubmed": "19560008", "title": "The IR Radlex Project: an interventional radiology lexicon--a collaborative project of the Radiological Society of North America and the Society of Interventional Radiology", "year": 2009 }, { "doi": "10.1016/j.jvir.2008.10.022", "pubmed": "19081735", "title": "The IR RadLex project: an interventional radiology lexicon--a collaborative project of the Radiological Society of North America and the Society of Interventional Radiology", "year": 2008 }, { "doi": "10.2214/ajr.174.5.1741463", "pubmed": "10789815", "title": "Radiology lexicon", "year": 2000 } ], "uri_format": "https://radlex.org/RID/$1", "version": "4.1" }, "rapdb.locus": { "description": "Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides locus information in RAP-DB.", "example": "Os01g0883800", "homepage": "https://rapdb.dna.affrc.go.jp/", "mappings": { "miriam": "rapdb.locus" }, "name": "RAP-DB Locus", "pattern": "^Os\\S+g\\d{7}$", "preferred_prefix": "rapdb.locus", "synonyms": [ "irgsp" ], "uri_format": "https://rapdb.dna.affrc.go.jp/locus/?name=$1" }, "rapdb.transcript": { "description": "Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides transcript information in RAP-DB.", "example": "Os01t0883800-02", "homepage": "https://rapdb.dna.affrc.go.jp/", "keywords": [ "dna", "genome" ], "mappings": { "go": "RAP-DB", "miriam": "rapdb.transcript", "ncbi": "RAP-DB", "prefixcommons": "rapdb" }, "name": "Rice annotation Project database", "pattern": "^Os\\S+t\\d{7}-\\d{2}$", "preferred_prefix": "rapdb.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/rapdb:$1" } ], "uri_format": "https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=$1" }, "ratmap": { "comment": "This resource doesn't exist on the web anymore", "deprecated": true, "description": "The Rat Genome Database RatMap is focused on presenting rat genes, DNA-markers, QTL:s etc that is localized to chromosome. The database is dedicated to rat gene nomenclature and should be consulted for queries in such matters", "example": "5", "homepage": "http://ratmap.org", "keywords": [ "dna", "gene", "genome" ], "mappings": { "ncbi": "RATMAP", "prefixcommons": "ratmap" }, "name": "Rat Genome Database", "preferred_prefix": "ratmap", "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/ratmap:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://ratmap.org/Showgene.php?gene_stable_id=$1" }, "rbk": { "contact": { "email": "oxburl@mmc.org", "name": "Leif Oxburgh", "orcid": "0000-0002-2825-7663" }, "description": "(Re)Building a Kidney is an NIDDK-funded consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function.", "example": "Q-2958", "homepage": "https://www.rebuildingakidney.org/", "keywords": [ "cell biology", "developmental biology", "genomics", "molecular biology" ], "mappings": { "biocontext": "RBK", "fairsharing": "FAIRsharing.78d3ad", "miriam": "rbk", "n2t": "rbk" }, "name": "Rebuilding a Kidney", "pattern": "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$", "preferred_prefix": "rbk", "publications": [ { "doi": "10.1681/asn.2016101077", "pmc": "PMC5407737", "pubmed": "28096308", "title": "(Re)Building a Kidney", "year": 2017 }, { "doi": "10.1681/ASN.2016101077", "title": "(Re)Building a Kidney." } ], "repository": "https://github.com/informatics-isi-edu/gudmap-rbk/wiki/Create-citable-datasets", "uri_format": "https://www.rebuildingakidney.org/id/$1" }, "rbo": { "contact": { "email": "daniel.c.berrios@nasa.gov", "github": "DanBerrios", "name": "Daniel C. Berrios", "orcid": "0000-0003-4312-9552" }, "depends_on": [ "bfo", "chmo", "envo", "obi", "pato", "ro", "uo" ], "description": "RBO is an ontology for the effects of radiation on biota in terrestrial and space environments.", "download_json": "http://purl.obolibrary.org/obo/rbo.json", "download_obo": "http://purl.obolibrary.org/obo/rbo.obo", "download_owl": "http://purl.obolibrary.org/obo/rbo.owl", "example": "00000105", "example_extras": [ "010007" ], "homepage": "https://github.com/Radiobiology-Informatics-Consortium/RBO", "keywords": [ "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "RBO", "bioportal": "RBO", "obofoundry": "rbo", "ols": "rbo", "ontobee": "RBO" }, "name": "Radiation Biology Ontology", "pattern": "^\\d{6,8}$", "preferred_prefix": "RBO", "rdf_uri_format": "http://purl.obolibrary.org/obo/RBO_$1", "repository": "https://github.com/Radiobiology-Informatics-Consortium/RBO", "uri_format": "http://purl.obolibrary.org/obo/RBO_$1", "version": "2025-02-28" }, "rcb": { "contact": { "email": "atsushi.yoshiki@riken.jp", "name": "Atsushi Yoshiki", "orcid": "0000-0002-9450-5151" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Collection of many cell lines derived from human and other various animals, preserved by the RIKEN BioResource Research Center.", "example": "RCB0002", "homepage": "https://cell.brc.riken.jp/en/rcb", "keywords": [ "animal", "bioresource", "cell", "cell line", "cultured cell", "cultured cell line", "dna", "embryo", "experimental animal", "experimental plant", "faseb list", "gene", "genetic material", "organ", "plant", "recombinant host", "seed", "sperm", "tissue", "virus" ], "mappings": { "cellosaurus": "RCB", "rrid": "IMSR_RBRC" }, "name": "RIKEN Bioresource Center Cell Bank", "pattern": "^RCB\\d+$", "preferred_prefix": "rcb", "publications": [ { "pubmed": "34532769" }, { "pubmed": "19448331" } ], "uri_format": "https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo=$1" }, "rdbsb": { "contact": { "email": "gqzhang@sinh.ac.cn", "name": "Guoqing Zhang", "orcid": "0000-0001-8827-7546" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "This database provides identifiers for catalytic bioparts which are fundamental to the design, construction, and optimization of biological systems for specific metabolic pathways. It provides basic information, function information (including catalytic functions, qualitative and quantitative parameters, and biopart expression), and sequence information (nucleotide sequence and amino acid sequence)", "example": "OENC205", "github_request_issue": 1473, "homepage": "https://www.biosino.org/rdbsb", "name": "Registry and database of bioparts for synthetic biology", "pattern": "^OENC\\d+$", "preferred_prefix": "rdbsb", "publications": [ { "doi": "10.1093/nar/gkae844", "pmc": "PMC11701600", "pubmed": "39360609", "title": "RDBSB: a database for catalytic bioparts with experimental evidence", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://www.biosino.org/rdbsb/bioparts_detail/$1" }, "rdf": { "contact": { "email": "rmrich5@gmail.com", "name": "Rafael Richards", "orcid": "0000-0001-5699-0515" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace, defined in RDF 1.1 Concepts", "example": "type", "homepage": "http://www.w3.org/1999/02/22-rdf-syntax-ns", "keywords": [ "computer science", "subject agnostic", "w3c rec" ], "mappings": { "biocontext": "rdf", "fairsharing": "FAIRsharing.p77ph9", "lov": "rdf", "zazuko": "rdf" }, "name": "Resource Description Framework", "preferred_prefix": "rdf", "uri_format": "http://www.w3.org/1999/02/22-rdf-syntax-ns#$1" }, "rdfa": { "contact": { "email": "ivan@w3.org", "github": "iherman", "name": "Ivan Herman", "orcid": "0000-0003-0782-2704" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "RDFa Core is a specification for attributes to express structured data in any markup language. The embedded data already available in the markup language (e.g., HTML) can often be reused by the RDFa markup, so that publishers don't need to repeat significant data in the document content. (from https://www.w3.org/TR/rdfa-core/)", "download_rdf": "http://www.w3.org/ns/rdfa.ttl", "example": "PrefixOrTermMapping", "homepage": "http://www.w3.org/ns/rdfa", "keywords": [ "rdf" ], "mappings": { "lov": "rdfa", "zazuko": "rdfa" }, "name": "RDFa Vocabulary for Term and Prefix Assignment, and for Processor Graph Reporting", "preferred_prefix": "rdfa", "uri_format": "http://www.w3.org/ns/rdfa#$1" }, "rdfs": { "contact": { "email": "danbri@w3.org", "name": "Dan Brickley", "orcid": "0000-0002-6450-7041" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary.", "download_owl": "https://triplydb.com/w3c/rdfs/download.trig.gz", "example": "label", "homepage": "https://www.w3.org/TR/rdf-schema/", "keywords": [ "bioinformatics", "life science", "linguistics", "ontology", "ontology and terminology", "w3c rec" ], "mappings": { "aberowl": "RDFS", "biocontext": "rdfs", "bioportal": "RDFS", "fairsharing": "FAIRsharing.v9n3gk", "lov": "rdfs", "ols": "rdfs", "zazuko": "rdfs" }, "name": "RDF Schema", "preferred_prefix": "rdfs", "uri_format": "http://www.w3.org/2000/01/rdf-schema#$1" }, "rdo": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Ontologies of diseases that integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms.", "download_obo": "https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/disease/RDO.obo", "download_owl": "https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/disease/RDO.owl", "example": "9002859", "homepage": "https://ratmine.mcw.edu/ontology/disease/", "keywords": [ "ontology" ], "name": "RGD Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "rdo", "uri_format": "http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#$1" }, "re3data": { "description": "Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines.", "example": "r3d100010772", "homepage": "https://datacite.org", "mappings": { "bartoc": "822", "miriam": "re3data" }, "name": "re3data", "pattern": "^r3d\\d{9,9}$", "preferred_prefix": "re3data", "uri_format": "https://www.re3data.org/repository/$1" }, "reactome": { "contact": { "email": "deustp01@med.nyu.edu", "github": "deustp01", "name": "Peter D'Eustachio", "orcid": "0000-0002-5494-626X" }, "contributor_extras": [ { "email": "smoxon@lbl.gov", "github": "sierra-moxon", "name": "Sierra Moxon", "orcid": "0000-0002-8719-7760" } ], "description": "The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology.", "example": "R-BTA-418592", "homepage": "https://www.reactome.org/", "keywords": [ "human", "pathway", "reaction" ], "license": "CC0-1.0", "mappings": { "biocontext": "REACTOME", "cheminf": "000411", "edam": "1155", "go": "Reactome", "integbio": "nbdc00185", "miriam": "reactome", "n2t": "reactome", "pathguide": "103", "prefixcommons": "reactome", "re3data": "r3d100010861", "togoid": "ReactomePathway", "wikidata": "P3937" }, "name": "Reactome", "pattern": "^R-[A-Z]{3}-\\d+(-\\d+)?(\\.\\d+)?$", "preferred_prefix": "reactome", "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/reactome:$1" }, { "code": "browser", "description": "An interactive view over pathways.", "homepage": "https://reactome.org/PathwayBrowser/", "name": "Reactome Pathway Browser", "uri_format": "https://reactome.org/PathwayBrowser/#/$1" }, { "code": "pathwaycommons", "description": "Pathway diagram drawn with Cytoscape", "homepage": "https://www.pathwaycommons.org", "name": "Pathway Commons", "uri_format": "https://apps.pathwaycommons.org/pathways?uri=http%3A%2F%2Fidentifiers.org%2Freactome%2F$1" } ], "publications": [ { "doi": "10.1093/nar/gki072", "pmc": "PMC540026", "pubmed": "15608231", "title": "Reactome: a knowledgebase of biological pathways", "year": 2005 } ], "references": [ "https://github.com/biopragmatics/bioregistry/pull/1086" ], "synonyms": [ "RE", "REACT", "Reactome", "reactome.pathway" ], "uri_format": "https://reactome.org/content/detail/$1" }, "reaxys": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Reaxys is a web-based tool for the retrieval of chemistry information and data from published literature, including journals and patents. The information includes chemical compounds, chemical reactions, chemical properties, related bibliographic data, substance data with synthesis planning information, as well as experimental procedures from selected journals and patents. It is licensed by Elsevier.", "example": "1257009", "homepage": "https://www.reaxys.com", "mappings": { "edam": "1003", "wikidata": "P1579" }, "name": "Reaxys", "pattern": "^\\d+$", "preferred_prefix": "reaxys", "synonyms": [ "Beilstein", "Reaxys" ] }, "rebase": { "contact": { "email": "roberts@neb.com", "name": "Richard John Roberts", "orcid": "0000-0002-4348-0169" }, "description": "REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.", "example": "101", "homepage": "http://rebase.neb.com/rebase/", "keywords": [ "dna", "enzyme", "genome", "life science", "protein", "rna", "small molecule", "structure" ], "mappings": { "biocontext": "REBASE", "edam": "2325", "fairsharing": "FAIRsharing.9sb9qh", "go": "REBASE", "integbio": "nbdc00648", "miriam": "rebase", "n2t": "rebase", "pathguide": "72", "prefixcommons": "rebase", "re3data": "r3d100012171", "uniprot": "DB-0089", "wikidata": "P4866" }, "name": "REBASE Enzyme Number", "pattern": "^\\d+$", "preferred_prefix": "rebase", "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/rebase:$1" } ], "publications": [ { "doi": "10.1093/nar/gku1046", "pmc": "PMC4383893", "pubmed": "25378308", "title": "REBASE--a database for DNA restriction and modification: enzymes, genes and genomes", "year": 2014 }, { "doi": "10.1093/nar/gkp874", "pmc": "PMC2808884", "pubmed": "19846593", "title": "REBASE--a database for DNA restriction and modification: enzymes, genes and genomes", "year": 2009 } ], "uri_format": "http://rebase.neb.com/rebase/enz/$1.html" }, "rebec": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Presents the new fast tracks for clinical research and observational studies on INDIGENOUS PEOPLE AND TRADITIONAL COMMUNITIES and on NEGLECTED TROPICAL DISEASES (NTDs). Fast-track can reduce the normal approval period for clinical trials to less than 48 hours, if the documentation, information and any mandatory changes requested are provided by the registrant.", "example": "RBR-6qvdftm", "homepage": "https://ensaiosclinicos.gov.br", "name": "Brazilian Registry of Clinical Trials", "pattern": "^RBR-\\w+$", "preferred_prefix": "rebec", "uri_format": "https://ensaiosclinicos.gov.br/rg/$1" }, "receptome.family": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The human receptor families involved in signaling (with the exception of channels) are presented in the Human Plasma Membrane Receptome database.", "example": "5.1", "homepage": "http://www.receptome.org", "keywords": [ "protein" ], "mappings": { "prefixcommons": "hpmr" }, "name": "Human Plasma Membrane Receptome Families", "preferred_prefix": "receptome.family", "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/hpmr:$1" } ], "uri_format": "http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId=$1" }, "redfly": { "comment": "This resource doesn't exist on the web anymore", "deprecated": true, "description": "REDflyis a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs).", "example": "8", "homepage": "http://redfly.ccr.buffalo.edu", "keywords": [ "regulation" ], "mappings": { "pathguide": "265", "prefixcommons": "redfly" }, "name": "Regulatory Elements Database for Drosophila", "preferred_prefix": "redfly", "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/redfly:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://redfly.ccr.buffalo.edu/?content=/view_detail.php&crm_id=$1" }, "refseq": { "contact": { "email": "pruitt@ncbi.nlm.nih.gov", "name": "Kim Dixon Pruitt", "orcid": "0000-0001-7950-1374" }, "contributor_extras": [ { "github": "slobentanzer", "name": "Sebastian Lobentanzer", "orcid": "0000-0003-3399-6695" } ], "description": "The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products.", "example": "NP_012345", "example_extras": [ "WP_029104145.1" ], "has_canonical": "ncbiprotein", "homepage": "https://www.ncbi.nlm.nih.gov/projects/RefSeq/", "keywords": [ "computational biology", "dna", "genetics", "life science", "protein", "rna" ], "mappings": { "biocontext": "RefSeq", "edam": "1098", "fairsharing": "FAIRsharing.4jg0qw", "go": "RefSeq", "hl7": "2.16.840.1.113883.6.280", "integbio": "nbdc00187", "miriam": "refseq", "n2t": "refseq", "prefixcommons": "refseq", "re3data": "r3d100010285", "uniprot": "DB-0117" }, "name": "Reference Sequence Collection", "pattern": "^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|WP|XM|XP|XR|YP|ZP)_\\d+)|(NZ_[A-Z]{2,4}\\d+))(\\.\\d+)?$", "preferred_prefix": "refseq", "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/refseq:$1" } ], "publications": [ { "doi": "10.1093/nar/gkae1038", "pubmed": "39526381", "title": "NCBI RefSeq: reference sequence standards through 25 years of curation and annotation", "year": 2024 }, { "doi": "10.1093/nar/gkv1189", "pmc": "PMC4702849", "pubmed": "26553804", "title": "Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation", "year": 2015 }, { "doi": "10.1093/nar/gkl842", "pmc": "PMC1716718", "pubmed": "17130148", "title": "NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins", "year": 2006 } ], "references": [ "https://github.com/biopragmatics/bioregistry/issues/545" ], "synonyms": [ "REFSEQ_PROT" ], "uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1" }, "reo": { "comment": "From James O.: It was an ontology for \"reagents\" developed by @Matthew Brush. Since OBI was interested in reagents, Matt developed it in coordination with OBI and had plans to submit it to OBO. I believe that REO was once included in Ontobee, and OBI even started using some REO terms. But REO was never submitted to OBO. I believe it was abandoned.", "contact": { "email": "matt@tislab.org", "github": "mbrush", "name": "Matthew Brush", "orcid": "0000-0002-1048-5019" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Reagent Ontology (ReO) adheres to OBO Foundry principles (obofoundry.org) to model the domain of biomedical research reagents, considered broadly to include materials applied “chemically” in scientific techniques to facilitate generation of data and research materials. ReO is a modular ontology that re-uses existing ontologies to facilitate cross-domain interoperability. It consists of reagents and their properties, linking diverse biological and experimental entities to which they are related. ReO supports community use cases by providing a flexible, extensible, and deeply integrated framework that can be adapted and extended with more specific modeling to meet application needs.", "download_owl": "https://github.com/tis-lab/reagent-ontology/raw/master/reo/ontology_files/reo_pre-merged_or_reasoned_files/reo_reasoned_9-6-12.owl", "example": "0000079", "homepage": "https://github.com/tis-lab/reagent-ontology", "keywords": [ "ontology" ], "mappings": { "ontobee": "REO" }, "name": "Reagent Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "reo", "references": [ "https://github.com/obi-ontology/obi/issues/1015", "https://code.google.com/archive/p/reagent-ontology/", "https://github.com/obi-ontology/obi/issues/1135" ], "repository": "https://github.com/tis-lab/reagent-ontology", "uri_format": "http://purl.obolibrary.org/obo/REO_$11" }, "repeatsdb.protein": { "description": "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references protein entries in the database.", "example": "P29894", "homepage": "https://repeatsdb.org/", "mappings": { "miriam": "repeatsdb.protein" }, "name": "RepeatsDB Protein", "pattern": "^[OPQopq][0-9][A-Za-z0-9]{3}[0-9]|[A-Na-nR-Zr-z][0-9]([A-Za-z][A-Za-z0-9]{2}[0-9]){1,2}$", "preferred_prefix": "repeatsdb.protein", "provides": "uniprot", "uri_format": "https://repeatsdb.org/protein/$1" }, "repeatsdb.structure": { "description": "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references structural entries in the database.", "example": "2gc4E", "homepage": "https://repeatsdb.org/", "mappings": { "miriam": "repeatsdb.structure" }, "name": "RepeatsDB Structure", "pattern": "^[0-9][A-Za-z0-9]{3}[A-Za-z0-9][A-Za-z0-9]?[0-9]?[0-9]?$", "preferred_prefix": "repeatsdb.structure", "uri_format": "https://repeatsdb.org/structure/$1" }, "repec": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Peruvian Clinical Trials Registry - REPEC is a non-profit online information system developed in 2007 by INS. It is a publicly accessible prospective registry aimed at providing information about clinical trials underway in Peru. REPEC also includes Registries for Trial Sites, Institutional Research Ethics Committees, Sponsors and Contract Research Organizations. REPEC contains records of clinical trials since 1995. Since December 14, 2012, the Peruvian National Institute of Health, by means of the General Office for Research and Technological Transfer (OGITT), has started a process to improve REPEC and to join the WHO International Clinical Trials Registry Platform (ICTRP) and to be acknowledged as a Primary Registry. More information about primary registries is available in ICRTP at http://apps.who.int/trialsearch/. (from website)", "example": "046-19", "homepage": "https://ensayosclinicos-repec.ins.gob.pe/en/", "logo": "https://ensayosclinicos-repec.ins.gob.pe/images/plantilla/img_logo_principal_repec_en.png", "name": "Peruvian Clinical Trial Registry", "pattern": "^\\d+-\\d+(-[A-Z])?$", "preferred_prefix": "repec", "uri_format": "https://www.ins.gob.pe/ensayosclinicos/rpec/recuperarECPBNuevo.asp?val=&NroPag=1&flg=0&ver=EN&numEC=$1" }, "reproduceme": { "contact": { "email": "sheeba.samuel@uni-jena.de", "name": "Sheeba Samuel", "orcid": "0000-0002-7981-8504" }, "description": "The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan ontology to describe a complete path of a scientific experiment. It expresses the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes and properties to represent a scientific experiment including its computational and non-computational steps to track the provenance of results. It describes a complete path of a scientific experiment considering the use-case of biological imaging and microscopy experiments, computational experiments, including Jupyter notebooks and scripts. It describes an experiment and its data, agents, activities, plans, steps, variables, instruments, materials, and settings required for its reproducibility.", "download_owl": "http://aber-owl.net/media/ontologies/REPRODUCE-ME/7/reproduce-me.owl", "example": "MicrobeamManipulation", "homepage": "https://w3id.org/reproduceme/research", "keywords": [ "ontology" ], "mappings": { "aberowl": "REPRODUCE-ME", "bioportal": "REPRODUCE-ME", "ols": "reproduceme" }, "name": "REPRODUCE-ME Ontology", "preferred_prefix": "reproduceme", "uri_format": "https://w3id.org/reproduceme#$1", "version": "1.1" }, "researchgate.profile": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "identifier for a person, used by ResearchGate profiles", "example": "Rita-Heuser", "homepage": "https://www.researchgate.net", "keywords": [ "person", "researcher" ], "mappings": { "wikidata": "P2038" }, "name": "ResearchGate profile ID", "pattern": "^[0-9A-Za-z_-]+$", "preferred_prefix": "researchgate.profile", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1171" ], "uri_format": "https://www.researchgate.net/profile/$1" }, "resid": { "contact": { "email": "john.garavelli@ebi.ac.uk", "name": "John Garavelli", "orcid": "0000-0002-4131-735X" }, "deprecated": true, "description": "The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.", "example": "AA0001", "homepage": "https://proteininformationresource.org/resid/", "keywords": [ "obo", "ontology", "protein", "small molecule", "structure" ], "mappings": { "biocontext": "RESID", "edam": "2619", "go": "RESID", "miriam": "resid", "n2t": "resid", "obofoundry": "resid", "prefixcommons": "resid" }, "name": "Protein covalent bond", "pattern": "^AA\\d{4}$", "preferred_prefix": "RESID", "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/resid:$1" } ], "publications": [ { "doi": "10.1002/pmic.200300764", "pubmed": "15174124", "title": "Annotation of post-translational modifications in the Swiss-Prot knowledge base", "year": 2004 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/RESID_$1", "uri_format": "https://proteininformationresource.org/cgi-bin/resid?id=$1" }, "reto": { "contact": { "email": "vladimir.n.mironov@gmail.com", "name": "Vladimir Mironov" }, "description": "Regulation of Transcription", "download_obo": "https://www.bio.ntnu.no/ontology/ReTO/reto.obo", "download_owl": "https://www.bio.ntnu.no/ontology/ReTO/reto.owl", "download_rdf": "http://www.bio.ntnu.no/ontology/ReTO/reto.rdf", "homepage": "http://www.semantic-systems-biology.org/apo", "keywords": [ "life science", "ontology", "regulation of gene expression", "transcript", "transcriptomics" ], "mappings": { "aberowl": "RETO", "bioportal": "RETO", "fairsharing": "FAIRsharing.4qyf0f", "ols": "reto" }, "name": "Regulation of Transcription Ontology", "no_own_terms": true, "preferred_prefix": "reto" }, "rex": { "contact": { "email": "amalik@ebi.ac.uk", "github": "amalik01", "name": "Adnan Malik", "orcid": "0000-0001-8123-5351" }, "deprecated": true, "description": "An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time.", "download_owl": "http://purl.obolibrary.org/obo/rex.owl", "example": "0000512", "homepage": "https://www.ebi.ac.uk/chebi/", "keywords": [ "biochemistry", "chemistry", "enzymatic reaction", "life science", "obo", "ontology", "reaction data" ], "mappings": { "aberowl": "REX", "biocontext": "REX", "bioportal": "REX", "fairsharing": "FAIRsharing.g0a7s0", "obofoundry": "rex", "ols": "rex", "ontobee": "REX", "prefixcommons": "rex" }, "name": "Physico-chemical process", "part_of": "chebi", "pattern": "^\\d{7}$", "preferred_prefix": "REX", "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/rex:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/REX_$1", "uri_format": "http://purl.obolibrary.org/obo/REX_$1", "version": "2017-11-19" }, "rexo": { "contact": { "email": "kuiper@bio.ntnu.no", "github": "makuintnu", "name": "Martin Kuiper", "orcid": "0000-0002-1171-9876" }, "description": "Regulation of Gene Expression", "download_obo": "https://www.bio.ntnu.no/ontology/ReXO/rexo.obo", "download_owl": "https://www.bio.ntnu.no/ontology/ReXO/rexo.owl", "download_rdf": "http://www.bio.ntnu.no/ontology/ReXO/rexo.rdf", "homepage": "http://www.semantic-systems-biology.org/apo", "keywords": [ "expression data", "life science", "ontology", "orthologous", "regulation of gene expression" ], "mappings": { "aberowl": "REXO", "bioportal": "REXO", "fairsharing": "FAIRsharing.recas1", "ols": "rexo" }, "name": "Regulation of Gene Expression Ontology", "no_own_terms": true, "preferred_prefix": "rexo", "publications": [ { "doi": "10.1186/s12859-014-0386-y", "pmc": "PMC4279962", "pubmed": "25490885", "title": "Finding gene regulatory network candidates using the gene expression knowledge base", "year": 2014 } ] }, "rfam": { "contact": { "email": "apetrov@ebi.ac.uk", "github": "AntonPetrov", "name": "Anton I Petrov", "orcid": "0000-0001-7279-2682" }, "description": "The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion.", "example": "RF00230", "homepage": "https://rfam.org/", "keywords": [ "genetics" ], "mappings": { "biocontext": "RFAM", "edam": "2356", "fairsharing": "FAIRsharing.fex4c8", "go": "Rfam", "integbio": "nbdc00654", "miriam": "rfam", "n2t": "rfam", "ncbi": "RFAM" }, "name": "Rfam database of RNA families", "pattern": "^RF\\d{5}$", "preferred_prefix": "rfam", "publications": [ { "doi": "10.1093/nar/gkae1023", "pubmed": "39526405", "title": "Rfam 15: RNA families database in 2025", "year": 2024 }, { "doi": "10.1093/nar/gkx1038", "pmc": "PMC5753348", "pubmed": "29112718", "title": "Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families", "year": 2018 }, { "doi": "10.1093/nar/gku1063", "pmc": "PMC4383904", "pubmed": "25392425", "title": "Rfam 12.0: updates to the RNA families database", "year": 2014 } ], "twitter": "RfamDB", "uri_format": "https://rfam.org/family/$1" }, "rfc": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Legacy site for IETF RFC proposals", "example": "5013", "homepage": "https://www.ietf.org/", "mappings": { "n2t": "rfc" }, "name": "Internet Standard -- IETF Request for Comments", "pattern": "^\\d+$", "preferred_prefix": "rfc", "uri_format": "https://tools.ietf.org/rfc/rfc$1" }, "rgap": { "comment": "This resource has been updated as of 19 November, 2024", "contact": { "email": "Robin.Buell@uga.edu", "name": "C. Robin Buell", "orcid": "0000-0002-6727-4677" }, "description": "This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes. These data are available through search pages and the Genome Browser that provides an integrated display of annotation data.", "example": "LOC_Os02g13300", "homepage": "https://rice.uga.edu", "keywords": [ "dna", "genome" ], "mappings": { "prefixcommons": "rgap" }, "name": "Rice Genome Annotation Project", "preferred_prefix": "rgap", "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/rgap:$1" } ], "publications": [ { "doi": "10.1093/nar/gkae1061", "pubmed": "39558187", "title": "The rice genome annotation project: an updated database for mining the rice genome", "year": 2024 }, { "doi": "10.1093/nar/gkl976", "pmc": "PMC1751532", "pubmed": "17145706", "title": "The TIGR Rice Genome Annotation Resource: improvements and new features", "year": 2006 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://rice.uga.edu/cgi-bin/ORF_infopage.cgi?orf=$1" }, "rgd": { "contact": { "email": "jrsmith@mcw.edu", "name": "Jennifer R Smith", "orcid": "0000-0002-6443-9376" }, "description": "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references genes.", "example": "7499841", "homepage": "http://rgd.mcw.edu/", "keywords": [ "behavior", "biomedical science", "comparative genomics", "congenic rat", "data analysis service", "disease", "dna", "est", "faseb list", "function", "gene", "genetic", "genome", "genomic", "genomics", "genotype", "gold standard", "human", "immunology", "inbred rat strain", "knockout", "map", "marker", "model organism", "molecular medicine", "mouse", "mutant", "ontology", "organism supplier", "pathway", "phenomics", "phenotype", "physiology", "proteomics", "qtl", "quantitative genetics", "rat", "recombinant inbred rat", "sequence", "strain", "translational medicine", "variation", "veterinary medicine" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "RGD", "biocontext": "RGD", "bioportal": "RGD", "cellosaurus": "RGD", "edam": "2620", "fairsharing": "FAIRsharing.pfg82t", "go": "RGD", "integbio": "nbdc00188", "miriam": "rgd", "n2t": "rgd", "ncbi": "RGD", "pathguide": "267", "prefixcommons": "rgd", "re3data": "r3d100010417", "rrid": "RGD", "togoid": "Rgd", "uniprot": "DB-0091", "wikidata": "P3853" }, "name": "Rat Genome Database", "pattern": "^\\d{4,}$", "preferred_prefix": "rgd", "providers": [ { "code": "agr", "description": "RGD through the Alliance of Genome Resources", "homepage": "https://www.alliancegenome.org", "name": "RGD through the Alliance of Genome Resources", "uri_format": "https://www.alliancegenome.org/gene/RGD:$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/rgd:$1" } ], "publications": [ { "doi": "10.1093/database/baae132", "pmc": "PMC11753291", "pubmed": "39841812", "title": "Standardized pipelines support and facilitate integration of diverse datasets at the Rat Genome Database" }, { "doi": "10.1093/genetics/iyac005", "pmc": "PMC8982048", "pubmed": "35380657", "title": "MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses", "year": 2022 }, { "doi": "10.1007/s00335-021-09932-x", "pmc": "PMC8570235", "pubmed": "34741192", "title": "The Rat Genome Database (RGD) facilitates genomic and phenotypic data integration across multiple species for biomedical research", "year": 2021 }, { "doi": "10.1093/nar/gkz1041", "pmc": "PMC7145519", "pubmed": "31713623", "title": "The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform", "year": 2020 }, { "doi": "10.1007/978-1-4939-9581-3_3", "pubmed": "31228152", "title": "Rat Genome Databases, Repositories, and Tools", "year": 2019 }, { "doi": "10.1007/978-1-4939-9581-3_2", "pubmed": "31228151", "title": "Rat Genome Assemblies, Annotation, and Variant Repository", "year": 2019 }, { "doi": "10.1007/978-1-4939-9581-3_1", "pubmed": "31228150", "title": "The Rat: A Model Used in Biomedical Research", "year": 2019 }, { "doi": "10.1093/database/baz037", "pmc": "PMC6444380", "pubmed": "30938777", "title": "Quantitative phenotype analysis to identify, validate and compare rat disease models", "year": 2019 }, { "doi": "10.1093/database/baz014", "pmc": "PMC6369425", "pubmed": "30753478", "title": "Integrated curation and data mining for disease and phenotype models at the Rat Genome Database", "year": 2019 }, { "doi": "10.1007/978-1-4939-7737-6_8", "pmc": "PMC6487669", "pubmed": "29761460", "title": "A Primer for the Rat Genome Database (RGD)", "year": 2018 }, { "doi": "10.1093/ilar/ilw041", "pmc": "PMC6057551", "pubmed": "28838068", "title": "Rat Genome and Model Resources", "year": 2017 }, { "doi": "10.1242/dmm.026021", "pmc": "PMC5087824", "pubmed": "27736745", "title": "Exploring human disease using the Rat Genome Database", "year": 2016 }, { "doi": "10.1016/j.csbj.2015.11.006", "pmc": "PMC4700298", "pubmed": "27602200", "title": "Disease, Models, Variants and Altered Pathways-Journeying RGD Through the Magnifying Glass", "year": 2015 }, { "doi": "10.1152/physiolgenomics.00046.2016", "pmc": "PMC5005459", "pubmed": "27287925", "title": "Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database", "year": 2016 }, { "doi": "10.1093/database/baw034", "pmc": "PMC4805243", "pubmed": "27009807", "title": "The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database", "year": 2016 }, { "doi": "10.1093/nar/gku1026", "pmc": "PMC4383884", "pubmed": "25355511", "title": "The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease", "year": 2014 }, { "doi": "10.1186/s40246-014-0017-8", "pmc": "PMC4191248", "pubmed": "25265995", "title": "Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease", "year": 2014 }, { "doi": "10.1093/database/bat015", "pmc": "PMC3630803", "pubmed": "23603846", "title": "PhenoMiner: quantitative phenotype curation at the rat genome database", "year": 2013 }, { "pubmed": "23434633" }, { "doi": "10.1371/journal.pcbi.1000582", "pmc": "PMC2775909", "pubmed": "19956751", "title": "The rat genome database curators: who, what, where, why", "year": 2009 }, { "pubmed": "18996890" }, { "doi": "10.1093/nar/gkl988", "pmc": "PMC1761441", "pubmed": "17151068", "title": "The Rat Genome Database, update 2007--easing the path from disease to data and back again", "year": 2006 }, { "pubmed": "10400928", "title": "A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat", "year": 1999 } ], "synonyms": [ "RGD" ], "twitter": "ratgenome", "uri_format": "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1" }, "rgd.qtl": { "description": "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references quantitative trait loci (qTLs), providing phenotype and disease descriptions, mapping, and strain information as well as links to markers and candidate genes.", "example": "1354581", "homepage": "http://rgd.mcw.edu/", "mappings": { "biocontext": "RGD.QTL", "miriam": "rgd.qtl", "n2t": "rgd.qtl" }, "name": "Rat Genome Database qTL", "pattern": "^\\d+$", "preferred_prefix": "rgd.qtl", "twitter": "ratgenome", "uri_format": "http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=$1" }, "rgd.strain": { "description": "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references strain reports, which include a description of strain origin, disease, phenotype, genetics and immunology.", "example": "5688061", "homepage": "http://rgd.mcw.edu/", "mappings": { "biocontext": "RGD.STRAIN", "miriam": "rgd.strain", "n2t": "rgd.strain" }, "name": "Rat Genome Database strain", "pattern": "^\\d+$", "preferred_prefix": "rgd.strain", "twitter": "ratgenome", "uri_format": "http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$1" }, "rhea": { "contact": { "email": "anne.morgat@sib.swiss", "name": "Anne Morgat", "orcid": "0000-0002-1216-2969" }, "description": " Rhea is an expert-curated knowledgebase of chemical and transport reactions of biological interest. Enzyme-catalyzed and spontaneously occurring reactions are curated from peer-reviewed literature and represented in a computationally tractable manner by using the ChEBI (Chemical Entities of Biological Interest) ontology to describe reaction participants.\n\nRhea covers the reactions described by the IUBMB Enzyme Nomenclature as well as many additional reactions and can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analyses. Rhea is the standard for enzyme and transporter annotation in UniProtKB.", "example": "12345", "homepage": "https://www.rhea-db.org/", "keywords": [ "biochemistry", "life science", "reaction", "small molecule" ], "license": "CC-BY-4.0", "mappings": { "biocontext": "RHEA", "edam": "2644", "fairsharing": "FAIRsharing.pn1sr5", "go": "RHEA", "integbio": "nbdc02083", "miriam": "rhea", "n2t": "rhea", "pathguide": "310", "prefixcommons": "rhea", "re3data": "r3d100010891", "togoid": "Rhea" }, "name": "Rhea, the Annotated Reactions Database", "pattern": "^\\d{5}$", "preferred_prefix": "rhea", "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/rhea:$1" } ], "publications": [ { "doi": "10.1093/nar/gkab1016", "pmc": "PMC8728268", "pubmed": "34755880", "title": "Rhea, the reaction knowledgebase in 2022", "year": 2022 }, { "doi": "10.1093/bioinformatics/btz817", "pmc": "PMC7162351", "pubmed": "31688925", "title": "Enzyme annotation in UniProtKB using Rhea", "year": 2020 }, { "doi": "10.1093/nar/gky876", "pmc": "PMC6324061", "pubmed": "30272209", "title": "Updates in Rhea: SPARQLing biochemical reaction data", "year": 2019 }, { "doi": "10.1093/nar/gkw990", "pmc": "PMC5210663", "pubmed": "27789701", "title": "Updates in Rhea - an expert curated resource of biochemical reactions", "year": 2016 }, { "doi": "10.1093/nar/gku961", "pmc": "PMC4384025", "pubmed": "25332395", "title": "Updates in Rhea--a manually curated resource of biochemical reactions", "year": 2014 }, { "doi": "10.1093/nar/gkr1126", "pmc": "PMC3245052", "pubmed": "22135291", "title": "Rhea--a manually curated resource of biochemical reactions", "year": 2011 } ], "synonyms": [ "RHEA" ], "twitter": "rhea_db", "uri_format": "https://www.rhea-db.org/rhea/$1" }, "ribocentre": { "contact": { "email": "huanglin36@mail.sysu.edu.cn", "name": "Lin Huang", "orcid": "0000-0002-2121-365X" }, "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "Ribocentre is designed to contain comprehensive information of all natural ribozymes.", "example": "hammer", "github_request_issue": 611, "homepage": "https://www.ribocentre.org/", "name": "Ribocentre", "pattern": "^[a-zA-Z0-9-]+$", "preferred_prefix": "ribocentre", "publications": [ { "doi": "10.1093/nar/gkac840", "pmc": "PMC9825448", "pubmed": "36177882", "title": "Ribocentre: a database of ribozymes", "year": 2023 } ], "repository": "https://github.com/ribocentre/ribocentre.github.io", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "ribocenter" ], "uri_format": "https://www.ribocentre.org/docs/$1" }, "ricecyc": { "description": "RiceCyc is a catalog of known and/or predicted biochemical pathways from rice (Oryza sativa). Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene database project", "example": "PWY-1042", "homepage": "http://www.gramene.org/pathway/ricecyc.html", "keywords": [ "gene", "pathway" ], "mappings": { "pathguide": "227", "prefixcommons": "ricecyc" }, "name": "Rice Metabolic Pathways", "preferred_prefix": "ricecyc", "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/ricecyc:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://pathway.gramene.org/RICE/NEW-IMAGE?type=PATHWAY&object=$1" }, "ricegap": { "description": "The objective of this project is to provide high quality annotation for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated with functional annotation including expression data, gene ontologies, and tagged lines.", "example": "LOC_Os02g13300", "homepage": "http://rice.plantbiology.msu.edu/annotation_pseudo_current.shtml", "mappings": { "biocontext": "RICEGAP", "miriam": "ricegap", "n2t": "ricegap" }, "name": "Rice Genome Annotation Project", "pattern": "^LOC\\_Os\\d{1,2}g\\d{5}$", "preferred_prefix": "ricegap", "uri_format": "http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=$1" }, "ricenetdb.compound": { "description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.", "example": "OSC1416", "homepage": "http://bis.zju.edu.cn/ricenetdb", "mappings": { "biocontext": "RICENETDB.COMPOUND", "miriam": "ricenetdb.compound", "n2t": "ricenetdb.compound" }, "name": "RiceNetDB Compound", "pattern": "^OSC\\d{4}$", "preferred_prefix": "ricenetdb.compound", "uri_format": "http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID=$1" }, "ricenetdb.gene": { "description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.", "example": "LOC_Os01g49190.1", "homepage": "http://bis.zju.edu.cn/ricenetdb/", "mappings": { "biocontext": "RICENETDB.GENE", "miriam": "ricenetdb.gene", "n2t": "ricenetdb.gene" }, "name": "RiceNetDB Gene", "pattern": "^LOC\\_Os\\d{1,2}g\\d{5}\\.\\d$", "preferred_prefix": "ricenetdb.gene", "uri_format": "http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID=$1" }, "ricenetdb.mirna": { "description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.", "example": "osa-miR446", "homepage": "http://bis.zju.edu.cn/ricenetdb", "mappings": { "biocontext": "RICENETDB.MIRNA", "miriam": "ricenetdb.mirna", "n2t": "ricenetdb.mirna" }, "name": "RiceNetDB miRNA", "pattern": "^osa-miR\\d{3,5}[a-z]{0,1}$", "preferred_prefix": "ricenetdb.mirna", "uri_format": "http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php?ID=$1" }, "ricenetdb.protein": { "description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.", "example": "LOC_Os01g49190", "homepage": "http://bis.zju.edu.cn/ricenetdb/", "mappings": { "biocontext": "RICENETDB.PROTEIN", "miriam": "ricenetdb.protein", "n2t": "ricenetdb.protein" }, "name": "RiceNetDB Protein", "pattern": "^LOC\\_Os\\d{1,2}g\\d{5}$", "preferred_prefix": "ricenetdb.protein", "uri_format": "http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID=$1" }, "ricenetdb.reaction": { "description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.", "example": "OSR0818", "homepage": "http://bis.zju.edu.cn/ricenetdb", "mappings": { "biocontext": "RICENETDB.REACTION", "miriam": "ricenetdb.reaction", "n2t": "ricenetdb.reaction" }, "name": "RiceNetDB Reaction", "pattern": "^OSR\\d{4}$", "preferred_prefix": "ricenetdb.reaction", "uri_format": "http://bis.zju.edu.cn/ricenetdb/reactiondetails.php?ID=$1" }, "rism": { "description": "RISM Online is a new service that will publish the bibliographic and authority data from the catalogue of the Répertoire International des Sources Musicales project.", "example": "people/11035", "homepage": "https://rism.digital/", "mappings": { "miriam": "rism" }, "name": "RISM Online", "pattern": "^[a-z]+/[0-9]+$", "preferred_prefix": "rism", "uri_format": "https://rism.online/$1" }, "rna_sstrand": { "description": "RNA STRAND contains known RNA secondary structures of any type and organism. The ultimate goal of this database is to incorporate a comprehensive collection of known RNA secondary structures, and to provide the scientific community with simple yet powerful ways of analysing, searching and updating the proposed database.", "example": "CRW_00469", "homepage": "http://www.rnasoft.ca/sstrand", "keywords": [ "rna", "structure" ], "mappings": { "prefixcommons": "rna_sstrand" }, "name": "RNA SSTRAND", "preferred_prefix": "rna_sstrand", "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/rna_sstrand:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.rnasoft.ca/sstrand/show_results.php?molecule_ID=$1" }, "rnacentral": { "contact": { "email": "bsweeney@ebi.ac.uk", "github": "blakesweeney", "name": "Blake A Sweeney", "orcid": "0000-0002-6497-2883" }, "description": "RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases.", "example": "URS0000759CF4", "homepage": "https://rnacentral.org/", "keywords": [ "bioinformatics", "biology" ], "mappings": { "biocontext": "RNACENTRAL", "edam": "3856", "fairsharing": "FAIRsharing.KcCjL7", "go": "RNAcentral", "integbio": "nbdc01215", "miriam": "rnacentral", "n2t": "rnacentral", "ncbi": "RNAcentral", "wikidata": "P8697" }, "name": "RNACentral", "pattern": "^URS[0-9A-F]{10}(\\_\\d+)?$", "preferred_prefix": "rnacentral", "publications": [ { "doi": "10.1093/nar/gky1034", "pmc": "PMC6324050", "pubmed": "30395267", "title": "RNAcentral: a hub of information for non-coding RNA sequences", "year": 2019 }, { "doi": "10.1093/nar/gkw1008", "pmc": "PMC5210518", "pubmed": "27794554", "title": "RNAcentral: a comprehensive database of non-coding RNA sequences", "year": 2016 } ], "repository": "https://github.com/RNAcentral/", "synonyms": [ "LNCRNADB" ], "twitter": "RNAcentral", "uri_format": "https://rnacentral.org/rna/$1" }, "rnajunction": { "contact": { "email": "ygyingli@ncsu.edu", "name": "Yaroslava G Yingling", "orcid": "0000-0002-8557-9992" }, "description": "RNAJunction is a database of RNA junctions and kissing loop structures. It contains structure and sequence information for RNA structural elements such as helical junctions, internal loops, bulges and loop–loop interactions. It allows searching by PDB code, structural classification, sequence, keyword or inter-helix angles. RNAJunction is designed to aid analysis of RNA structures as well as design of novel RNA structures on a nanoscale. ", "example": "8668", "homepage": "http://rnajunction.abcc.ncifcrf.gov", "keywords": [ "rna", "structural biology", "structure" ], "mappings": { "fairsharing": "FAIRsharing.zzgvrv", "prefixcommons": "rnajunction" }, "name": "Database of RNA Junctions and Kissing loop Structures", "preferred_prefix": "rnajunction", "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/rnajunction:$1" } ], "publications": [ { "doi": "10.1093/nar/gkm842", "pmc": "PMC2238914", "pubmed": "17947325", "title": "RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign", "year": 2007 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://rnajunction.ncifcrf.gov/JunctionPage.php?jid=$1" }, "rnaloops": { "contact": { "email": "Maciej.Antczak@cs.put.poznan.pl", "github": "mantczak", "name": "Maciej Antczak", "orcid": "0000-0002-5320-2023" }, "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "Rnaloops stores the information about n-way junctions (where n≥3) found in experimentally determined rna 3d structures deposited in the protein data bank.", "example": "91792", "github_request_issue": 601, "homepage": "https://rnaloops.cs.put.poznan.pl", "keywords": [ "rna", "structural bioinformatcs" ], "name": "RNAloops", "pattern": "^\\d+$", "preferred_prefix": "rnaloops", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://rnaloops.cs.put.poznan.pl/search/details/$1" }, "rnamod": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A comprehensive listing of post-transcriptionally modified nucleosides from RNA -", "example": "051", "homepage": "http://rna.rega.kuleuven.be/rnamods/", "keywords": [ "post-transcriptional modification", "rna", "structural bioinformatcs" ], "name": "The RNA Modification Database", "pattern": "^\\d{3}$", "preferred_prefix": "rnamod", "uri_format": "http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?$1" }, "rnamods": { "description": "The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA.", "example": "101", "homepage": "http://rna-mdb.cas.albany.edu/RNAmods/rnaover.htm", "keywords": [ "rna", "structure" ], "mappings": { "biocontext": "RNAMODS", "go": "RNAmods", "miriam": "rnamods", "n2t": "rnamods", "prefixcommons": "rnamods" }, "name": "RNA Modification Database", "pattern": "^\\d{3}$", "preferred_prefix": "rnamods", "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/rnamods:$1" } ], "uri_format": "http://mods.rna.albany.edu/mods/modifications/view/$1" }, "rnao": { "contact": { "email": "BatchelorC@rsc.org", "name": "Colin Batchelor", "orcid": "0000-0001-5985-7429" }, "deprecated": true, "description": "Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures.", "download_obo": "http://purl.obolibrary.org/obo/rnao.obo", "download_owl": "http://purl.obolibrary.org/obo/rnao.owl", "example": "0000128", "homepage": "https://github.com/bgsu-rna/rnao", "keywords": [ "biochemistry", "life science", "molecular structure", "obo", "ontology", "ribonucleic acid", "rna secondary structure", "sequence motif" ], "license": "CC0-1.0", "mappings": { "aberowl": "RNAO", "biocontext": "RNAO", "bioportal": "RNAO", "fairsharing": "FAIRsharing.kqt2h2", "obofoundry": "rnao", "ols": "rnao", "ontobee": "RNAO", "prefixcommons": "rnao" }, "name": "RNA ontology", "pattern": "^\\d{7}$", "preferred_prefix": "RNAO", "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/rnao:$1" } ], "publications": [ { "doi": "10.1261/rna.2343206", "pmc": "PMC1421088", "pubmed": "16484377", "title": "The RNA Ontology Consortium: an open invitation to the RNA community", "year": 2006 }, { "doi": "10.3233/ao-2011-0082", "title": "The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data", "year": 2011 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/RNAO_$1", "repository": "https://github.com/BGSU-RNA/rnao", "uri_format": "http://purl.obolibrary.org/obo/RNAO_$1", "version": "2019-04-15" }, "rnavdb": { "description": "The RNA Virus Database is a database and web application describing the genome organization and providing analytical tools for the 938 known species of RNA virus. It can identify submitted nucleotide sequences, can place them into multiple whole-genome alignments and contains translated genome sequences for all species.", "example": "164750", "homepage": "http://virus.zoo.ox.ac.uk/rnavirusdb/", "keywords": [ "genome", "rna" ], "mappings": { "prefixcommons": "rvd" }, "name": "RNA Virus Database", "preferred_prefix": "rnavdb", "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/rvd:$1" } ], "uri_format": "http://virus.zoo.ox.ac.uk/rnavirusdb/virus.php?id=$1" }, "ro": { "appears_in": [ "agro", "aism", "cdno", "cl", "clao", "clyh", "colao", "cteno", "ecao", "ecocore", "ecto", "envo", "foodon", "fovt", "gallont", "genepio", "go", "hso", "lepao", "maxo", "ons", "ontoavida", "pcl", "pco", "plana", "planp", "poro", "proco", "psdo", "pso", "rbo", "uberon", "upa", "xpo", "zp" ], "banana": "RO", "banana_peel": "_", "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "description": "The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies.", "download_json": "http://purl.obolibrary.org/obo/ro.json", "download_obo": "http://purl.obolibrary.org/obo/ro.obo", "download_owl": "http://purl.obolibrary.org/obo/ro.owl", "example": "0002533", "example_extras": [ "HOM0000022" ], "homepage": "https://oborel.github.io/", "keywords": [ "life science", "obo", "ontology", "relations" ], "license": "CC0-1.0", "mappings": { "aberowl": "RO", "agroportal": "RO", "biocontext": "RO", "biolink": "RO", "bioportal": "OBOREL", "fairsharing": "FAIRsharing.9w8ea0", "go": "RO", "miriam": "ro", "n2t": "ro", "obofoundry": "ro", "ols": "ro", "ontobee": "RO", "prefixcommons": "ro", "wikidata": "P3590" }, "name": "Relation Ontology", "namespace_in_lui": true, "pattern": "^(HOM)?\\d{7}$", "preferred_prefix": "RO", "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/ro:$1" } ], "publications": [ { "doi": "10.1186/2041-1480-5-41", "pmc": "PMC4177597", "pubmed": "25276335", "title": "Structuring research methods and data with the research object model: genomics workflows as a case study", "year": 2014 }, { "doi": "10.1186/gb-2005-6-5-r46", "pmc": "PMC1175958", "pubmed": "15892874", "title": "Relations in biomedical ontologies", "year": 2005 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/RO_$1", "repository": "https://github.com/oborel/obo-relations", "synonyms": [ "RO_proposed_relation", "obo_rel", "oborel" ], "uri_format": "http://purl.obolibrary.org/obo/RO_$1", "version": "2025-03-05" }, "roleo": { "banana": "RoleO", "banana_peel": "_", "comment": "This resource doesn't exist on the web anymore", "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", "name": "Yongqun Oliver He", "orcid": "0000-0001-9189-9661" }, "deprecated": true, "description": "The Role Ontology (RoleO) is a ontology in the domain of role classification. RoleO aims to standardize role classification and support computer-assisted reasoning. RoleO is a community-based ontology, and its development follows the OBO Foundry principles.", "download_owl": "http://aber-owl.net/media/ontologies/ROLEO/1/roleo.owl", "example": "0000002", "homepage": "http://sourceforge.net/projects/roleo", "keywords": [ "obo", "ontology" ], "mappings": { "aberowl": "ROLEO", "bioportal": "ROLEO", "prefixcommons": "roleo" }, "name": "Role Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "RoleO", "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/roleo:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://purl.obolibrary.org/obo/RoleO_$1" }, "ror": { "contact": { "email": "maria.gould@ucop.edu", "github": "mariagould", "name": "Maria Gould", "orcid": "0000-0002-2916-3423" }, "description": "ROR (Research Organization Registry) is a global, community-led registry\nof open persistent identifiers for research organizations. ROR is jointly\noperated by California Digital Library, Crossref, and Datacite.", "download_owl": "https://w3id.org/rorio/rorio.owl", "example": "03yrm5c26", "homepage": "https://ror.org", "keywords": [ "data management", "ontology" ], "license": "CC0-1.0", "mappings": { "bartoc": "20474", "fairsharing": "FAIRsharing.1jKfji", "miriam": "ror", "n2t": "ror" }, "mastodon": "ResearchOrgs@mastodon.social", "name": "Research Organization Registry", "pattern": "^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$", "preferred_prefix": "ror", "repository": "https://github.com/ror-community", "twitter": "ResearchOrgs", "uri_format": "https://ror.org/$1" }, "rouge": { "contact": { "email": "ohara@kazusa.or.jp", "name": "Osamu Ohara", "orcid": "0000-0002-3328-9571" }, "description": "The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.", "example": "mKIAA4200", "homepage": "http://www.kazusa.or.jp/rouge/", "keywords": [ "dna", "life science", "protein" ], "mappings": { "biocontext": "ROUGE", "fairsharing": "FAIRsharing.vdbagq", "integbio": "nbdc00672", "miriam": "rouge", "n2t": "rouge", "prefixcommons": "rouge", "uniprot": "DB-0092" }, "name": "Rodent Unidentified Gene-Encoded Large Proteins", "pattern": "^m\\w+$", "preferred_prefix": "rouge", "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/rouge:$1" } ], "publications": [ { "doi": "10.1093/nar/gkh035", "pmc": "PMC308769", "pubmed": "14681467", "title": "HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE", "year": 2004 } ], "uri_format": "https://www.kazusa.or.jp/rouge/gfpage/$1" }, "rpcec": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Cuban Public Registry of Clinical Trials (RPCEC) is a website with a database of clinical trials, with national coverage. It was established in 2007 under the leadership of the National Coordinating Center of Clinical Trials (CENCEC) and with INFOMED collaboration. (from homepage)", "example": "RPCEC00000423", "homepage": "https://rpcec.sld.cu/en/home", "name": "Cuban Registry of Clinical Trials", "pattern": "^RPCEC\\d+$", "preferred_prefix": "rpcec", "uri_format": "https://rpcec.sld.cu/en/trials/$1" }, "rrid": { "banana": "RRID", "contact": { "email": "bandrow@gmail.com", "github": "bandrow", "name": "Anita Bandrowski", "orcid": "0000-0002-5497-0243" }, "contributor_extras": [ { "email": "bandrow@gmail.com", "github": "bandrow", "name": "Anita Bandrowski", "orcid": "0000-0002-5497-0243" } ], "description": "The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools.: Antibodies, Model Organisms, and Databases / Software tools.\nThe initiative works with participating journals to intercept manuscripts in the publication process that use these resources, and allows publication authors to incorporate RRIDs within the methods sections. It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch.", "example": "AB_262044", "homepage": "https://rrid.site", "keywords": [ "annotation", "centrally registered identifier", "chemistry", "citation", "data retrieval", "knowledge and information systems", "life science", "omics", "resource metadata" ], "mappings": { "biocontext": "RRID", "fairsharing": "FAIRsharing.ATwSZG", "miriam": "rrid", "n2t": "rrid" }, "name": "Research Resource Identification", "namespace_in_lui": true, "pattern": "^[a-zA-Z]+.+$", "preferred_prefix": "rrid", "publications": [ { "doi": "10.1093/nar/gkac927", "pmc": "PMC9825422", "pubmed": "36370112", "title": "The Antibody Registry: ten years of registering antibodies", "year": 2023 }, { "doi": "10.1093/gigascience/giac058", "pmc": "PMC9197678", "pubmed": "35701373", "title": "A decade of GigaScience: What can be learned from half a million RRIDs in the scientific literature?", "year": 2022 }, { "doi": "10.1371/journal.pcbi.1008967", "pmc": "PMC8189493", "pubmed": "34043624", "title": "Antibody Watch: Text mining antibody specificity from the literature", "year": 2021 }, { "doi": "10.1002/cnr2.1150", "pmc": "PMC7941525", "pubmed": "32721132", "title": "Improving transparency and scientific rigor in academic publishing", "year": 2018 }, { "doi": "10.7554/elife.41676", "pmc": "PMC6351100", "pubmed": "30693867", "title": "Incidences of problematic cell lines are lower in papers that use RRIDs to identify cell lines", "year": 2019 }, { "doi": "10.1038/nmeth.3995", "pmc": "PMC10335836", "pubmed": "27595404", "title": "A proposal for validation of antibodies", "year": 2016 }, { "doi": "10.1016/j.neuron.2016.04.030", "pmc": "PMC5854161", "pubmed": "27151636", "title": "RRIDs: A Simple Step toward Improving Reproducibility through Rigor and Transparency of Experimental Methods", "year": 2016 }, { "doi": "10.1002/cne.23913", "pmc": "PMC4684178", "pubmed": "26599696", "title": "The Resource Identification Initiative: A Cultural Shift in Publishing", "year": 2016 }, { "doi": "10.12688/f1000research.6555.2", "pmc": "PMC4648211", "pubmed": "26594330", "title": "The Resource Identification Initiative: A cultural shift in publishing", "year": 2015 }, { "doi": "10.7717/peerj.148", "pmc": "PMC3771067", "pubmed": "24032093", "title": "On the reproducibility of science: unique identification of research resources in the biomedical literature", "year": 2013 } ], "uri_format": "https://scicrunch.org/resolver/RRID:$1" }, "rrrc": { "description": "Supplies biomedical investigators with rat models, embryonic stem cells, related reagents, and protocols they require for their research. In addition to repository, cryostorage and distribution functions, RRRC can facilitate acquisition of rat strains from other international repositories as well as provide consultation and technical training to investigators using rat models. [from RRID]", "example": "961", "homepage": "http://www.rrrc.us/", "keywords": [ "animal", "biomedical", "catalog", "cell line", "cryopreserved", "database", "disease", "drug", "embryo", "embryonic stem cell", "gamete", "genome", "genotyping", "germplasma", "human", "hybrid", "inbred", "infectious", "molecular", "mutant", "nuclear", "ovarian", "pathogen", "protocol", "rat", "rat model", "reagent", "research", "stem cell", "strain", "tissue" ], "mappings": { "rrid": "RRRC" }, "name": "Rat Resource and Research Center", "pattern": "^\\d+$", "preferred_prefix": "rrrc", "uri_format": "https://www.rrrc.us/Strain/?x=$1" }, "rs": { "contact": { "email": "sjwang@mcw.edu", "github": "shurjenw", "name": "Shur-Jen Wang", "orcid": "0000-0001-5256-8683" }, "description": "Ontology of rat strains", "download_obo": "https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.obo", "download_owl": "https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.owl", "example": "0001807", "homepage": "http://rgd.mcw.edu/rgdweb/search/strains.html", "keywords": [ "genetic strain", "life science", "mutation", "obo", "ontology" ], "license": "CC-BY-4.0", "logo": "http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif", "mappings": { "aberowl": "RS", "biocontext": "RS", "bioportal": "RS", "cellosaurus": "RS", "fairsharing": "FAIRsharing.vajn3f", "obofoundry": "rs", "ols": "rs", "ontobee": "RS", "prefixcommons": "rs" }, "name": "Rat Strain Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "RS", "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/rs:$1" } ], "publications": [ { "doi": "10.1186/2041-1480-4-36", "pmc": "PMC4177145", "pubmed": "24267899", "title": "Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD", "year": 2013 }, { "doi": "10.1093/database/bat015", "pmc": "PMC3630803", "pubmed": "23603846", "title": "PhenoMiner: quantitative phenotype curation at the rat genome database", "year": 2013 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/RS_$1", "repository": "https://github.com/rat-genome-database/RS-Rat-Strain-Ontology", "twitter": "ratgenome", "uri_format": "http://purl.obolibrary.org/obo/RS_$1", "version": "6.245" }, "rtecs": { "contact": { "email": "vep1@cdc.gov", "name": "Vernon Putz-Anderson", "orcid": "0000-0002-3588-3259" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "RTECS is a compendium of data extracted from the open scientific literature. The data are recorded in the format developed by the RTECS staff and arranged in alphabetical order by prime chemical name. Six types of toxicity data are included in the file: (1) primary irritation; (2) mutagenic effects; (3) reproductive effects; (4) tumorigenic effects; (5) acute toxicity; and (6) other multiple dose toxicity. Specific numeric toxicity values such as LD50, LC50, TDLo, and TCLo are noted as well as species studied and route of administration used. For each citation, the bibliographic source is listed thereby enabling the user to access the actual studies cited. No attempt has been made to evaluate the studies cited in RTECS. The user has the responsibility of making such assessments.", "example": "AB1925000", "homepage": "https://www.cdc.gov/niosh/rtecs/", "mappings": { "cheminf": "000566" }, "name": "Registry of Toxic Effects of Chemical Substances", "pattern": "^AB\\d+$", "preferred_prefix": "rtecs", "proprietary": true, "publications": [ { "doi": "10.1016/s1074-9098%2899%2900058-1", "title": "An overview of the Registry of Toxic Effects of Chemical Substances (RTECS): Critical information on chemical hazards", "year": 1999 } ], "references": [ "https://www.cdc.gov/niosh/docs/97-119/pdfs/97-119.pdf", "https://www.cdc.gov/niosh/npg/npgdrtec.html" ] }, "rubygems": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A repository of software packages written in Ruby.", "example": "bel", "homepage": "https://rubygems.org", "name": "RubyGems", "preferred_prefix": "rubygems", "uri_format": "https://rubygems.org/gems/$1" }, "runbiosimulations": { "description": "runBioSimulations is a platform for sharing simulation experiments and their results. runBioSimulations enables investigators to use a wide range of simulation tools to execute a wide range of simulations. runBioSimulations permanently saves the results of these simulations, and investigators can share results by sharing URLs similar to sharing URLs for files with DropBox and Google Drive.", "example": "5fde96bdc5f1aa9ff0cce18a", "homepage": "https://icahn.mssm.edu/", "mappings": { "miriam": "runbiosimulations" }, "name": "runBioSimulations", "pattern": "^[0-9a-z]{24,24}$", "preferred_prefix": "runbiosimulations", "uri_format": "https://run.biosimulations.org/simulations/$1" }, "rxno": { "contact": { "email": "batchelorc@rsc.org", "github": "batchelorc", "name": "Colin Batchelor", "orcid": "0000-0001-5985-7429" }, "description": "RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the Diels–Alder cyclization.", "download_obo": "https://github.com/rsc-ontologies/rxno/raw/master/rxno.obo", "download_owl": "http://purl.obolibrary.org/obo/rxno.owl", "example": "0000253", "homepage": "https://github.com/rsc-ontologies/rxno", "keywords": [ "molecular chemistry", "obo", "ontology", "reaction data" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "RXNO", "biocontext": "RXNO", "bioportal": "RXNO", "fairsharing": "FAIRsharing.w4tncg", "obofoundry": "rxno", "ols": "rxno", "ontobee": "RXNO", "wikidata": "P2106" }, "name": "Name Reaction Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "RXNO", "rdf_uri_format": "http://purl.obolibrary.org/obo/RXNO_$1", "repository": "https://github.com/rsc-ontologies/rxno", "uri_format": "http://purl.obolibrary.org/obo/RXNO_$1", "version": "2021-12-16" }, "rxnorm": { "contact": { "email": "rxnorminfo@nlm.nih.gov", "name": "RxNorm Customer Service" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, and Gold Standard Drug Database. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary.", "example": "221058", "homepage": "https://www.nlm.nih.gov/research/umls/rxnorm/", "keywords": [ "biomedical science", "drug", "drug name", "ontology", "preclinical studies" ], "license": "https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf", "mappings": { "aberowl": "RXNORM", "biocontext": "RXCUI", "biolink": "RXNORM", "bioportal": "RXNORM", "fairsharing": "FAIRsharing.36pf8q", "hl7": "2.16.840.1.113883.6.88", "wikidata": "P3345" }, "name": "RxNorm", "pattern": "^[0-9]{1,7}$", "preferred_prefix": "rxnorm", "providers": [ { "code": "bp", "description": "RxNorm in BioPortal", "homepage": "http://purl.bioontology.org/ontology/RXNORM", "name": "BioPortal", "uri_format": "http://purl.bioontology.org/ontology/RXNORM/$1" } ], "publications": [ { "doi": "10.1136/amiajnl-2011-000116", "pmc": "PMC3128404", "pubmed": "21515544", "title": "Normalized names for clinical drugs: RxNorm at 6 years", "year": 2011 }, { "pmc": "PMC2655997", "pubmed": "18998891", "title": "RxTerms - a drug interface terminology derived from RxNorm", "year": 2008 }, { "doi": "10.1109/mitp.2005.122", "title": "RxNorm: prescription for electronic drug information exchange", "year": 2005 } ], "synonyms": [ "RXCUI" ], "uri_format": "https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=$1" }, "s_mart_db": { "description": "S/MARt DB collects information about scaffold/matrix attached regions and the nuclear matrix proteins that are supposed be involved in the interaction of these elements with the nuclear matrix.", "example": "SM0000020", "homepage": "http://smartdb.bioinf.med.uni-goettingen.de/", "keywords": [ "protein" ], "mappings": { "integbio": "nbdc00674", "pathguide": "47", "prefixcommons": "s_mart_db" }, "name": "The S/MAR transaction DataBase", "preferred_prefix": "s_mart_db", "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/s_mart_db:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/getSMAR.cgi?$1" }, "sabiork.compound": { "description": "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The compound data set provides information regarding the reactions in which a compound participates as substrate, product or modifier (e.g. inhibitor, cofactor), and links to further information.", "example": "75", "homepage": "http://sabiork.h-its.org/", "mappings": { "miriam": "sabiork.compound", "n2t": "sabiork.compound" }, "name": "SABIO-RK Compound", "pattern": "^\\d+$", "preferred_prefix": "sabiork.compound", "uri_format": "http://sabiork.h-its.org/newSearch?q=$1" }, "sabiork.ec": { "contact": { "email": "ulrike.wittig@h-its.org", "name": "Ulrike Wittig", "orcid": "0000-0002-9077-5664" }, "description": "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data.", "example": "2.7.1.1", "homepage": "http://sabiork.h-its.org/", "keywords": [ "reaction" ], "mappings": { "biocontext": "SABIORK.EC", "miriam": "sabiork.ec", "n2t": "sabiork.ec", "prefixcommons": "sabiork.ec" }, "name": "SABIO-RK EC Record", "pattern": "^((\\d+)|(\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$", "preferred_prefix": "sabiork.ec", "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/sabiork.ec:$1" } ], "provides": "ec", "publications": [ { "pubmed": "17822389", "title": "Storing and annotating of kinetic data", "year": 2007 } ], "uri_format": "http://sabiork.h-its.org/newSearch?q=ecnumber:$1" }, "sabiork.kineticrecord": { "contact": { "email": "ulrike.wittig@h-its.org", "name": "Ulrike Wittig", "orcid": "0000-0002-9077-5664" }, "description": "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The kinetic record data set provides information regarding the kinetic law, measurement conditions, parameter details and other reference information.", "example": "5046", "homepage": "http://sabiork.h-its.org/", "keywords": [ "classification", "enzyme", "kinetics" ], "mappings": { "biocontext": "SABIORK.KINETICRECORD", "go": "SABIO-RK", "miriam": "sabiork.kineticrecord", "n2t": "sabiork.kineticrecord", "prefixcommons": "sabiork.kinetic" }, "name": "SABIO Reaction Kinetics", "pattern": "^\\d+$", "preferred_prefix": "sabiork.kineticrecord", "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/sabiork.kinetic:$1" } ], "publications": [ { "pubmed": "17822389", "title": "Storing and annotating of kinetic data", "year": 2007 } ], "uri_format": "http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid=$1" }, "sabiork.reaction": { "contact": { "email": "ulrike.wittig@h-its.org", "name": "Ulrike Wittig", "orcid": "0000-0002-9077-5664" }, "description": "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The reaction data set provides information regarding the organism in which a reaction is observed, pathways in which it participates, and links to further information.", "example": "75", "homepage": "http://sabiork.h-its.org/", "keywords": [ "biochemistry", "kinetics", "life science", "pathway", "reaction" ], "mappings": { "biocontext": "SABIORK.REACTION", "edam": "2309", "fairsharing": "FAIRsharing.cwx04e", "miriam": "sabiork.reaction", "n2t": "sabiork.reaction", "pathguide": "226", "prefixcommons": "sabiork.reaction", "re3data": "r3d100011052", "uniprot": "DB-0177" }, "name": "SABIO-RK Reaction", "pattern": "^\\d+$", "preferred_prefix": "sabiork.reaction", "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/sabiork.reaction:$1" } ], "publications": [ { "doi": "10.1093/nar/gkx1065", "pubmed": "29092055" }, { "doi": "10.1093/nar/gkr1046", "pmc": "PMC3245076", "pubmed": "22102587", "title": "SABIO-RK--database for biochemical reaction kinetics", "year": 2011 } ], "synonyms": [ "SABIO-RK" ], "uri_format": "http://sabiork.h-its.org/reacdetails.jsp?reactid=$1" }, "sael": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "name": "Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List", "preferred_prefix": "sael", "publications": [ { "doi": "10.1002/cfg.434", "pmc": "PMC2447422", "pubmed": "18629134", "title": "The SOFG Anatomy Entry List (SAEL): an annotation tool for functional genomics data", "year": 2004 } ] }, "salk": { "appears_in": [ "efo" ], "comment": "spider stuff!", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Scientific research institute for neuroscience, genetics, immunology, plant biology and more.", "example": "037727", "homepage": "https://www.salk.edu/", "name": "Salk Institute for Biological Studies", "pattern": "^\\d{6}$", "preferred_prefix": "salk", "uri_format": "https://abrc.osu.edu/stocks/number/SALK_$1" }, "salmon": { "contact": { "email": "brycemecum@gmail.com", "github": "amoeba", "name": "Bryce Mecum", "orcid": "0000-0002-0381-3766" }, "description": "An ontology representing knowledge about salmon, features of their habitats, salmon stakeholders, and related entities. This ontology is considered to be in the early stages of development, though it is based upon considerable previous work. Contributions of all kinds are welcome and encouraged, including alignments, updates to existing terms, and new terms.", "download_owl": "http://aber-owl.net/media/ontologies/SALMON/2/salmon.owl", "example": "00000674", "homepage": "https://github.com/DataONEorg/sem-prov-ontologies/", "keywords": [ "ontology" ], "mappings": { "aberowl": "SALMON", "bioportal": "SALMON" }, "name": "Salmon Ontology", "pattern": "^\\d+$", "preferred_prefix": "salmon", "uri_format": "https://purl.dataone.org/odo/SALMON_$1" }, "sao": { "contact": { "email": "slarson@ncmir.ucsd.edu", "name": "Stephen Larson" }, "deprecated": true, "description": "SAO describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules.", "download_owl": "http://aber-owl.net/media/ontologies/SAO/2/sao.owl", "example": "5277619", "homepage": "http://ccdb.ucsd.edu/CCDBWebSite/sao.html", "keywords": [ "biochemistry", "obo", "ontology", "owl" ], "mappings": { "aberowl": "SAO", "biocontext": "SAO", "bioportal": "SAO", "obofoundry": "sao", "prefixcommons": "sao" }, "name": "Subcellular Anatomy Ontology", "pattern": "^\\d+$", "preferred_prefix": "SAO", "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/sao:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/SAO_$1", "references": [ "http://www.ontobee.org/ontology/SAO" ], "uri_format": "http://uri.neuinfo.org/nif/nifstd/sao$1" }, "sasap": { "contact": { "email": "brycemecum@gmail.com", "github": "amoeba", "name": "Bryce Mecum", "orcid": "0000-0002-0381-3766" }, "description": "An ontology which represents information about the State of Alaska's Salmon and People (SASAP) project, as well as knowledge about salmon, features of their habitats, salmon stakeholders, and related entities.", "download_owl": "http://aber-owl.net/media/ontologies/SASAP/2/sasap.owl", "example": "00000101", "homepage": "https://github.com/DataONEorg/sem-prov-ontologies", "keywords": [ "ontology" ], "mappings": { "aberowl": "SASAP", "bioportal": "SASAP" }, "name": "The State of Alaska's Salmon and People Ontology", "pattern": "^\\d+$", "preferred_prefix": "sasap", "uri_format": "https://purl.dataone.org/odo/SASAP_$1" }, "sasbdb": { "contact": { "email": "a.kikhney@embl-hamburg.de", "name": "Al Kikhney", "orcid": "0000-0003-1321-3956" }, "description": "Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data.", "example": "SASDAX8", "homepage": "http://www.sasbdb.org/", "keywords": [ "life science", "molecular biology" ], "mappings": { "biocontext": "SASBDB", "fairsharing": "FAIRsharing.i1F3Hb", "miriam": "sasbdb", "n2t": "sasbdb", "re3data": "r3d100012273", "uniprot": "DB-0258" }, "name": "Small Angle Scattering Biological Data Bank", "pattern": "^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$", "preferred_prefix": "sasbdb", "publications": [ { "doi": "10.1002/pro.3731", "pmc": "PMC6933840", "pubmed": "31576635", "title": "SASBDB: Towards an automatically curated and validated repository for biological scattering data", "year": 2019 }, { "doi": "10.1093/nar/gku1047", "pmc": "PMC4383894", "pubmed": "25352555", "title": "SASBDB, a repository for biological small-angle scattering data", "year": 2014 } ], "uri_format": "http://www.sasbdb.org/data/$1" }, "sbo": { "appears_in": [ "proco", "scdo" ], "banana": "SBO", "contact": { "email": "sheriff@ebi.ac.uk", "github": "rsmsheriff", "name": "Rahuman Sheriff", "orcid": "0000-0003-0705-9809" }, "description": "The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort.", "download_obo": "http://purl.obolibrary.org/obo/sbo.obo", "download_owl": "http://purl.obolibrary.org/obo/sbo.owl", "example": "0000485", "homepage": "http://www.ebi.ac.uk/sbo/", "keywords": [ "mathematical model", "modeling and simulation", "molecular interaction", "obo", "ontology", "pathway model", "systems biology" ], "license": "Artistic License 2.0", "mappings": { "aberowl": "SBO", "biocontext": "SBO", "bioportal": "SBO", "fairsharing": "FAIRsharing.s19src", "miriam": "sbo", "n2t": "sbo", "obofoundry": "sbo", "ols": "sbo", "ontobee": "SBO", "prefixcommons": "sbo" }, "name": "Systems Biology Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "SBO", "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/sbo:$1" }, { "code": "biomodels", "description": "Provider for SBO at BioModels", "homepage": "http://biomodels.net", "name": "BioModels", "uri_format": "http://biomodels.net/SBO/SBO_$1" } ], "publications": [ { "doi": "10.1038/msb.2011.77", "pmc": "PMC3261705", "pubmed": "22027554", "title": "Controlled vocabularies and semantics in systems biology", "year": 2011 }, { "doi": "10.1186/1471-2202-7-s1-s11", "pmc": "PMC1775041", "pubmed": "17118155", "title": "Model storage, exchange and integration", "year": 2006 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/SBO_$1", "repository": "https://github.com/EBI-BioModels/SBO", "twitter": "biomodels", "uri_format": "http://purl.obolibrary.org/obo/SBO_$1", "version": "2021-08-28" }, "scancerrna": { "contact": { "email": "zty2009@hit.edu.cn", "name": "Tianyi Zhao", "orcid": "0000-0001-7352-2959" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "SCancerRNA provides identifiers for non-coding RNA biomarkers, including long ncRNA, microRNA, PIWI-interacting RNA, small nucleolar RNA, and circular RNA, with data on their differential expression at the cellular level in cancer.", "example": "9530", "github_request_issue": 1215, "homepage": "http://www.scancerrna.com/", "name": "SCancerRNA", "pattern": "^\\d+$", "preferred_prefix": "scancerrna", "publications": [ { "doi": "10.1093/gpbjnl/qzae023", "pubmed": "39341795", "title": "SCancerRNA: Expression at the Single-cell Level and Interaction Resource of Non-coding RNA Biomarkers for Cancers", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. 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"https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBbWtCIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--69320a8be8ca6a407eaf142714307b4c7e6b5f45/cropped-Screenshot-from-2020-05-23-20-20-32-2.png?disposition=inline", "mappings": { "aberowl": "SCDO", "bioportal": "SCDO", "fairsharing": "FAIRsharing.kkq6pw", "obofoundry": "scdo", "ols": "scdo", "ontobee": "SCDO" }, "name": "Sickle Cell Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "SCDO", "publications": [ { "doi": "10.1093/database/baac014", "pmc": "PMC9216550", "pubmed": "35363306", "title": "The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation", "year": 2022 }, { "doi": "10.1089/omi.2020.0153", "pmc": "PMC7549008", "pubmed": "33021900", "title": "The Sickle Cell Disease Ontology: Enabling Collaborative Research and Co-Designing of New Planetary Health Applications", "year": 2020 }, { "doi": "10.1093/database/baz118", "pmc": "PMC6878945", "pubmed": "31769834", "title": "The Sickle Cell Disease Ontology: enabling universal sickle cell-based knowledge representation", "year": 2019 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/SCDO_$1", "repository": "https://github.com/scdodev/scdo-ontology", "uri_format": "http://purl.obolibrary.org/obo/SCDO_$1", "version": "2021-04-15" }, "schem": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Selventa legacy chemical namespace used with the Biological Expression Language", "example": "A0001", "homepage": "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-legacy-chemical-names.txt", "keywords": [ "bel", "chemistry", "selventa" ], "license": "Apache-2.0", "name": "Selventa Chemicals", "pattern": "^A\\d{4}$", "preferred_prefix": "schem", "uri_format": "https://biopragmatics.github.io/providers/schem/$1" }, "schema": { "contact": { "email": "johardi@stanford.edu", "name": "Josef Hardi" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Schema.org is a collaborative, community activity with a mission to create, maintain, and promote schemas for structured data on the Internet, on web pages, in email messages, and beyond.", "download_owl": "http://aber-owl.net/media/ontologies/SCHEMAORG/2/schemaorg.owl", "download_rdf": "https://schema.org/version/latest/schemaorg-all-http.rdf", "example": "Person", "homepage": "https://schema.org", "keywords": [ "computer science", "general & upper", "ontology", "subject agnostic" ], "mappings": { "aberowl": "SCHEMAORG", "biolink": "schema", "bioportal": "SCHEMA", "fairsharing": "FAIRsharing.hzdzq8", "lov": "schema", "ols": "schemaorg_http", "zazuko": "schema" }, "name": "Schema.org", "preferred_prefix": "schema", "repository": "http://github.com/schemaorg/schemaorg", "synonyms": [ "schemaorg" ], "uri_format": "https://schema.org/$1" }, "scholia.resource": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A frontend to Wikidata", "example": "doi", "homepage": "https://scholia.toolforge.org/", "keywords": [ "registry", "wikidata" ], "name": "Scholia Registry", "preferred_prefix": "scholia.resource", "uri_format": "https://bioregistry.io/metaregistry/scholia/$1" }, "sciflection": { "description": "Sciflection is a public repository for experiments and associated spectra, usually uploaded from Electronic Lab Notebooks, shared under FAIR conditions", "example": "5ede4273-b26c-4ea4-adb7-3ce294ab3397", "homepage": "https://sciformation.com/sciflection.html", "mappings": { "miriam": "sciflection", "re3data": "r3d100013413" }, "name": "Sciflection", "pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$", "preferred_prefix": "sciflection", "uri_format": "https://sciflection.com/$1" }, "sciprofiles": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "numerical identifier for an author in SciProfiles by MDPI", "example": "118021", "homepage": "https://sciprofiles.com/", "keywords": [ "person", "researcher" ], "mappings": { "wikidata": "P8159" }, "name": "SciProfiles ID", "pattern": "^[1-9]\\d*$", "preferred_prefix": "sciprofiles", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1171" ], "uri_format": "https://sciprofiles.com/profile/$1" }, "scomp": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Selventa legacy complex namespace used with the Biological Expression Language", "example": "C0001", "homepage": "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-named-complexes.txt", "keywords": [ "bel", "protein complexes", "selventa" ], "license": "Apache-2.0", "name": "Selventa Complexes", "pattern": "^C\\d{4}$", "preferred_prefix": "scomp", "uri_format": "https://biopragmatics.github.io/providers/scomp/$1" }, "scop": { "contact": { "email": "JMChandonia@lbl.gov", "github": "jmchandonia", "name": "John-Marc Chandonia", "orcid": "0000-0002-5153-9079" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "SCOP(e) unique identifier. This is simply a number that may be used to reference any entry in the SCOP(e) hierarchy, from root to leaves (Fold, Superfamily, Family, etc.).", "example": "47419", "homepage": "https://scop.berkeley.edu", "keywords": [ "protein", "structure" ], "mappings": { "biocontext": "SCOP", "edam": "1042", "miriam": "scop", "n2t": "scop", "prefixcommons": "scop" }, "name": "Structural Classification of Proteins - Unique Identifier", "pattern": "^\\d+$", "preferred_prefix": "scop", "providers": [ { "code": "CURATOR_REVIEW", "description": "SCOP at Berkeley", "homepage": "http://scop.berkeley.edu/", "name": "SCOP at Berkeley", "uri_format": "http://scop.berkeley.edu/sunid=$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/scop:$1" }, { "code": "mrc", "description": "SCOP at UK Medical Research council (MRC)", "homepage": "https://scop.mrc-lmb.cam.ac.uk", "name": "SCOP at UK Medical Research council (MRC)", "uri_format": "https://scop.mrc-lmb.cam.ac.uk/term/$1" } ], "publications": [ { "doi": "10.1093/nar/27.1.254", "pmc": "PMC148149", "pubmed": "9847194", "title": "SCOP: a Structural Classification of Proteins database", "year": 1999 }, { "doi": "10.1093/nar/25.1.236", "pmc": "PMC146380", "pubmed": "9016544", "title": "SCOP: a structural classification of proteins database", "year": 1997 }, { "doi": "10.1093/nar/28.1.257", "pmc": "PMC102479", "pubmed": "10592240", "title": "SCOP: a structural classification of proteins database", "year": 2000 }, { "doi": "10.1107/s0907444998009172", "pubmed": "10089491", "title": "SCOP, Structural Classification of Proteins database: applications to evaluation of the effectiveness of sequence alignment methods and statistics of protein structural data", "year": 1998 } ], "references": [ "https://scop.berkeley.edu/help/#stableidentifiers" ], "synonyms": [ "scop.sun", "scop.sunid" ], "uri_format": "http://scop.berkeley.edu/sunid=$1" }, "scop.sccs": { "contact": { "email": "JMChandonia@lbl.gov", "github": "jmchandonia", "name": "John-Marc Chandonia", "orcid": "0000-0002-5153-9079" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This is a dot notation used to concisely describe a SCOP(e) class, fold, superfamily, and family. For example, a.39.1.1 references the 'Calbindin D9K' family, where 'a' represents the class, '39' represents the fold, '1' represents the superfamily, and the last '1' represents the family.", "example": "a.39.1.1", "example_extras": [ "a", "a.39", "a.39.1" ], "homepage": "https://scop.berkeley.edu", "mappings": { "edam": "1041" }, "name": "SCOP(e) concise classification string", "preferred_prefix": "scop.sccs", "references": [ "https://scop.berkeley.edu/help/#stableidentifiers" ], "uri_format": "http://scop.berkeley.edu/sccs=$1" }, "scop.sid": { "contact": { "email": "JMChandonia@lbl.gov", "github": "jmchandonia", "name": "John-Marc Chandonia", "orcid": "0000-0002-5153-9079" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": " A 7-character sid consists of \"d\" followed by the 4-character PDB ID of the file of origin, the PDB chain ID ('_' if none, '.' if multiple as is the case in genetic domains), and a single character (usually an integer) if needed to specify the domain uniquely ('_' if not). Sids are currently all lower case, even when the chain letter is upper case. Example sids include d4akea1, d9hvpa_, and d1cph.1.", "example": "d4akea1", "example_extras": [ "d1cph.1", "d9hvpa_" ], "homepage": "https://scop.berkeley.edu", "mappings": { "edam": "1039" }, "name": "Structural Classification of Protein - Stable Domain Identifier", "preferred_prefix": "scop.sid", "references": [ "https://scop.berkeley.edu/help/#stableidentifiers" ], "uri_format": "http://scop.berkeley.edu/sid=$1" }, "scopus": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Scopus is the largest abstract and citation database of peer-reviewed literature: scientific journals, books and conference proceedings. \nDelivering a comprehensive overview of the world's research output in the fields of science, technology, medicine, social sciences, and arts \nand humanities, Scopus features smart tools to track, analyze and visualize research.", "example": "56305849200", "homepage": "https://www.scopus.com", "keywords": [ "subject agnostic" ], "mappings": { "biolink": "ScopusID", "fairsharing": "FAIRsharing.0a674c", "wikidata": "P1153" }, "name": "Scopus Researcher", "pattern": "^\\d+$", "preferred_prefix": "scopus", "synonyms": [ "scopus.author" ], "twitter": "Scopus", "uri_format": "https://www.scopus.com/authid/detail.uri?authorId=$1" }, "scopus.affiliation": { "description": "identifier for an organisation in author affiliations per Scopus", "example": "60025709", "homepage": "http://info.sciencedirect.com/scopus/scopus-in-detail/tools/affiliationidentifier", "mappings": { "wikidata": "P1155" }, "name": "Scopus affiliation ID", "preferred_prefix": "scopus.affiliation", "uri_format": "https://www.scopus.com/affil/profile.uri?afid=$1" }, "scopus.publication": { "description": "identifier for a source/publication venue (journal, conference, etc) in Scopus", "example": "16129", "homepage": "https://www.scopus.com/", "mappings": { "wikidata": "P1156" }, "name": "Scopus Publication", "pattern": "^[1-9]\\d{0,11}$", "preferred_prefix": "scopus.publication", "uri_format": "https://www.scopus.com/sourceid/$1" }, "scopus.work": { "description": "unique academic work identifier assigned in Scopus bibliographic database", "example": "2-s2.0-0030770923", "homepage": "https://www.scopus.com/", "mappings": { "wikidata": "P1154" }, "name": "Scopus Work", "pattern": "^2-s2\\.0-\\d+$", "preferred_prefix": "scopus.work", "synonyms": [ "scopus.eid" ], "uri_format": "http://www.scopus.com/record/display.url?origin=inward&eid=$1" }, "scoro": { "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 based on PRO for describing the contributions that may be made, and the roles that may be held by a person with respect to a journal article or other publication (e.g. the role of article guarantor or illustrator).", "example": "IntellectualContribution", "homepage": "http://www.sparontologies.net/ontologies/scoro", "keywords": [ "academy", "bibliography", "citation", "data model", "report", "subject agnostic" ], "mappings": { "fairsharing": "FAIRsharing.c86b48", "lov": "scoro" }, "name": "Scholarly Contributions and Roles Ontology", "preferred_prefix": "SCoRO", "publications": [ { "doi": "10.3233/sw-150177", "title": "The Document Components Ontology (DoCO)", "year": 2016 } ], "repository": "https://github.com/sparontologies/scoro", "twitter": "sparontologies", "uri_format": "http://purl.org/spar/scoro/$1" }, "scpd": { "comment": "This resource doesn't exist on the web anymore", "deprecated": true, "description": "Database containing promotor sequences found in Saccharomyces cerevisiae.", "example": "CDC2", "homepage": "http://rulai.cshl.edu/SCPD/", "keywords": [ "dna", "rna" ], "mappings": { "pathguide": "130", "prefixcommons": "scpd" }, "name": "Saccharomyces cerevisiae promoter database", "preferred_prefix": "scpd", "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/scpd:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://rulai.cshl.edu/cgi-bin/SCPD/getgene2?$1" }, "scr": { "contact": { "email": "abandrowski@ncmir.ucsd.edu", "name": "Anita Bandrowski", "orcid": "0000-0002-5497-0243" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The SciCrunch Registry holds metadata records that describe digital resources, e.g., software, databases, projects and also services. Most of these are produced as a result of government funding and are available to the scientific community. Resources are manually curated to make sure the information is accurate. We also use a web crawler to find literature mentions for the resources.", "example": "022586", "github_request_issue": 421, "homepage": "https://scicrunch.org/browse/resourcedashboard", "keywords": [ "interactive portal", "life science", "neurobiology", "nih initiative", "rrid" ], "mappings": { "fairsharing": "FAIRsharing.kj4pvk", "integbio": "nbdc01937", "rrid": "SCR" }, "name": "SciCrunch Registry", "pattern": "^\\d+$", "preferred_prefix": "scr", "publications": [ { "doi": "10.1002/cne.23913", "pmc": "PMC4684178", "pubmed": "26599696", "title": "The Resource Identification Initiative: A Cultural Shift in Publishing", "year": 2016 }, { "pubmed": "22434839" } ], "synonyms": [ "scicrunch" ], "uri_format": "http://scicrunch.org/resolver/SCR_$1" }, "scretf": { "description": "ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor.", "example": "RSC3", "homepage": "http://stormo.wustl.edu/ScerTF/", "mappings": { "biocontext": "SCRETF", "miriam": "scretf", "n2t": "scretf" }, "name": "ScerTF", "pattern": "^\\w+$", "preferred_prefix": "scretf", "uri_format": "http://stormo.wustl.edu/ScerTF/details/$1" }, "sdap": { "description": "SDAP is a Web server that integrates a database of allergenic proteins with various bioinformatics tools for performing structural studies related to allergens and characterization of their epitopes.", "example": "610", "homepage": "http://fermi.utmb.edu/SDAP", "keywords": [ "protein", "structure" ], "mappings": { "prefixcommons": "sdap" }, "name": "Structural Database of Allergenic Proteins", "preferred_prefix": "sdap", "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/sdap:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://fermi.utmb.edu/cgi-bin/SDAP/sdap_02?dB_Type=0&allid=$1" }, "sdbs": { "description": "The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds. 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It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.", "example": "cpd15380", "homepage": "http://modelseed.org/", "mappings": { "biocontext": "SEED.COMPOUND", "miriam": "seed.compound", "n2t": "seed.compound" }, "name": "SEED Compound", "pattern": "^cpd\\d+$", "preferred_prefix": "seed.compound", "repository": "https://github.com/TheSEED", "uri_format": "http://modelseed.org/biochem/compounds/$1" }, "seed.reaction": { "description": "ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions.", "example": "rxn00001", "homepage": "http://modelseed.org/biochem/reactions/", "mappings": { "biolink": "SEED.REACTION", "miriam": "seed.reaction", "n2t": "seed.reaction" }, "name": "SEED Reactions", "pattern": "^rxn\\d+$", "preferred_prefix": "seed.reaction", "uri_format": "http://modelseed.org/biochem/reactions/$1" }, "seed.role": { "contributor": { "github": "samseaver", "name": "Sam Seaver", "orcid": "0000-0002-7674-5194" }, "description": "With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [Fellowship for Interpretation of Genomes (FIG)](http://thefig.info/) as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data.\nThis prefix provides identifiers for molecular roles that describe the function of one or more proteins in microbes and plants.", "example": "Histidinol dehydrogenase (EC 1.1.1.23)", "example_extras": [ "Archease", "Xylan oligosaccharide ABC transporter, substrate-binding component" ], "github_request_issue": 1340, "homepage": "https://theseed.org/", "license": "MIT", "name": "The SEED", "preferred_prefix": "seed.role", "publications": [ { "doi": "10.1093/nar/gki866", "pmc": "PMC1251668", "pubmed": "16214803", "title": "The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes", "year": 2005 } ], "repository": "https://github.com/orgs/TheSEED", "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. 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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/sep:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/SEP_$1", "uri_format": "http://purl.obolibrary.org/obo/SEP_$1" }, "sepio": { "contact": { "email": "mhb120@gmail.com", "github": "mbrush", "name": "Matthew Brush", "orcid": "0000-0002-1048-5019" }, "description": "An ontology for representing the provenance of scientific claims and the evidence that supports them.", "download_owl": "http://purl.obolibrary.org/obo/sepio.owl", "example": "0000048", "homepage": "https://github.com/monarch-initiative/SEPIO-ontology", "keywords": [ "obo", "ontology" ], "license": "CC-BY-3.0", "logo": "https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/SEPIO-LOGOS/sepio_logo_black-banner.png", "mappings": { "aberowl": "SEPIO", "biocontext": "SEPIO", "bioportal": "SEPIO", "obofoundry": "sepio", "ols": "sepio", "ontobee": "SEPIO" }, "name": "Scientific Evidence and Provenance Information Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "SEPIO", "rdf_uri_format": "http://purl.obolibrary.org/obo/SEPIO_$1", "repository": "https://github.com/monarch-initiative/SEPIO-ontology", "uri_format": "http://purl.obolibrary.org/obo/SEPIO_$1", "version": "2023-06-13" }, "sfam": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Selventa legacy protein family namespace used with the Biological Expression Language", "example": "F0001", "homepage": "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-protein-families.txt", "keywords": [ "bel", "protein families", "selventa" ], "license": "Apache-2.0", "name": "Selventa Families", "pattern": "^F\\d{4}$", "preferred_prefix": "sfam", "uri_format": "https://biopragmatics.github.io/providers/sfam/$1" }, "sgd": { "contact": { "email": "cherry@genome.stanford.edu", "name": "J. 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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/signaling-gateway:$1" } ], "publications": [ { "doi": "10.1093/bioinformatics/btr190", "pmc": "PMC3106186", "pubmed": "21505029", "title": "Signaling gateway molecule pages--a data model perspective", "year": 2011 }, { "doi": "10.1093/nar/gkm907", "pmc": "PMC2238911", "pubmed": "17965093", "title": "The Molecule Pages database", "year": 2007 }, { "doi": "10.1038/nature01307", "pubmed": "12478304", "title": "The Molecule Pages database", "year": 2002 } ], "uri_format": "http://www.signaling-gateway.org/molecule/query?afcsid=$1" }, "signor": { "contact": { "email": "gianni.cesareni@torvergata.it", "name": "Gianni Cesareni", "orcid": "0000-0002-9528-6018" }, "description": "SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature.", "example": "SIGNOR-C41", "homepage": "https://signor.uniroma2.it/", "keywords": [ "biology" ], "license": "CC-BY-NC-4.0", "mappings": { "fairsharing": "FAIRsharing.ss78t4", "miriam": "signor", "pathguide": "599", "uniprot": "DB-0206" }, "name": "Signaling Network Open Resource", "pattern": "^SIGNOR\\-[A-Z]+\\d+$", "preferred_prefix": "signor", "publications": [ { "doi": "10.1093/nar/gkac883", "pmc": "PMC9825604", "pubmed": "36243968", "title": "SIGNOR 3.0, the SIGnaling network open resource 3.0: 2022 update", "year": 2022 }, { "doi": "10.1093/nar/gkv1048", "pmc": "PMC4702784", "pubmed": "26467481", "title": "SIGNOR: a database of causal relationships between biological entities", "year": 2015 } ], "synonyms": [ "SIGNOR" ], "uri_format": "https://signor.uniroma2.it/relation_result.php?id=$1" }, "signor.relation": { "comment": "Currently, you can put a SIGNOR relation ID into the main page search box and it will resolve, but there is not currently a way to resolve them via a URL pattern", "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "Identifiers for relationships between proteins and complexes, along with their type and provenance", "example": "SIGNOR-252737", "github_request_issue": 604, "homepage": "https://signor.uniroma2.it", "keywords": [ "protein-protein interactions" ], "name": "SIGNOR Relation", "part_of": "signor", "pattern": "^SIGNOR-\\d+$", "preferred_prefix": "signor.relation", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } }, "silva.taxon": { "contact": { "email": "lorenz.reimer@dsmz.de", "name": "Lorenz Reimer", "orcid": "0000-0002-7805-0660" }, "contributor": { "email": "jplfaria@anl.gov", "github": "jplfaria", "name": "Jose P. Faria", "orcid": "0000-0001-9302-7250" }, "description": "SILVA is a resource of aligned ribosomal RNA (rRNA) gene sequences for Bacteria, Archaea, and Eukaryotes.\n\nIt assigns internal, auto-incremented integer identifiers to taxa. However, these identifiers are not persistent nor unique - if the label for a taxon is changed, it assigned a new identifier and the old identifier is removed.", "example": "11084", "github_request_issue": 1306, "homepage": "https://www.arb-silva.de", "license": "CC-BY-SA-4.0", "logo": "https://www.arb-silva.de/fileadmin/graphics_general/main/dissemination/silva-sticker-1_2_ext_33.png", "name": "SILVA Taxon", "pattern": "^\\d+$", "preferred_prefix": "silva.taxon", "publications": [ { "doi": "10.1093/nar/gkt1209", "pmc": "PMC3965112", "pubmed": "24293649", "title": "The SILVA and \"All-species Living Tree Project (LTP)\" taxonomic frameworks", "year": 2014 }, { "doi": "10.1093/nar/gks1219", "pmc": "PMC3531112", "pubmed": "23193283", "title": "The SILVA ribosomal RNA gene database project: improved data processing and web-based tools", "year": 2012 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" } }, "sio": { "banana": "SIO", "banana_peel": "_", "contact": { "email": "michel.dumontier@gmail.com", "github": "micheldumontier", "name": "Michel Dumontier", "orcid": "0000-0003-4727-9435" }, "description": "The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities.", "download_owl": "http://semanticscience.org/ontology/sio/v1.59/sio-release.owl", "example": "000912", "homepage": "https://github.com/micheldumontier/semanticscience", "keywords": [ "biology", "knowledge representation", "natural science", "ontology", "subject agnostic" ], "mappings": { "aberowl": "SIO", "agroportal": "SIO", "biocontext": "SIO", "biolink": "SIO", "bioportal": "SIO", "fairsharing": "FAIRsharing.dpkb5f", "lov": "sio", "miriam": "sio", "ols": "sio", "ontobee": "SIO" }, "name": "Semanticscience Integrated Ontology", "pattern": "^\\d{6}$", "preferred_prefix": "sio", "publications": [ { "doi": "10.1186/2041-1480-5-14", "pmc": "PMC4015691", "pubmed": "24602174", "title": "The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery", "year": 2014 } ], "repository": "https://github.com/micheldumontier/semanticscience", "uri_format": "https://semanticscience.org/resource/SIO_$1", "version": "1.59" }, "siren": { "comment": "appears in FOODON, there is no website other than the spreadsheet referenced below on langual's site", "contact": { "email": "patrice.buche@inrae.fr", "name": "Patrice Buche", "orcid": "0000-0002-9134-5404" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A modern method of records management and an automated cross-referenced subject index for accurate and comprehensive information retrieval developed by the US FDA's Bureau of Foods", "example": "F11903", "homepage": "https://www.langual.org/langual_indexed_datasets.asp", "mappings": { "agroportal": "SIREN" }, "name": "Scientific Information Retrieval and Exchange Network", "pattern": "^F\\d+$", "preferred_prefix": "siren", "publications": [ { "doi": "10.1093/jaoac/65.5.1268", "title": "SIREN: Data Base Approach to Scientific Information Handling in the Bureau of Foods, Food and Drug Administration", "year": 1982 } ], "references": [ "https://github.com/FoodOntology/foodon/issues/267", "https://www.langual.org/download/IndexedDatasets/FDA/SIREN%20(updated).TXT" ], "synonyms": [ "SUBSET_SIREN" ] }, "sisu": { "contact": { "email": "hannele.laivuori@helsinki.fi", "name": "Hannele Laivuori", "orcid": "0000-0003-3212-7826" }, "description": "The Sequencing Initiative Suomi (SISu) project is an international collaboration to harmonize and aggregate whole genome and exome sequence data from Finnish samples, providing data for researchers and clinicians. The SISu project allows for the search of variants to determine their attributes and occurrence in Finnish cohorts, and provides summary data on single nucleotide variants and indels from exomes, sequenced in disease-specific and population genetic studies.", "example": "17:41223048", "homepage": "http://www.sisuproject.fi/", "keywords": [ "biomedical science", "epidemiology", "genomics", "medicine", "preclinical studies" ], "mappings": { "biocontext": "SISU", "fairsharing": "FAIRsharing.t1a232", "miriam": "sisu", "n2t": "sisu" }, "name": "Sequencing Initiative Suomi", "pattern": "^[0-9]+:[0-9]+$", "preferred_prefix": "sisu", "publications": [ { "doi": "10.1371/journal.pone.0128524", "pmc": "PMC4452275", "pubmed": "26030606", "title": "Targeted resequencing of the pericentromere of chromosome 2 linked to constitutional delay of growth and puberty", "year": 2015 }, { "doi": "10.1371/journal.pgen.1004494", "pmc": "PMC4117444", "pubmed": "25078778", "title": "Distribution and medical impact of loss-of-function variants in the Finnish founder population", "year": 2014 } ], "uri_format": "http://search.sisuproject.fi/#/variant/$1" }, "sitex": { "contact": { "email": "imedvedeva@celgene.com", "github": "imedvedeva-celgene", "name": "Irina Medvedeva", "orcid": "0000-0003-2802-8198" }, "description": "SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments.", "example": "1000", "homepage": "http://www-bionet.sscc.ru/sitex/", "keywords": [ "domain", "eukaryotic", "life science", "sequence", "structure" ], "mappings": { "biocontext": "SITEX", "fairsharing": "FAIRsharing.5mr9c5", "miriam": "sitex", "n2t": "sitex", "prefixcommons": "sitex" }, "name": "SitEx", "pattern": "^\\d+$", "preferred_prefix": "sitex", "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/sitex:$1" } ], "publications": [ { "doi": "10.1093/nar/gkr1187", "pmc": "PMC3245165", "pubmed": "22139920", "title": "SitEx: a computer system for analysis of projections of protein functional sites on eukaryotic genes", "year": 2011 } ], "uri_format": "http://www-bionet.sscc.ru/sitex/index.php?siteid=$1" }, "skip": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "SKIP is aiming to promote the exchange of information and joint research between researchers by aggregating various information of stem cells (iPS cells, iPS cells derived from patients, etc.) to stimulate research on disease and regenerative medicine.", "example": "SKIP001214", "homepage": "https://skip.stemcellinformatics.org/en/", "mappings": { "cellosaurus": "SKIP" }, "name": "Stemcell Knowledge and Information Portal", "pattern": "^SKIP\\d+$", "preferred_prefix": "skip", "uri_format": "https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1" }, "skm": { "description": "Stress Knowledge Map (SKM, available at https://skm.nib.si) is a knowledge graph resulting from the integration of dispersed published information on plant molecular responses to biotic and abiotic stressors. ", "example": "rx00408", "homepage": "http://www.nib.si/eng/", "mappings": { "miriam": "skm" }, "name": "Stress Knowledge Map", "pattern": "^rx[0-9]{5}$", "preferred_prefix": "skm", "uri_format": "https://skm.nib.si/api/pss/reactions?reaction_id=$1&return_field=summary" }, "skos": { "contact": { "email": "alistair.miles@linacre.ox.ac.uk", "github": "alimanfoo", "name": "Alistair Miles", "orcid": "0000-0001-9018-4680" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "SKOS is an area of work developing specifications and standards to support the use of knowledge organization systems (KOS) such as thesauri, classification schemes, subject heading lists and taxonomies within the framework of the Semantic Web", "download_owl": "http://aber-owl.net/media/ontologies/skos/1/skos.owl", "download_rdf": "http://www.w3.org/TR/skos-reference/skos.rdf", "example": "prefLabel", "homepage": "https://www.w3.org/2004/02/skos/", "keywords": [ "ontology", "subject agnostic", "w3c rec" ], "mappings": { "aberowl": "skos", "bartoc": "18274", "biocontext": "skos", "fairsharing": "FAIRsharing.48e326", "lov": "skos", "ols": "skos", "zazuko": "skos" }, "name": "Simple Knowledge Organization System", "preferred_prefix": "skos", "uri_format": "http://www.w3.org/2004/02/skos/core#$1" }, "skosxl": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Simple Knowledge Organization System (SKOS) is a common data model for sharing and linking knowledge organization systems via the Semantic Web. SKOS-XL defines an extension for the Simple Knowledge Organization System, providing additional support for describing and linking lexical entities.This document provides a brief description of the SKOS-XL vocabulary.", "example": "literalForm", "homepage": "http://www.w3.org/2008/05/skos-xl#", "keywords": [ "data model", "metadata", "semantic web", "skos", "w3c rec" ], "mappings": { "lov": "skosxl", "zazuko": "skosxl" }, "name": "Simple Knowledge Organization System eXtension for Labels", "preferred_prefix": "skosxl", "uri_format": "http://www.w3.org/2008/05/skos-xl#$1" }, "slctr": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Sri Lanka Clinical Trials Registry (SLCTR) is a Registry for clinical trials involving human subjects, conducted in Sri Lanka or overseas. The SLCTR is a Primary Registry linked to the Registry Network of the International Clinical Trials Registry Platform of the WHO (WHO-ICTRP). It is a not-for-profit Registry, with free and open access to researchers, clinicians, and the general public. (from homepage)", "example": "SLCTR/2023/010", "homepage": "https://slctr.lk/", "logo": "https://slctr.lk/images/logo.png", "name": "Sri Lanka Clinical Trials Registry", "pattern": "^SLCTR/\\d{4}/\\d+$", "preferred_prefix": "slctr", "references": [ "https://slctr.lk/trials/slctr-2023-010" ] }, "slkbase": { "description": "Cell line databases/resources", "example": "3618", "homepage": "https://sumlineknowledgebase.com/", "mappings": { "cellosaurus": "SLKBase" }, "name": "SUM Breast Cancer Cell Line Knowledge Base", "pattern": "^\\d+$", "preferred_prefix": "slkbase", "uri_format": "https://sumlineknowledgebase.com/?page_id=$1" }, "slm": { "banana": "SLM", "contact": { "email": "swisslipids@isb-sib.ch", "name": "Alan Bridge", "orcid": "0000-0003-2148-9135" }, "description": "SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions.", "download_rdf": "file:///nfs/production/parkinso/spot/ols4/prod/local_ontologies/swisslipids.ttl", "example": "000000341", "homepage": "http://www.swisslipids.org/#/", "keywords": [ "life science", "metabolomics" ], "license": "CC-BY-4.0", "mappings": { "biocontext": "SWISSLIPID", "fairsharing": "FAIRsharing.pxr7x2", "integbio": "nbdc02026", "miriam": "slm", "n2t": "swisslipid", "ols": "slm", "pathguide": "687", "re3data": "r3d100012603", "togoid": "Swisslipids", "uniprot": "DB-0197", "wikidata": "P8691" }, "name": "SwissLipid", "namespace_in_lui": true, "pattern": "^\\d+$", "preferred_prefix": "SLM", "publications": [ { "doi": "10.1093/bioinformatics/btv285", "pmc": "PMC4547616", "pubmed": "25943471", "title": "The SwissLipids knowledgebase for lipid biology", "year": 2015 } ], "synonyms": [ "swisslipid", "swisslipids" ], "uri_format": "https://www.swisslipids.org/#/entity/SLM:$1" }, "slso": { "contact": { "email": "daniel.c.berrios@nasa.gov", "github": "DanBerrios", "name": "Dan Berrios", "orcid": "0000-0003-4312-9552" }, "description": "The Space Life Sciences Ontology is an application ontology and is intended to support the operation of NASA's Life Sciences Data Archive and other systems that contain space life science research data.", "download_json": "https://github.com/nasa/LSDAO/raw/refs/heads/master/slso.json", "download_obo": "http://purl.obolibrary.org/obo/slso.obo", "download_owl": "http://purl.obolibrary.org/obo/slso.owl", "example": "0000000", "homepage": "https://github.com/nasa/LSDAO", "keywords": [ "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "SLSO", "bioportal": "SLSO", "obofoundry": "slso", "ontobee": "SLSO" }, "name": "Space Life Sciences Ontology", "preferred_prefix": "SLSO", "rdf_uri_format": "http://purl.obolibrary.org/obo/SLSO_$1", "repository": "https://github.com/nasa/LSDAO", "uri_format": "http://purl.obolibrary.org/obo/SLSO_$1" }, "smart": { "contact": { "email": "chris.ponting@ed.ac.uk", "name": "Chris P. Ponting", "orcid": "0000-0003-0202-7816" }, "description": "The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures.", "example": "SM00015", "homepage": "http://smart.embl-heidelberg.de/", "keywords": [ "domain", "life science", "protein", "structure" ], "mappings": { "biocontext": "SMART", "fairsharing": "FAIRsharing.hsbpq3", "go": "SMART", "integbio": "nbdc00682", "miriam": "smart", "n2t": "smart", "prefixcommons": "smart", "togoid": "Smart", "uniprot": "DB-0097" }, "name": "Simple Modular Architecture Research Tool", "pattern": "^SM\\d{5}$", "preferred_prefix": "smart", "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/smart:$1" } ], "publications": [ { "doi": "10.1093/nar/27.1.229", "pmc": "PMC148142", "pubmed": "9847187", "title": "SMART: identification and annotation of domains from signalling and extracellular protein sequences", "year": 1999 }, { "doi": "10.1093/nar/gkx922", "pmc": "PMC5753352", "pubmed": "29040681", "title": "20 years of the SMART protein domain annotation resource", "year": 2018 }, { "doi": "10.1093/nar/gku949", "pmc": "PMC4384020", "pubmed": "25300481", "title": "SMART: recent updates, new developments and status in 2015", "year": 2014 }, { "doi": "10.1093/nar/gkr931", "pmc": "PMC3245027", "pubmed": "22053084", "title": "SMART 7: recent updates to the protein domain annotation resource", "year": 2011 }, { "doi": "10.1093/nar/gkn808", "pmc": "PMC2686533", "pubmed": "18978020", "title": "SMART 6: recent updates and new developments", "year": 2008 }, { "doi": "10.1093/nar/gkj079", "pmc": "PMC1347442", "pubmed": "16381859", "title": "SMART 5: domains in the context of genomes and networks", "year": 2006 }, { "doi": "10.1093/nar/gkh088", "pmc": "PMC308822", "pubmed": "14681379", "title": "SMART 4.0: towards genomic data integration", "year": 2004 }, { "doi": "10.1093/nar/30.1.242", "pmc": "PMC99073", "pubmed": "11752305", "title": "Recent improvements to the SMART domain-based sequence annotation resource", "year": 2002 }, { "doi": "10.1093/nar/28.1.231", "pmc": "PMC102444", "pubmed": "10592234", "title": "SMART: a web-based tool for the study of genetically mobile domains", "year": 2000 }, { "doi": "10.1016/s0959-440x(99)80055-4", "pubmed": "10361098", "title": "Protein families in multicellular organisms", "year": 1999 }, { "doi": "10.1016/S0959-440X(99)80055-4", "title": "Protein families in multicellular organisms." } ], "uri_format": "http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1" }, "smc.bgc": { "contact": { "email": "dwudwary@lbl.gov", "name": "Daniel W Udwary", "orcid": "0000-0002-3491-0198" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "The secondary metabolism collaboratory is a database for secondary metabolite biosynthetic gene clusters. This prefix represents identifiers for individual biosynthetic gene clusters (BGCs) linked to their corresponding bacterial or archaeal source.", "example": "12039302", "github_request_issue": 1301, "homepage": "https://smc.jgi.doe.gov", "name": "Secondary Metabolism Collaboratory", "pattern": "^\\d+$", "preferred_prefix": "smc.bgc", "publications": [ { "doi": "10.1093/nar/gkae1060", "pubmed": "39540430", "title": "The secondary metabolism collaboratory: a database and web discussion portal for secondary metabolite biosynthetic gene clusters", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://smc.jgi.doe.gov/bgc/$1" }, "smc.source": { "contact": { "email": "dwudwary@lbl.gov", "name": "Daniel W Udwary", "orcid": "0000-0002-3491-0198" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "The secondary metabolism collaboratory is a database for secondary metabolite biosynthetic gene clusters. This prefix represents identifiers for bacteria and archaea sources linked to their associated set of biosynthetic gene clusters (BGCs).", "example": "1", "github_request_issue": 1301, "homepage": "https://smc.jgi.doe.gov", "name": "Secondary Metabolism Collaboratory", "pattern": "^\\d+$", "preferred_prefix": "smc.source", "publications": [ { "doi": "10.1093/nar/gkae1060", "pubmed": "39540430", "title": "The secondary metabolism collaboratory: a database and web discussion portal for secondary metabolite biosynthetic gene clusters", "year": 2024 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://smc.jgi.doe.gov/sources/$1" }, "smid": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "SMIDs (Small Molecule Identifiers) represent gene-style identifiers for small molecules newly identified in C. elegans and other nematodes. SMIDs aim to make life easier for describing biogenic small molecules in metabolomic and genomic applications. ", "example": "137", "homepage": "https://smid-db.org/", "name": "C. elegans Small Molecule Identifier Database", "pattern": "^\\d+$", "preferred_prefix": "smid", "synonyms": [ "SMID-DB" ], "uri_format": "https://smid-db.org/smid/$1" }, "smiles": { "contact": { "email": "tim.vandermeersch@gmail.com", "github": "timvdm", "name": "Tim Vandermeersch" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "github": "NishaSharma14", "name": "Nisha Sharma", "orcid": "0009-0006-4755-1039" } ], "description": "Documentation of SMILES (Simplified Molecular Input Line Entry System), a line notation (a typographical method using printable characters) for entering and representing molecules and reactions.", "example": "CC2(C)C\\1CCC(C)/C=C/12", "homepage": "https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html", "keywords": [ "chemistry", "life science" ], "mappings": { "fairsharing": "FAIRsharing.qv4b3c", "wikidata": "P233" }, "name": "Simplified molecular-input line-entry system", "pattern": "^[A-Za-z0-9+\\-\\*=#$:().>/\\\\\\[\\]%]+$", "preferred_prefix": "smiles", "providers": [ { "code": "cms.canonicalize", "description": "Canonicalizes a given SMILES string according to the allowed toolkits.", "homepage": "https://api.naturalproducts.net/latest/docs#/convert/SMILES_Canonicalise_convert_canonicalsmiles_get", "name": "Canonicalizes a SMILES via the Cheminformatics Microservice", "uri_format": "https://api.naturalproducts.net/latest/convert/canonicalsmiles?smiles=$1" }, { "code": "cms.convert", "description": "Convert SMILES to various molecular formats using different toolkits.", "homepage": "https://api.naturalproducts.net/latest/docs#/convert/SMILES_convert_to_Formats_convert_formats_get", "name": "Convert SMILES to various molecular formats via the Cheminformatics Microservice", "uri_format": "https://api.naturalproducts.net/latest/convert/formats?smiles=$1" }, { "code": "cms.coordinates2d", "description": "Generates 2D Coordinates using the CDK Structure diagram generator/RDKit/Open Babel and returns the mol block.", "homepage": "https://api.naturalproducts.net/latest/docs#/convert/Create2D_Coordinates_convert_mol2D_get", "name": "Generate 2D coordinates via the Cheminformatics Microservice", "uri_format": "https://api.naturalproducts.net/latest/convert/mol2D?smiles=$1" }, { "code": "cms.coordinates3d", "description": "Generates a random 3D conformer from SMILES using the specified molecule toolkit.", "homepage": "https://api.naturalproducts.net/latest/docs#/convert/Create3D_Coordinates_convert_mol3D_get", "name": "Generate 3D conformer via the Cheminformatics Microservice", "uri_format": "https://api.naturalproducts.net/latest/convert/mol3D?smiles=$1" }, { "code": "cms.cxsmiles", "description": "Convert SMILES to CXSMILES. For more informations.", "homepage": "https://api.naturalproducts.net/latest/docs#/convert/SMILES_to_CXSMILES_convert_cxsmiles_get", "name": "Convert SMILES to CXSMILES via the Cheminformatics Microservice", "uri_format": "https://api.naturalproducts.net/latest/convert/cxsmiles?smiles=$1" }, { "code": "cms.depict2d", "description": "Generates a 2D depiction of a molecule using CDK or RDKit with the given parameters.", "homepage": "https://api.naturalproducts.net/latest/docs#/depict/Depict2D_molecule_depict_2D_get", "name": "Depict 2D via the Cheminformatics Microservice", "uri_format": "https://api.naturalproducts.net/latest/depict/2D?smiles=$1" }, { "code": "cms.depict3d", "description": "Generate 3D depictions of molecules using OpenBabel or RDKit.", "homepage": "https://api.naturalproducts.net/latest/docs#/depict/Depict3D_Molecule_depict_3D_get", "name": "Depict 3D via the Cheminformatics Microservice", "uri_format": "https://api.naturalproducts.net/latest/depict/3D?smiles=$1" }, { "code": "cms.descriptor", "description": "Returns descriptors calculated from the molecule with RDKit", "homepage": "https://api.naturalproducts.net/latest/docs#/chem/get_descriptors_chem_descriptors_get", "name": "RDKit Descriptor via the Cheminformatics Microservice", "uri_format": "https://api.naturalproducts.net/latest/chem/descriptors?smiles=$1" }, { "code": "cms.inchi", "description": "Convert SMILES to InChI.", "homepage": "https://api.naturalproducts.net/latest/docs#/convert/SMILES_to_InChI_convert_inchi_get", "name": "Convert SMILES to InChI via the Cheminformatics Microservice", "uri_format": "https://api.naturalproducts.net/latest/convert/inchi?smiles=$1" }, { "code": "cms.inchikey", "description": "Convert SMILES to InChIKey.", "homepage": "https://api.naturalproducts.net/latest/docs#/convert/SMILES_to_InChIKey_convert_inchikey_get", "name": "Convert SMILES to InChIKey via the Cheminformatics Microservice", "uri_format": "https://api.naturalproducts.net/latest/convert/inchikey?smiles=$1" }, { "code": "cms.iupac", "description": "Generates IUPAC name for given SMILES using [STOUT](https://jcheminf.biomedcentral.com/articles/10.1186/s13321-021-00512-4) package.", "homepage": "https://api.naturalproducts.net/latest/docs#/convert/SMILES_to_IUPACname_convert_iupac_get", "name": "Generate IUPAC name from SMILES via the Cheminformatics Microservice", "uri_format": "https://api.naturalproducts.net/latest/convert/iupac?smiles=$1" }, { "code": "cms.selfies", "description": "Generates SELFIES string for a given SMILES string.", "homepage": "https://api.naturalproducts.net/latest/docs#/convert/encode_SELFIES_convert_selfies_get", "name": "Generates SELFIES for a SMILES via the Cheminformatics Microservice", "uri_format": "https://api.naturalproducts.net/latest/convert/selfies?smiles=$1" } ], "publications": [ { "doi": "10.1186/1758-2946-4-24", "pmc": "PMC3551648", "pubmed": "23031664", "title": "mol2chemfig, a tool for rendering chemical structures from molfile or SMILES format to LATE X code", "year": 2012 }, { "doi": "10.1021/ci00067a005", "title": "SMILES. 3. DEPICT. Graphical depiction of chemical structures", "year": 1990 }, { "doi": "10.1021/ci00062a008", "title": "SMILES. 2. Algorithm for generation of unique SMILES notation", "year": 1989 }, { "doi": "10.1021/ci00057a005", "title": "SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules", "year": 1988 } ], "references": [ "https://github.com/biopragmatics/bioregistry/issues/931" ], "repository": "https://github.com/timvdm/OpenSMILES/blob/master/discussion_summary.txt", "uri_format": "https://www.simolecule.com/cdkdepict/depict/bow/svg?smi=$1&zoom=2.0&annotate=cip" }, "smpdb": { "contact": { "email": "david.wishart@ualberta.ca", "github": "DavidWishartLab", "name": "David S. Wishart", "orcid": "0000-0002-3207-2434" }, "description": "The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram.", "example": "SMP0000219", "homepage": "https://smpdb.ca/", "keywords": [ "chemical", "human", "life science", "metabolite", "pathway" ], "mappings": { "biocontext": "SMPDB", "biolink": "PathWhiz", "edam": "2659", "fairsharing": "FAIRsharing.y1zyaq", "integbio": "nbdc00908", "miriam": "smpdb", "n2t": "smpdb", "pathguide": "311", "prefixcommons": "smpdb" }, "name": "Small Molecule Pathway Database", "pattern": "^SMP\\d+$", "preferred_prefix": "smpdb", "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/smpdb:$1" } ], "publications": [ { "doi": "10.1093/nar/gkt1067", "pmc": "PMC3965088", "pubmed": "24203708", "title": "SMPDB 2.0: big improvements to the Small Molecule Pathway Database", "year": 2013 }, { "doi": "10.1093/nar/gkp1002", "pmc": "PMC2808928", "pubmed": "19948758", "title": "SMPDB: The Small Molecule Pathway Database", "year": 2009 }, { "doi": "doi:10.1093/nar/gkp1002", "title": "SMPDB: The Small Molecule Pathway Database." } ], "synonyms": [ "SMP" ], "twitter": "WishartLab", "uri_format": "https://smpdb.ca/view/$1" }, "snap": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Theoretical explanation of a purely spatial ontology supporting snapshot views of the world at successive instants of time, as part of a modular ontology of the dynamic features of reality.", "example": "Quality", "homepage": "http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf", "keywords": [ "gene", "interaction", "pathway", "protein" ], "mappings": { "pathguide": "494", "prefixcommons": "snap" }, "name": "Snapshot", "preferred_prefix": "snap", "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/snap:$1" } ], "synonyms": [ "bfo11snap" ], "uri_format": "http://www.ifomis.org/bfo/1.1/snap#$1" }, "snctp": { "comment": "it appears they cede information into WHO", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The SNCTP (Swiss National Clinical Trials Portal) is the portal where clinical trials in Switzerland are published. It contains data from two sources: from BASEC, the national platform for submitting applications for research projects to ethics committees, and from the ICTRP (the WHO International Clinical Trials Registry Platform), which covers the 17 primary registries worldwide. The ICTRP clinical trials shown on the SNCTP are limited to those conducted in Switzerland; there is also an option to display trials conducted in one of Switzerland's neighbouring countries. [from homepage]", "example": "SNCTP000005580", "homepage": "https://kofam.ch/en/snctp-portal", "name": "Swiss National Clinical Trials Portal", "preferred_prefix": "snctp" }, "snomedct": { "contact": { "email": "custserv@nlm.nih.gov", "name": "NLM Customer Service" }, "contributor_extras": [ { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" } ], "description": "SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc.", "download_owl": "http://snomed.info/sct/900000000000207008/version/20200131", "example": "284196006", "homepage": "https://browser.ihtsdotools.org/", "keywords": [ "biomedical science", "health science", "medicine", "ontology", "preclinical studies" ], "license": "https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf", "mappings": { "aberowl": "SNOMEDCT", "bartoc": "20686", "biocontext": "SNOMEDCT", "biolink": "SNOMEDCT", "bioportal": "SNOMEDCT", "fairsharing": "FAIRsharing.d88s6e", "hl7": "2.16.840.1.113883.6.96", "miriam": "snomedct", "n2t": "snomedct", "ols": "snomed", "prefixcommons": "snomedct", "wikidata": "P5806" }, "name": "SNOMED CT (International Edition)", "pattern": "^(\\w+)?\\d+$", "preferred_prefix": "snomedct", "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/snomedct:$1" }, { "code": "bioportal.purl", "description": "BioPortal PURL", "homepage": "https://bioontology.org", "name": "BioPortal PURL", "uri_format": "http://purl.bioontology.org/ontology/SNOMEDCT/$1" } ], "publications": [ { "doi": "10.1097/00024665-200609000-00011", "pubmed": "16980782", "title": "Standardized nursing language in the systematized nomenclature of medicine clinical terms: A cross-mapping validation method", "year": 2006 } ], "rdf_uri_format": "http://snomed.info/id/$1", "synonyms": [ "SCTID", "SCTID_2010_1_31", "SNOMECT", "SNOMED", "SNOMEDCT", "SNOMEDCTCT", "SNOMEDCTCT_2018_03_01", "SNOMEDCTCT_2019_03_01", "SNOMEDCT_2005_07_31", "SNOMEDCT_2010_1_31", "SNOMEDCT_2020_03_01", "SNOMEDCT_US", "SNOMEDCT_US_2015_03_01", "SNOMEDCT_US_2016_03_01", "SNOMEDCT_US_2018_03_01", "SNOMEDCT_US_2018_09_01", "SNOMEDCT_US_2019_03_01", "SNOMEDCT_US_2019_09_01", "SNOMEDCT_US_2020_03_01", "SNOMEDCT_US_2020_09_01", "SNOMEDCT_US_2021_03_01", "SNOMEDCT_US_2021_07_31", "SNOMEDCT_US_2021_09_01", "SNOMEDCT_US_2022_07_31", "SNOMEDCT_US_2022_09_01", "SNOMEDCT_US_2022_12_31", "SNOMEDCT_US_2023_02_28", "SNOMEDCT_US_2023_03_01", "SNOMEDCT_US_2023_09_01", "SNOMEDCT_US_2023_10_01", "SNOMEDCT_US_2023_11_01", "SNOMEDCT_US_2024_03_01", "SNOMED_CT", "SNOMED_CT_US_2018_03_01", "SNOWMEDCT", "SNOWMEDCT_US", "SNOWMEDCT_US_2018_03_01" ], "uri_format": "http://snomed.info/id/$1", "version": "20200131" }, "snornabase": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A comprehensive database of\n\nhuman H/ACA and C/D box snoRNAs.", "example": "SR0000178", "homepage": "https://www-snorna.biotoul.fr/", "keywords": [ "rna" ], "mappings": { "integbio": "nbdc00323", "prefixcommons": "snornalbmedb" }, "name": "snoRNABase", "preferred_prefix": "snornabase", "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/snornalbmedb:$1" } ], "uri_format": "http://www-snorna.biotoul.fr/plus.php?id=$1" }, "snp2tfbs": { "description": "SNP2TFBS is aimed at studying variations (SNPs/indels) that affect transcription factor binding (TFB) in the Human genome.", "example": "rs11603840", "homepage": "https://ccg.epfl.ch/snp2tfbs/", "mappings": { "miriam": "snp2tfbs" }, "name": "SNP to Transcription Factor Binding Sites", "pattern": "^rs[0-9]+$", "preferred_prefix": "snp2tfbs", "provides": "dbsnp", "uri_format": "https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1" }, "snp500cancer": { "comment": "This resource doesn't exist on the web anymore", "deprecated": true, "description": "The goal of the SNP500Cancer project is to resequence 102 reference samples to find known or newly discovered single nucleotide polymorphisms (SNPs) which are of immediate importance to molecular epidemiology studies in cancer.", "example": "TP53-47", "homepage": "http://snp500cancer.nci.nih.gov", "keywords": [ "dna" ], "mappings": { "prefixcommons": "snp500cancer" }, "name": "SNP500Cancer", "preferred_prefix": "snp500cancer", "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/snp500cancer:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://snp500cancer.nci.nih.gov/snp.cfm?both_snp_id=$1" }, "so": { "appears_in": [ "pcl" ], "banana": "SO", "contact": { "email": "keilbeck@genetics.utah.edu", "github": "keilbeck", "name": "Karen Eilbeck", "orcid": "0000-0002-0831-6427" }, "description": "The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data.", "download_obo": "https://github.com/The-Sequence-Ontology/SO-Ontologies/raw/master/Ontology_Files/so.obo", "download_owl": "http://purl.obolibrary.org/obo/so.owl", "example": "0001157", "homepage": "http://www.sequenceontology.org/", "keywords": [ "bioinformatics", "biology", "deoxyribonucleic acid", "dna", "gene", "genome", "life science", "obo", "ontology", "ribonucleic acid", "rna", "sequence", "sequence annotation", "sequence feature", "structure" ], "license": "CC-BY-4.0", "logo": "https://obofoundry.org/images/so_logo.png", "mappings": { "aberowl": "SO", "agroportal": "SO", "biocontext": "SO", "bioportal": "SO", "fairsharing": "FAIRsharing.6bc7h9", "go": "SO", "miriam": "so", "n2t": "so", "obofoundry": "so", "ols": "so", "ontobee": "SO", "prefixcommons": "so" }, "name": "Sequence types and features ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "SO", "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/so:$1" } ], "publications": [ { "doi": "10.1186/gb-2010-11-8-r88", "pmc": "PMC2945790", "pubmed": "20796305", "title": "A standard variation file format for human genome sequences", "year": 2010 }, { "doi": "10.1016/j.jbi.2010.03.002", "pmc": "PMC3052763", "pubmed": "20226267", "title": "Evolution of the Sequence Ontology terms and relationships", "year": 2010 }, { "doi": "10.1186/gb-2005-6-5-r44", "pmc": "PMC1175956", "pubmed": "15892872", "title": "The Sequence Ontology: a tool for the unification of genome annotations", "year": 2005 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/SO_$1", "repository": "https://github.com/The-Sequence-Ontology/SO-Ontologies", "uri_format": "http://purl.obolibrary.org/obo/SO_$1", "version": "2024-11-18" }, "sopharm": { "contact": { "email": "adrien.coulet@loria.fr", "name": "Adrien Coulet", "orcid": "0000-0002-1466-062X" }, "deprecated": true, "description": "SO-Pharm (Suggested Ontology for Pharmacogenomics) is a domain ontology implemented in OWL-DL, which proposes a formal description of pharmacogenomic knowledge. SO-Pharm articulates different ontologies that represent complementary sub-domains of pharmacogenomics, i.e. related to genotype, phenotype, drugs, and clinical trials. SO-Pharm enables to represent pharmacogenomic relationships between a drug, a genomic variation and a phenotype trait. In addition, it enables to represent patient and more largely panel included in trials, and populations. SO-Pharm enables the representation of measured items on this patients such as results from the observation of a phenotype trait or of genomic variations. SO-Pharm supports knowledge about pharmacogenomic hypothesis, case study, and investigations in pharmacogenomics. SO-Pharm is designed to facilitate data integration and knowledge discovery in pharmacogenomics. In addition it provides a consistent articulation of ontologies of pharmacogenomic sub-domains.", "download_owl": "http://aber-owl.net/media/ontologies/SOPHARM/18/sopharm.owl", "homepage": "http://www.loria.fr/~coulet/sopharm2.0_description.php", "keywords": [ "obo", "ontology" ], "mappings": { "aberowl": "SOPHARM", "biocontext": "SOPHARM", "bioportal": "SOPHARM", "obofoundry": "sopharm" }, "name": "Suggested Ontology for Pharmacogenomics", "preferred_prefix": "SOPHARM", "rdf_uri_format": "http://purl.obolibrary.org/obo/SOPHARM_$1", "uri_format": "http://purl.obolibrary.org/obo/SOPHARM_$1" }, "sosa": { "contact": { "email": "dr.shorthair@pm.me", "github": "dr-shorthair", "name": "Simon Cox", "orcid": "0000-0002-3884-3420" }, "contributor": { "github": "StroemPhi", "name": "Philip Strömert", "orcid": "0000-0002-1595-3213" }, "description": "This ontology is based on the SSN Ontology by the W3C Semantic Sensor Networks Incubator Group (SSN-XG), together with considerations from the W3C/OGC Spatial Data on the Web Working Group.", "download_rdf": "https://www.w3.org/ns/sosa/", "example": "FeatureOfInterest", "github_request_issue": 1274, "homepage": "https://www.w3.org/TR/vocab-ssn/", "keywords": [ "environment", "iot" ], "license": "http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document", "mappings": { "agroportal": "SOSA", "lov": "sosa", "zazuko": "sosa" }, "name": "Sensor, Observation, Sample, and Actuator Ontology", "preferred_prefix": "sosa", "publications": [ { "doi": "10.1016/j.websem.2018.06.003", "title": "SOSA: A lightweight ontology for sensors, observations, samples, and actuators", "year": 2019 } ], "repository": "https://github.com/w3c/sdw", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.w3.org/ns/sosa/$1" }, "soybase": { "contact": { "email": "Jacqueline.Campbell@usda.gov", "name": "Jacqueline Campbell", "orcid": "0000-0003-2787-3955" }, "description": "SoyBase is a repository for curated genetics, genomics and related data resources for soybean.", "example": "BARC-013845-01256", "homepage": "http://soybase.org/", "keywords": [ "agriculture", "comparative genomics", "development", "life science", "obo", "phenotype", "plant breeding", "spider" ], "mappings": { "biocontext": "SOYBASE", "fairsharing": "FAIRsharing.z4agsr", "integbio": "nbdc01817", "miriam": "soybase", "n2t": "soybase", "ncbi": "SoyBase", "pathguide": "44", "prefixcommons": "soy", "re3data": "r3d100010846" }, "name": "SoyBase", "pattern": "^\\w+(\\-)?\\w+(\\-)?\\w+$", "preferred_prefix": "soybase", "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/soy:$1" } ], "publications": [ { "doi": "10.1093/nar/gkp798", "pmc": "PMC2808871", "pubmed": "20008513", "title": "SoyBase, the USDA-ARS soybean genetics and genomics database", "year": 2009 } ], "twitter": "SoyBaseDatabase", "uri_format": "http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$1" }, "span": { "comment": "see also snap. This ontology only exists in description in the paper and does not have an associated web resource", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Theoretical explanation of to a purely spatiotemporal ontology of change and process, as part of a modular ontology of the dynamic features of reality.", "homepage": "http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf", "keywords": [ "ontology", "upper-level ontology" ], "name": "Span", "preferred_prefix": "span", "synonyms": [ "bfo11span" ] }, "spbase": { "comment": "This resource doesn't exist on the web anymore", "deprecated": true, "description": "SpBase, is designed to present the results of the genome sequencing project for the purple sea urchin. THe sequences and annotations emerging from this effort are organized in a database that provides the research community access to those data not normally presented through NCBI and other large databases.", "example": "SPU_000001", "homepage": "http://spbase.org", "keywords": [ "dna", "genome", "rna" ], "mappings": { "integbio": "nbdc00686", "prefixcommons": "spbase" }, "name": "SpBase", "preferred_prefix": "spbase", "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/spbase:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.spbase.org/SpBase/search/viewAnnoGeneInfo.php?spu_id=$1" }, "spd": { "contact": { "email": "ramirez@macn.gov.ar", "github": "martinjramirez", "name": "Martin Ramirez", "orcid": "0000-0002-0358-0130" }, "description": "An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow).", "download_obo": "http://purl.obolibrary.org/obo/spd.obo", "download_owl": "http://purl.obolibrary.org/obo/spd.owl", "example": "0000001", "homepage": "http://research.amnh.org/atol/files/", "keywords": [ "anatomy", "behavior", "life science", "obo", "ontology", "spider" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "SPD", "biocontext": "SPD", "bioportal": "SPD", "fairsharing": "FAIRsharing.yecp83", "obofoundry": "spd", "ols": "spd", "ontobee": "SPD", "prefixcommons": "spdo", "wikidata": "P4537" }, "name": "Spider Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "SPD", "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/spdo:$1" } ], "publications": [ { "doi": "10.3390/d11100202", "title": "The Spider Anatomy Ontology (SPD)—A Versatile Tool to Link Anatomy with Cross-Disciplinary Data", "year": 2019 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/SPD_$1", "repository": "https://github.com/obophenotype/spider-ontology", "uri_format": "http://purl.obolibrary.org/obo/SPD_$1" }, "spdx": { "description": "The SPDX License List is a list of commonly found licenses and exceptions used in free and open source and other collaborative software or documentation. The purpose of the SPDX License List is to enable easy and efficient identification of such licenses and exceptions in an SPDX document, in source files or elsewhere. The SPDX License List includes a standardized short identifier, full name, vetted license text including matching guidelines markup as appropriate, and a canonical permanent URL for each license and exception.", "example": "CC-BY-1.0", "homepage": "https://spdx.org/licenses", "mappings": { "miriam": "spdx", "n2t": "spdx" }, "name": "Software Package Data Exchange License", "pattern": "^[0-9A-Za-z\\-.]+$", "preferred_prefix": "spdx", "uri_format": "https://spdx.org/licenses/$1" }, "sphn": { "contact": { "email": "Sabine.Oesterle@sib.swiss", "name": "Sabine Oesterle", "orcid": "0000-0003-3248-7899" }, "contributor": { "email": "deepak.unni3@gmail.com", "github": "deepakunni3", "name": "Deepak Unni", "orcid": "0000-0002-3583-7340" }, "description": "The Swiss Personalized Health Network is a national infrastructure initiative with the aim to develop, implement, and validate coordinated data infrastructures in order to make health-relevant data interoperable and shareable for research in Switzerland. The sphn RDF schema builds the foundation for all data exchanges within the sphn by integrating semantic information defined in the [sphn dataset](https://sphn.ch/document/sphn-dataset/).", "download_owl": "https://git.dcc.sib.swiss/sphn-semantic-framework/sphn-ontology/-/raw/master/rdf_schema/sphn_rdf_schema.owl", "download_rdf": "https://git.dcc.sib.swiss/sphn-semantic-framework/sphn-ontology/-/raw/master/rdf_schema/sphn_rdf_schema.ttl", "example": "Allergy", "github_request_issue": 535, "homepage": "https://www.sphn.ch", "keywords": [ "ontology" ], "license": "CC-BY-4.0", "name": "Swiss Personalized Health Network Schema", "pattern": "^\\S+$", "preferred_prefix": "sphn", "repository": "https://git.dcc.sib.swiss/sphn-semantic-framework/sphn-ontology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://biomedit.ch/rdf/sphn-ontology/sphn#$1" }, "spike.map": { "contact": { "email": "Yossih@tauex.tau.ac.il", "name": "Yosef Shiloh", "orcid": "0000-0002-1538-6060" }, "description": "SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository that can store, organise and allow retrieval of pathway information in a way that will be useful for the research community. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. This collection references pathway maps.", "example": "spike00001", "homepage": "http://www.cs.tau.ac.il/~spike/", "keywords": [ "dna", "gene expression", "pathway" ], "mappings": { "biocontext": "SPIKE.MAP", "miriam": "spike.map", "n2t": "spike.map", "prefixcommons": "spike" }, "name": "SPIKE Map", "pattern": "^spike\\d{5}$", "preferred_prefix": "spike.map", "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/spike:$1" } ], "publications": [ { "doi": "10.1093/nar/gkq1167", "pmc": "PMC3014840", "pubmed": "21097778", "title": "SPIKE: a database of highly curated human signaling pathways", "year": 2010 }, { "doi": "10.1186/1471-2105-9-110", "pmc": "PMC2263022", "pubmed": "18289391", "title": "SPIKE--a database, visualization and analysis tool of cellular signaling pathways", "year": 2008 } ], "uri_format": "http://www.cs.tau.ac.il/~spike/maps/$1.html" }, "splash": { "description": "The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance.", "example": "splash10-0zq2000000-77302b0326a418630a84", "homepage": "http://mona.fiehnlab.ucdavis.edu/", "mappings": { "biocontext": "SPLASH", "miriam": "splash", "n2t": "splash" }, "name": "Spectra Hash Code", "pattern": "^splash\\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$", "preferred_prefix": "splash", "uri_format": "http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$1" }, "splicenest": { "comment": "This resource doesn't exist on the web anymore", "deprecated": true, "description": "SpliceNest [1] is a web based graphical tool to explore gene structure, including alternative splicing, based on a mapping on the EST consensus sequences (contigs) from GeneNest [2] to the complete human genome.", "example": "Hs635", "homepage": "http://splicenest.molgen.mpg.de/", "keywords": [ "dna", "gene", "genome" ], "mappings": { "prefixcommons": "splicenest" }, "name": "SpliceNest", "preferred_prefix": "splicenest", "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/splicenest:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://splicenest.molgen.mpg.de/cgi-bin/splicegraph.cgi?cluster=$1" }, "spp": { "contact": { "email": "nmckenna@bcm.edu", "name": "Neil McKenna", "orcid": "0000-0001-6689-0104" }, "description": "The Signaling Pathways Project is an integrated 'omics knowledgebase based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Our goal is to create a resource where scientists can routinely generate research hypotheses or validate bench data relevant to cellular signaling pathways.", "example": "10.1621/vwN2g2HaX3", "homepage": "https://www.signalingpathways.org/index.jsf", "keywords": [ "omics", "transcriptomics" ], "mappings": { "fairsharing": "FAIRsharing.WxI96O", "miriam": "spp", "re3data": "r3d100013650" }, "name": "Signaling Pathways Project", "pattern": "^10.\\w{4}/\\w{10}$", "preferred_prefix": "spp", "publications": [ { "doi": "10.1038/s41597-019-0193-4", "pmc": "PMC6823428", "pubmed": "31672983", "title": "The Signaling Pathways Project, an integrated 'omics knowledgebase for mammalian cellular signaling pathways", "year": 2019 } ], "twitter": "sigpathproject", "uri_format": "https://www.signalingpathways.org/datasets/dataset.jsf?doi=$1" }, "srao": { "contact": { "email": "allyson.lister@oerc.ox.ac.uk", "github": "allysonlister", "name": "Allyson Lister", "orcid": "0000-0002-7702-4495" }, "description": "The FAIRsharing Subject Ontology (SRAO) is an application ontology for the categorization of research disciplines across all research domains, from the humanities to the natural sciences. It utilizes multiple external vocabularies.", "download_obo": "https://github.com/FAIRsharing/subject-ontology/raw/refs/heads/master/SRAO.obo", "download_owl": "https://github.com/FAIRsharing/subject-ontology/raw/refs/heads/master/SRAO.owl", "example": "0000400", "homepage": "https://github.com/FAIRsharing/subject-ontology", "keywords": [ "agriculture", "biomedical science", "classification", "computer science", "earth science", "environmental science", "fair", "humanities", "life science", "metadata standardization", "metascience", "natural science", "ontology", "resource metadata", "topics" ], "mappings": { "fairsharing": "FAIRsharing.b1xD9f", "ols": "srao" }, "name": "FAIRsharing Subject Ontology", "part_of": "fairsharing", "pattern": "^\\d{7}$", "preferred_prefix": "srao", "repository": "https://github.com/FAIRsharing/subject-ontology", "twitter": "FAIRsharing_org", "uri_format": "http://www.fairsharing.org/ontology/subject/SRAO_$1", "version": "2025-02-23" }, "ssbd.dataset": { "contact": { "email": "sonami@riken.jp", "name": "Shuichi Onami", "orcid": "0000-0002-8255-1724" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations.", "example": "1", "homepage": "https://ssbd.riken.jp", "keywords": [ "cell biology", "developmental biology", "molecular dynamics" ], "mappings": { "fairsharing": "FAIRsharing.we2r5a" }, "name": "System Science of Biological Dynamics dataset", "pattern": "^\\d+$", "preferred_prefix": "ssbd.dataset", "publications": [ { "doi": "10.1093/bioinformatics/btw417", "pmc": "PMC5181557", "pubmed": "27412095", "title": "SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena", "year": 2016 } ], "uri_format": "https://ssbd.riken.jp/database/dataset/$1" }, "ssbd.project": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations.", "example": "1", "homepage": "https://ssbd.riken.jp", "name": "System Science of Biological Dynamics project", "pattern": "^\\d+$", "preferred_prefix": "ssbd.project", "uri_format": "https://ssbd.riken.jp/database/project/$1" }, "ssn": { "contact": { "email": "dr.shorthair@pm.me", "github": "dr-shorthair", "name": "Simon Cox", "orcid": "0000-0002-3884-3420" }, "contributor": { "github": "StroemPhi", "name": "Philip Strömert", "orcid": "0000-0002-1595-3213" }, "description": "This ontology describes sensors, actuators and observations, and related concepts. It does not describe domain concepts, time, locations, etc. these are intended to be included from other ontologies via OWL imports.", "download_owl": "http://aber-owl.net/media/ontologies/SSN/2/ssn.owl", "download_rdf": "https://www.w3.org/ns/ssn/", "example": "hasProperty", "github_request_issue": 1272, "homepage": "https://www.w3.org/TR/vocab-ssn", "keywords": [ "imaging", "iot", "methods", "monitoring", "ontology", "remote sensing", "resource metadata", "sensor data", "w3c rec", "web of things" ], "license": "http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document", "mappings": { "aberowl": "SSN", "agroportal": "SSN", "bioportal": "SSN", "fairsharing": "FAIRsharing.c0bvcy", "lov": "ssn", "zazuko": "ssn" }, "name": "Semantic Sensor Network Ontology", "preferred_prefix": "ssn", "publications": [ { "doi": "10.3233/sw-180320", "title": "The Modular SSN Ontology: A Joint W3C and OGC Standard Specifying the Semantics of Sensors, Observations, Sampling, and Actuation", "year": 2019 }, { "doi": "10.1016/j.websem.2018.06.003", "title": "SOSA: A lightweight ontology for sensors, observations, samples, and actuators", "year": 2018 }, { "doi": "10.1016/j.websem.2012.05.003", "title": "The SSN ontology of the W3C semantic sensor network incubator group", "year": 2012 } ], "repository": "https://github.com/w3c/sdw-sosa-ssn", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.w3.org/ns/ssn/$1" }, "ssn.system": { "contact": { "email": "dr.shorthair@pm.me", "github": "dr-shorthair", "name": "Simon Cox", "orcid": "0000-0002-3884-3420" }, "contributor": { "email": "philip.stroemert@tib.eu", "github": "StroemPhi", "name": "Philip Strömert", "orcid": "0000-0002-1595-3213" }, "description": "This ontology describes system capabilities, operating ranges, and survival ranges. Please report any errors to the W3C Spatial Data on the Web Working Group via the SDW WG Public List public-sdw-wg@w3.org", "download_rdf": "http://www.w3.org/ns/ssn/systems", "example": "qualityOfObservation", "github_request_issue": 1270, "homepage": "https://www.w3.org/TR/vocab-ssn/", "license": "http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document", "name": "System capabilities, operating ranges, and survival ranges ontology", "preferred_prefix": "ssn.system", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://www.w3.org/ns/ssn/systems/$1" }, "ssrn.article": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "identifier for an article/paper at the SSRN", "example": "1667659", "homepage": "https://ssrn.com", "mappings": { "wikidata": "P893" }, "name": "Social Science Research Network Article", "preferred_prefix": "ssrn.article", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1171" ], "uri_format": "https://ssrn.com/abstract=$1" }, "ssrn.author": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "identifier for an author at the Social Science Research Network", "example": "112517", "homepage": "https://ssrn.com", "keywords": [ "person", "researcher" ], "mappings": { "wikidata": "P3747" }, "name": "Social Science Research Network Author", "pattern": "^[1-9]\\d{0,6}$", "preferred_prefix": "ssrn.author", "references": [ "https://github.com/biopragmatics/bioregistry/pull/1171" ], "uri_format": "https://ssrn.com/author=$1" }, "sssom": { "contact": { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" }, "contributor": { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" }, "description": "SSSOM is a Simple Standard for Sharing Ontological Mappings, providing - a TSV-based representation for ontology term mappings - a comprehensive set of standard metadata elements to describe mappings and - a standard translation between the TSV and the Web Ontology Language (OWL). Most metadata elements, such as \"sssom:mapping_justification\" are defined in the sssom namespace.", "example": "mapping_justification", "example_extras": [ "superClassOf" ], "github_request_issue": 759, "homepage": "https://w3id.org/sssom", "license": "BSD-3-Clause", "name": "Simple Standard for Sharing Ontological Mappings", "pattern": "^[A-Za-z_]+$", "preferred_prefix": "sssom", "repository": "https://github.com/mapping-commons/sssom", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://w3id.org/sssom/$1" }, "sstoss": { "comment": "This resource doesn't exist on the web anymore", "deprecated": true, "description": "SSToSS is a database which provides sequence-structural templates of single member protein domain superfamilies like PASS2. Sequence-structural templates are recognized by considering the content and overlap of sequence similarity and structural parameters like, solvent inaccessibility, secondary structural content, hydrogen bonding and spatial packing of the residues among the protein of single member superfamilies.", "example": "01.01.005", "homepage": "http://caps.ncbs.res.in/SSTOSS/index.htm", "keywords": [ "protein", "structure" ], "mappings": { "prefixcommons": "sstoss" }, "name": "Sequence-Structural Templates of Single-member Superfamilies", "preferred_prefix": "sstoss", "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/sstoss:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://caps.ncbs.res.in/cgi-bin/mini/databases/SSTOSS/sstoss.cgi?code=$1" }, "stap": { "contact": { "email": "bhsung@kribb.re.kr", "name": "Bong Hyun Sung", "orcid": "0000-0002-8992-1118" }, "deprecated": true, "description": "STAP (Statistical Torsional Angles Potentials) was developed since, according to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, are less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. The refined NMR solution structures (statistical torsion angle potentials; STAP) in the database are refined from the Protein Data Bank (PDB).", "example": "1a24", "homepage": "http://psb.kobic.re.kr/STAP/refinement/", "keywords": [ "life science", "statistics" ], "mappings": { "biocontext": "STAP", "fairsharing": "FAIRsharing.ja9cdq", "miriam": "stap", "n2t": "stap" }, "name": "Statistical Torsional Angles Potentials", "pattern": "^[0-9][A-Za-z0-9]{3}$", "preferred_prefix": "stap", "publications": [ { "doi": "10.1093/bioinformatics/btv595", "pubmed": "26504145", "title": "NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores", "year": 2015 }, { "doi": "10.1371/journal.pone.0108888", "pmc": "PMC4184813", "pubmed": "25279564", "title": "Protein NMR structures refined without NOE data", "year": 2014 }, { "doi": "10.1002/prot.24265", "pubmed": "23408564", "title": "Statistical torsion angle potential energy functions for protein structure modeling: a bicubic interpolation approach", "year": 2013 }, { "doi": "10.1093/nar/gkr1021", "pmc": "PMC3245188", "pubmed": "22102572", "title": "STAP Refinement of the NMR database: a database of 2405 refined solution NMR structures", "year": 2011 } ], "uri_format": "http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$1" }, "stato": { "appears_in": [ "ontoavida", "psdo", "scdo" ], "banana": "STATO", "contact": { "email": "proccaserra@gmail.com", "github": "proccaserra", "name": "Philippe Rocca-Serra", "orcid": "0000-0001-9853-5668" }, "description": "STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots.", "download_owl": "http://purl.obolibrary.org/obo/stato.owl", "example": "0000288", "homepage": "http://stato-ontology.org/", "keywords": [ "data visualization", "experimental measurement", "graph", "obo", "omics", "omics data analysis", "ontology", "protocol", "statistics", "study design" ], "license": "CC-BY-3.0", "logo": "https://raw.githubusercontent.com/ISA-tools/stato/dev/images/stato-logo-3.png", "mappings": { "aberowl": "STATO", "biocontext": "STATO", "bioportal": "STATO", "fairsharing": "FAIRsharing.na5xp", "miriam": "stato", "obofoundry": "stato", "ols": "stato", "ontobee": "STATO" }, "name": "The Statistical Methods Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "STATO", "publications": [ { "pubmed": "32109232", "title": "Semantic concept schema of the linear mixed model of experimental observations" }, { "pubmed": "31831744", "title": "Experiment design driven FAIRification of omics data matrices, an exemplar" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/STATO_$1", "repository": "https://github.com/ISA-tools/stato", "uri_format": "http://purl.obolibrary.org/obo/STATO_$1", "version": "2025-02-23" }, "stitch": { "contact": { "email": "bork@embl.de", "name": "Peer Bork", "orcid": "0000-0002-2627-833X" }, "description": "STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.", "example": "BQJCRHHNABKAKU", "homepage": "http://stitch.embl.de/", "keywords": [ "interaction", "life science", "protein", "small molecule" ], "mappings": { "biocontext": "STITCH", "fairsharing": "FAIRsharing.zhwa8x", "miriam": "stitch", "n2t": "stitch", "pathguide": "313", "prefixcommons": "stitch", "re3data": "r3d100012165" }, "name": "Search Tool for Interactions of Chemicals", "pattern": "^\\w{14}$", "preferred_prefix": "stitch", "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/stitch:$1" } ], "publications": [ { "doi": "10.1093/nar/gkt1207", "pmc": "PMC3964996", "pubmed": "24293645", "title": "STITCH 4: integration of protein-chemical interactions with user data", "year": 2013 }, { "doi": "10.1093/nar/gkr1011", "pmc": "PMC3245073", "pubmed": "22075997", "title": "STITCH 3: zooming in on protein-chemical interactions", "year": 2011 }, { "doi": "10.1093/nar/gkp937", "pmc": "PMC2808890", "pubmed": "19897548", "title": "STITCH 2: an interaction network database for small molecules and proteins", "year": 2009 }, { "doi": "10.1093/nar/gkm795", "pmc": "PMC2238848", "pubmed": "18084021", "title": "STITCH: interaction networks of chemicals and proteins", "year": 2007 } ], "uri_format": "http://stitch.embl.de/interactions/$1" }, "stn": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The pre-IND tracking number for submissions to the FDA", "example": "125768", "homepage": "https://www.fda.gov/media/128698/download", "name": "FDA Submission Tracking Number", "preferred_prefix": "stn" }, "storedb": { "banana": "STOREDB", "contact": { "email": "PNS12@cam.ac.uk", "name": "Dr Paul Schofield", "orcid": "0000-0002-5111-7263" }, "description": "STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons.", "example": "STUDY1040", "homepage": "https://www.storedb.org/", "keywords": [ "biomedical science", "ecology", "epidemiology", "life science", "preclinical studies" ], "mappings": { "biocontext": "STOREDB", "fairsharing": "FAIRsharing.6h8d2r", "integbio": "nbdc02191", "miriam": "storedb", "n2t": "storedb", "re3data": "r3d100011049" }, "name": "Store DB", "namespace_in_lui": true, "pattern": "^(STUDY|FILE|DATASET)\\d+$", "preferred_prefix": "storedb", "uri_format": "https://www.storedb.org/?$1" }, "storedb.dataset": { "comment": "Unfortunately, the resolver itself doesn't work since datasets are actually hierarchically assigned within studies.", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "description": "Datasets inside StoreDB", "example": "1251", "homepage": "https://www.storedb.org/", "name": "STOREDB at University of Cambridge", "part_of": "storedb", "pattern": "^\\d+$", "preferred_prefix": "storedb.dataset", "uri_format": "https://www.storedb.org/?STOREDB:DATASET$1" }, "storedb.file": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "File inside StoreDB", "example": "12929", "homepage": "https://www.storedb.org/", "name": "STOREDB at University of Cambridge", "part_of": "storedb", "pattern": "^\\d+$", "preferred_prefix": "storedb.file", "uri_format": "https://www.storedb.org/store_v3/download.jsp?fileId=$1" }, "storedb.study": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Study inside StoreDB", "example": "1174", "homepage": "https://www.storedb.org/", "name": "STOREDB at University of Cambridge", "part_of": "storedb", "pattern": "^\\d+$", "preferred_prefix": "storedb.study", "providers": [ { "code": "doi", "description": "DOIs for studies", "homepage": "https://www.storedb.org/", "name": "StoreDB DOI", "uri_format": "http://dx.doi.org/doi:10.20348/STOREDB/$1" } ], "uri_format": "https://www.storedb.org/store_v3/study.jsp?studyId=$1" }, "streptomedb": { "contact": { "email": "stefan.guenther@pharmazie.uni-freiburg.de", "name": "Stefan Günther", "orcid": "0000-0003-3744-189X" }, "contributor": { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" }, "description": "Identifers for natural products isolated or mutasynthesized by bacteria of the genus Streptomyces.", "example": "15753", "github_request_issue": 1287, "homepage": "http://streptomedb.vm.uni-freiburg.de:8000/streptomedb", "name": "StreptomeDB", "pattern": "^\\d+$", "preferred_prefix": "streptomedb", "publications": [ { "doi": "10.1093/nar/gkae1030", "pubmed": "39498494", "title": "StreptomeDB 4.0: a comprehensive database of streptomycetes natural products enriched with protein interactions and interactive spectral visualization", "year": 2024 }, { "doi": "10.1093/nar/gkaa868", "pmc": "PMC7779017", "pubmed": "33051671", "title": "StreptomeDB 3.0: an updated compendium of streptomycetes natural products", "year": 2020 }, { "doi": "10.1093/nar/gkv1319", "pmc": "PMC4702922", "pubmed": "26615197", "title": "StreptomeDB 2.0--an extended resource of natural products produced by streptomycetes", "year": 2015 }, { "doi": "10.1093/nar/gks1253", "pmc": "PMC3531085", "pubmed": "23193280", "title": "StreptomeDB: a resource for natural compounds isolated from Streptomyces species", "year": 2012 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "http://streptomedb.vm.uni-freiburg.de:8000/streptomedb/get_drugcard/$1" }, "string": { "contact": { "email": "bork@embl.de", "name": "Peer Bork", "orcid": "0000-0002-2627-833X" }, "description": "STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions.\nThe interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression, Previous Knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable.", "example": "P53350", "homepage": "http://string-db.org/", "keywords": [ "biology", "interaction", "life science", "protein" ], "mappings": { "biocontext": "STRING", "edam": "2302", "fairsharing": "FAIRsharing.9b7wvk", "integbio": "nbdc00690", "miriam": "string", "n2t": "string", "pathguide": "93", "prefixcommons": "string", "re3data": "r3d100010604", "uniprot": "DB-0141" }, "name": "Search Tool for Retrieval of Interacting Genes/Proteins", "pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$", "preferred_prefix": "string", "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/string:$1" } ], "provides": "uniprot", "publications": [ { "doi": "10.1093/nar/gkae1113", "pubmed": "39558183", "title": "The STRING database in 2025: protein networks with directionality of regulation", "year": 2024 }, { "doi": "10.1093/nar/gky1131", "pmc": "PMC6323986", "pubmed": "30476243", "title": "STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets", "year": 2019 }, { "doi": "10.1093/nar/gkw937", "pmc": "PMC5210637", "pubmed": "27924014", "title": "The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible", "year": 2016 }, { "doi": "10.1093/bioinformatics/btv696", "pmc": "PMC4896368", "pubmed": "26614125", "title": "SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles", "year": 2015 }, { "doi": "10.1093/nar/gku1003", "pmc": "PMC4383874", "pubmed": "25352553", "title": "STRING v10: protein-protein interaction networks, integrated over the tree of life", "year": 2014 }, { "doi": "10.1093/nar/gks1094", "pmc": "PMC3531103", "pubmed": "23203871", "title": "STRING v9.1: protein-protein interaction networks, with increased coverage and integration", "year": 2012 }, { "doi": "10.1093/nar/gkn760", "pmc": "PMC2686466", "pubmed": "18940858", "title": "STRING 8--a global view on proteins and their functional interactions in 630 organisms", "year": 2008 } ], "uri_format": "https://string-db.org/cgi/network?identifier=$1" }, "sty": { "contact": { "email": "olivier@nlm.nih.gov", "name": "Olivier Bodenreider", "orcid": "0000-0003-4769-4217" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "email": "tiago.lubiana.alves@usp.br", "github": "lubianat", "name": "Tiago Lubiana", "orcid": "0000-0003-2473-2313" } ], "description": "UMLS Semantic Network The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types.", "example": "T039", "homepage": "https://lhncbc.nlm.nih.gov/semanticnetwork/", "keywords": [ "ontology" ], "mappings": { "aberowl": "STY", "agroportal": "STY", "biolink": "UMLSSG", "bioportal": "STY", "ecoportal": "STY", "wikidata": "P11955" }, "name": "UMLS Semantic Types Ontology", "pattern": "^T\\d{3}$", "preferred_prefix": "sty", "providers": [ { "code": "bioportal.purl", "description": "BioPortal PURL", "homepage": "http://purl.bioontology.org/ontology/STY", "name": "BioPortal PURL", "uri_format": "http://purl.bioontology.org/ontology/STY/$1" } ], "synonyms": [ "UMLSSG", "umls.st", "umls.sty" ], "uri_format": "https://uts.nlm.nih.gov/uts/umls/semantic-network/$1" }, "subtilist": { "contact": { "email": "antoine.danchin@normalesup.org", "name": "Antoine Danchin", "orcid": "0000-0002-6350-5001" }, "description": "SubtiList serves to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria.\nSubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments.", "example": "BG11523", "homepage": "http://genolist.pasteur.fr/SubtiList/", "keywords": [ "dna", "genome", "protein" ], "mappings": { "biocontext": "SUBTILIST", "fairsharing": "FAIRsharing.40j2vd", "miriam": "subtilist", "n2t": "subtilist", "ncbi": "SubtiList", "prefixcommons": "subtilist" }, "name": "Bacillus subtilis genome sequencing project", "pattern": "^BG\\d+$", "preferred_prefix": "subtilist", "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/subtilist:$1" } ], "publications": [ { "doi": "10.1093/nar/30.1.62", "pmc": "PMC99059", "pubmed": "11752255", "title": "SubtiList: the reference database for the Bacillus subtilis genome", "year": 2002 } ], "uri_format": "http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+$1" }, "subtiwiki": { "contact": { "email": "jstuelk@gwdg.de", "name": "Jörg Stülke", "orcid": "0000-0001-5881-5390" }, "description": "SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis. It provides comprehensive information on all genes and their proteins and RNA products, as well as information related to the current investigation of the gene/protein. \nNote: Currently, direct access to RNA products is restricted. This is expected to be rectified soon.", "example": "BSU29180", "homepage": "http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page", "keywords": [ "dna", "gene", "life science", "protein", "rna" ], "mappings": { "biocontext": "SUBTIWIKI", "fairsharing": "FAIRsharing.2ck3st", "integbio": "nbdc00693", "miriam": "subtiwiki", "n2t": "subtiwiki", "prefixcommons": "subtiwiki" }, "name": "SubtiWiki", "pattern": "^BSU\\d{5}$", "preferred_prefix": "subtiwiki", "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/subtiwiki:$1" } ], "publications": [ { "doi": "10.1093/nar/gkv1006", "pmc": "PMC4702770", "pubmed": "26433225", "title": "SubtiWiki 2.0--an integrated database for the model organism Bacillus subtilis", "year": 2015 }, { "doi": "10.1093/database/bap012", "pmc": "PMC2790307", "pubmed": "20157485", "title": "A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki", "year": 2009 }, { "doi": "10.1099/mic.0.035790-0", "pubmed": "19959575", "title": "Connecting parts with processes: SubtiWiki and SubtiPathways integrate gene and pathway annotation for Bacillus subtilis", "year": 2009 } ], "uri_format": "http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$1" }, "sugarbind": { "contact": { "email": "frederique.lisacek@isb-sib.ch", "name": "Frederique Lisacek", "orcid": "0000-0002-0948-4537" }, "description": "The SugarBind Database captures knowledge of glycan binding of human pathogen lectins and adhesins, where each glycan-protein binding pair is associated with at least one published reference. It provides information on the pathogen agent, the lectin/adhesin involved, and the human glycan ligand. This collection provides information on ligands.", "download_owl": "http://aber-owl.net/media/ontologies/SUGARBIND/1/sugarbind.owl", "example": "lectins/172", "homepage": "http://sugarbind.expasy.org/", "keywords": [ "biomedical science", "glycomics", "ontology" ], "mappings": { "aberowl": "SUGARBIND", "biocontext": "SUGARBIND", "bioportal": "SUGARBIND", "fairsharing": "FAIRsharing.d064y6", "integbio": "nbdc02224", "miriam": "sugarbind", "n2t": "sugarbind" }, "name": "SugarBind", "pattern": "^[A-Za-z]+\\/[0-9]+$", "preferred_prefix": "sugarbind", "publications": [ { "doi": "10.1093/nar/gkv1247", "pmc": "PMC4702881", "pubmed": "26578555", "title": "SugarBindDB, a resource of glycan-mediated host-pathogen interactions", "year": 2015 }, { "doi": "10.1007/978-4-431-56454-6_13", "title": "SugarBindDB", "year": 2016 } ], "twitter": "ISBSIB", "uri_format": "http://sugarbind.expasy.org/$1" }, "sulo": { "contact": { "email": "michel.dumontier@gmail.com", "github": "micheldumontier", "name": "Michel Dumontier", "orcid": "0000-0003-4727-9435" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Simplified Upper Level Ontology (SULO) is ontology with a minimal set of classes and relations to guide the development of a personal health knowledge graph. 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It was produced by the Federative International Committee on Anatomical Terminology on behalf of the International Federation of Associations of Anatomists and posted on the Internet since 2010. [wikipedia]", "example": "E5.11.2.0.0.0.4", "homepage": "https://ifaa.unifr.ch/", "mappings": { "wikidata": "P1693" }, "name": "Terminologia Embryologica", "preferred_prefix": "te", "references": [ "https://en.wikipedia.org/wiki/Terminologia_Embryologica" ] }, "tfclass": { "contact": { "email": "edgar.wingender@edgar-wingender.de", "name": "Edgar Wingender", "orcid": "0000-0002-7729-8453" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "TFClass is a classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains. It comprises four general levels (superclass, class, family, subfamily) and two levels of instantiation (genus and molecular species). Two of them (subfamily and factor species) are optional. More detailed explanations about the classification scheme and its criteria are given here..", "example": "2.1.1", "homepage": "http://tfclass.bioinf.med.uni-goettingen.de", "keywords": [ "binding", "binding site", "bioinformatics", "expression data", "phylogenetics", "transcription factor", "transcription factor binding site prediction", "transcriptomics" ], "mappings": { "fairsharing": "FAIRsharing.XykycZ", "go": "TFClass", "pathguide": "666" }, "name": "Classification of Transcription Factors in Mammalia", "preferred_prefix": "tfclass", "publications": [ { "doi": "10.1093/nar/gkx987", "pmc": "PMC5753292", "pubmed": "29087517", "title": "TFClass: expanding the classification of human transcription factors to their mammalian orthologs", "year": 2018 } ], "uri_format": "http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=$1" }, "tgd": { "description": "The Tetrahymena Genome Database (TGD) Wiki is a database of information about the Tetrahymena thermophila genome sequence. It provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus, gene product annotations utilizing the Gene Ontology, and links to published literature.", "example": "TTHERM_00648910", "homepage": "http://ciliate.org/index.php/", "keywords": [ "genome" ], "mappings": { "biocontext": "TGD", "go": "TGD", "miriam": "tgd", "n2t": "tgd", "prefixcommons": "tgd" }, "name": "Tetrahymena Genome Database", "pattern": "^TTHERM\\_\\d+$", "preferred_prefix": "tgd", "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/tgd:$1" } ], "uri_format": "http://ciliate.org/index.php/feature/details/$1" }, "tgma": { "contact": { "email": "topalis@imbb.forth.gr", "name": "Pantelis Topalis", "orcid": "0000-0002-1635-4810" }, "deprecated": true, "description": "A structured controlled vocabulary of the anatomy of mosquitoes.", "download_obo": "http://purl.obolibrary.org/obo/tgma.obo", "download_owl": "http://purl.obolibrary.org/obo/tgma.owl", "example": "0000984", "homepage": "https://www.vectorbase.org/ontology-browser", "keywords": [ "anatomy", "life science", "mosquito", "obo", "ontology" ], "license": "CC0-1.0", "mappings": { "aberowl": "TGMA", "biocontext": "TGMA", "bioportal": "TGMA", "fairsharing": "FAIRsharing.dqnfkg", "obofoundry": "tgma", "ols": "tgma", "ontobee": "TGMA", "prefixcommons": "tgma" }, "name": "Mosquito gross anatomy ontology", "pattern": "^\\d{7}$", "preferred_prefix": "TGMA", "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/tgma:$1" } ], "publications": [ { "doi": "10.1111/j.1365-2583.2008.00781.x", "pubmed": "18237287", "title": "Anatomical ontologies of mosquitoes and ticks, and their web browsers in VectorBase", "year": 2008 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/TGMA_$1", "repository": "https://github.com/VEuPathDB-ontology/TGMA", "uri_format": "http://purl.obolibrary.org/obo/TGMA_$1", "version": "2013-06-03" }, "tgn": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "description": "TGN is a structured vocabulary currently containing around 1,106,000 names and other information about places. Names for a place may include names in the vernacular language, English, other languages, historical names, names and in natural order and inverted order. Among these names, one is flagged as the preferred name. TGN is a thesaurus, compliant with ISO and NISO standards for thesaurus construction; it contains hierarchical, equivalence, and associative relationships. Note that TGN is not a GIS (Geographic Information System). While many records in TGN include coordinates, these coordinates are approximate and are intended for reference only. The focus of each TGN record is a place. There are around 912,000 places in the TGN. In the database, each place record (also called a subject) is identified by a unique numeric ID. Linked to the record for the place are names, the place's parent or position in the hierarchy, other relationships, geographic coordinates, notes, sources for the data, and place types, which are terms describing the role of the place (e.g., inhabited place and state capital). The temporal coverage of the TGN ranges from prehistory to the present and the scope is global. The TGN is a hierarchical database; its trees branch from a root called Top of the TGN hierarchies (Subject_ID: 1000000). Currently there are two TGN facets, World and Extraterrestrial Places. Under the facet World, places are arranged in hierarchies generally representing the current political and physical world, although some historical nations and empires are also included. There may be multiple broader contexts, making the TGN polyhierarchical. The primary users of the Getty vocabularies include museums, art libraries, archives, visual resource collection catalogers, bibliographic projects concerned with art, researchers in art and art history, and the information specialists who are dealing with the needs of these users. In addition, a significant number of users of the Getty vocabularies are students or members of the general public.", "example": "1023371", "homepage": "https://www.getty.edu/research/tools/vocabularies/tgn/", "mappings": { "bartoc": "109" }, "name": "Getty Thesaurus of Geographic Names", "pattern": "^\\d+$", "preferred_prefix": "tgn", "references": [ "https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638380238036200" ], "uri_format": "http://vocab.getty.edu/page/tgn/$1" }, "th": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Terminologia Histologica (TH) is the controlled vocabulary for use in cytology and histology. It was intended to replace Nomina Histologica. [wikipedia]", "example": "H3.03.00.0.00007", "homepage": "https://ifaa.unifr.ch/", "keywords": [ "biology", "cytology", "histology", "life sciences" ], "mappings": { "wikidata": "P1694" }, "name": "Terminologia Histologica", "pattern": "^H\\d\\.\\d{2}\\.\\d{2}\\.\\d\\.\\d{5}$", "preferred_prefix": "th", "references": [ "https://en.wikipedia.org/wiki/Terminologia_Histologica" ] }, "theiler": { "appears_in": [ "mmusdv" ], "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Stages 1-28 of mouse embryo development", "example": "10", "example_decoys": [ "10e" ], "example_extras": [ "10b" ], "homepage": "https://embryology.med.unsw.edu.au/embryology/index.php?title=Mouse_Stages", "name": "Theiler Stage", "pattern": "^\\d+[a-d]?$", "preferred_prefix": "theiler", "providers": [ { "code": "legacy", "description": "Legacy URL at UNSW", "homepage": "https://embryology.med.unsw.edu.au/embryology/index.php?title=Mouse_Stages", "name": "Legacy URL at UNSW", "uri_format": "https://embryology.med.unsw.edu.au/embryology/index.php?title=Mouse_Stages#Theiler_Stage_$1" } ], "synonyms": [ "thielerstage" ], "uri_format": "http://php.med.unsw.edu.au/embryology/index.php?title=Mouse_Stages#Theiler_Stage_$1" }, "thermofisher": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "ThermoFisher is a life sciences supply vendor.", "example": "OSR00185W", "homepage": "https://www.thermofisher.com", "keywords": [ "biology", "chemistry", "life sciences", "vendor" ], "name": "Thermo Fisher Scientific", "pattern": "^\\w+$", "preferred_prefix": "thermofisher", "uri_format": "https://www.thermofisher.com/antibody/product/$1" }, "tigrfam": { "contributor_extras": [ { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" } ], "description": "TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins.", "example": "TIGR00010", "homepage": "http://www.jcvi.org/cgi-bin/tigrfams/Listing.cgi", "keywords": [ "protein" ], "mappings": { "biocontext": "TIGRFAM", "edam": "1141", "miriam": "tigrfam", "n2t": "tigrfam", "ncbi": "TIGRFAM", "prefixcommons": "tigrfams" }, "name": "TIGR protein families", "pattern": "^TIGR\\d+$", "preferred_prefix": "tigrfam", "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/tigrfams:$1" } ], "references": [ "https://ftp.ncbi.nlm.nih.gov/hmm/TIGRFAMs/license_and_availability.txt", "https://github.com/biopragmatics/bioregistry/issues/366" ], "uri_format": "https://www.ncbi.nlm.nih.gov/cdd?term=$1" }, "time": { "contact": { "email": "dr.shorthair@pm.me", "github": "dr-shorthair", "name": "Simon Cox", "orcid": "0000-0002-3884-3420" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Owl-time is an owl-2 dl ontology of temporal concepts, for describing the temporal properties of resources in the world or described in web pages. the ontology provides a vocabulary for expressing facts about topological (ordering) relations among instants and intervals, together with information about durations, and about temporal position including date-time information. time positions and durations may be expressed using either the conventional (gregorian) calendar and clock, or using another temporal reference system such as unix-time, geologic time, or different calendars.", "download_owl": "http://aber-owl.net/media/ontologies/TIME/2/time.owl", "example": "DateTimeDescription", "github_request_issue": 505, "homepage": "https://www.w3.org/TR/owl-time/", "keywords": [ "data coordination", "data model", "metadata standardization", "ontology", "resource metadata", "subject agnostic", "time" ], "mappings": { "aberowl": "TIME", "bartoc": "18311", "bioportal": "TIME", "fairsharing": "FAIRsharing.hw3bh2", "lov": "time", "zazuko": "time" }, "name": "Time Ontology in OWL", "preferred_prefix": "time", "repository": "https://github.com/w3c/sdw/", "uri_format": "http://www.w3.org/2006/time#$1" }, "tkg": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Collection of cell lines by Tohoku University. This includes transplantable animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series) cell lines as well as human, murine cell lines and hybridoma cells.", "example": "0221", "homepage": "http://www2.idac.tohoku.ac.jp/dep/ccr/", "mappings": { "cellosaurus": "TKG" }, "name": "Tohoku University cell line catalog", "pattern": "^\\d+$", "preferred_prefix": "tkg", "uri_format": "http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html" }, "tngb": { "description": "Cell line collections (Providers)", "example": "67035", "homepage": "http://biobanknetwork.telethon.it/", "mappings": { "cellosaurus": "TNGB" }, "name": "Telethon Network of Genetic Biobanks", "pattern": "^\\d+$", "preferred_prefix": "tngb", "uri_format": "http://biobanknetwork.telethon.it/Sample/View?sampleId=$1" }, "to": { "appears_in": [ "agro" ], "contact": { "email": "jaiswalp@science.oregonstate.edu", "github": "jaiswalp", "name": "Pankaj Jaiswal", "orcid": "0000-0002-1005-8383" }, "description": "A controlled vocabulary to describe phenotypic traits in plants.", "download_obo": "http://purl.obolibrary.org/obo/to.obo", "download_owl": "http://purl.obolibrary.org/obo/to.owl", "example": "0000630", "homepage": "http://browser.planteome.org/amigo", "keywords": [ "botany", "life cycle", "obo", "ontology", "phenotype", "plant", "structure", "trait" ], "license": "CC-BY-4.0", "logo": "http://planteome.org/sites/default/files/garland_logo.PNG", "mappings": { "aberowl": "TO", "agroportal": "TO", "biocontext": "TO", "bioportal": "PTO", "fairsharing": "FAIRsharing.w69t6r", "obofoundry": "to", "ols": "to", "ontobee": "TO", "prefixcommons": "pto" }, "name": "Plant Trait Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "TO", "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/pto:$1" } ], "publications": [ { "doi": "10.1093/nar/gkx1152", "pmc": "PMC5753347", "pubmed": "29186578", "title": "The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics", "year": 2018 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/TO_$1", "repository": "https://github.com/Planteome/plant-trait-ontology", "uri_format": "http://purl.obolibrary.org/obo/TO_$1", "version": "2023-07-17" }, "togoid": { "contact": { "email": "ktym@dbcls.jp", "github": "ktym", "name": "Toshiaki Katayama", "orcid": "0000-0003-2391-0384" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "TogoID is an ID conversion service implementing unique features with an intuitive web interface and an API for programmatic access. TogoID supports datasets from various biological categories such as gene, protein, chemical compound, pathway, disease, etc. TogoID users can perform exploratory multistep conversions to find a path among IDs. To guide the interpretation of biological meanings in the conversions, we crafted an ontology that defines the semantics of the dataset relations. (from https://togoid.dbcls.jp/)", "download_rdf": "https://raw.githubusercontent.com/togoid/togoid-config/main/ontology/togoid-ontology.ttl", "example": "AffyProbeset", "homepage": "https://togoid.dbcls.jp/ontology", "name": "TogoID Ontology", "preferred_prefix": "togoid", "publications": [ { "doi": "10.1093/bioinformatics/btac491", "pmc": "PMC9438948", "pubmed": "35801937", "title": "TogoID: an exploratory ID converter to bridge biological datasets", "year": 2022 } ], "rdf_uri_format": "https://togoid.dbcls.jp/ontology#$1", "repository": "https://github.com/dbcls/togoid/togoid-config", "uri_format": "https://togoid.dbcls.jp/#$1" }, "togovar": { "description": "TogoVar (A comprehensive Japanese genetic variation database) is a database that has collected and organized genome sequence differences between individuals (variants) in the Japanese population and disease information associated with them.", "example": "tgv139393198", "homepage": "https://grch38.togovar.org/", "mappings": { "integbio": "nbdc02359", "miriam": "togovar", "togoid": "Togovar" }, "name": "TogoVar", "pattern": "^tgv[0-9]+$", "preferred_prefix": "togovar", "uri_format": "https://grch38.togovar.org/variant/$1" }, "tokue": { "deprecated": true, "description": "Cell line databases/resources", "homepage": "http://cell-lines.toku-e.com", "mappings": { "cellosaurus": "TOKU-E" }, "name": "TOKU-E Cell-culture Database", "preferred_prefix": "tokue", "uri_format": "http://cell-lines.toku-e.com/Cell-Lines_$1.html" }, "tol": { "contributor_extras": [ { "email": "meghan.balk@gmail.com", "github": "megbalk", "name": "Meghan Balk", "orcid": "0000-0003-2699-3066" } ], "description": "The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web pages, the project provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history (phylogeny). \n\nEach page contains information about a particular group, with pages linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things.", "example": "98034", "homepage": "http://tolweb.org/tree/", "mappings": { "bartoc": "400", "biocontext": "TOL", "miriam": "tol", "n2t": "tol", "wikidata": "P5221" }, "name": "Tree of Life Web Project", "pattern": "^\\d+$", "preferred_prefix": "tol", "synonyms": [ "tol.webproj" ], "uri_format": "http://tolweb.org/$1" }, "topdb": { "description": "The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection of transmembrane protein datasets containing experimentally derived topology information. It contains information gathered from the literature and from public databases availableon transmembrane proteins. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases.", "example": "AP00378", "homepage": "http://topdb.enzim.hu/", "keywords": [ "protein" ], "mappings": { "biocontext": "TOPDB", "edam": "2789", "miriam": "topdb", "n2t": "topdb", "prefixcommons": "topdb" }, "name": "Topology Data Bank of Transmembrane Proteins", "pattern": "^[A-Z0-9]+$", "preferred_prefix": "topdb", "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/topdb:$1" } ], "uri_format": "http://topdb.enzim.hu/?m=show&id=$1" }, "topfind": { "contact": { "email": "chris.overall@ubc.ca", "name": "Christopher M. Overall", "orcid": "0000-0001-5844-2731" }, "description": "TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli.", "example": "Q9UKQ2", "homepage": "https://topfind.clip.msl.ubc.ca", "keywords": [ "life science" ], "mappings": { "biocontext": "TOPFIND", "fairsharing": "FAIRsharing.rkpmhn", "miriam": "topfind", "n2t": "topfind", "re3data": "r3d100012721" }, "name": "TopFind", "pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$", "preferred_prefix": "topfind", "provides": "uniprot", "publications": [ { "doi": "10.1093/nar/gku1012", "pmc": "PMC4383881", "pubmed": "25332401", "title": "Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events", "year": 2014 }, { "doi": "10.1093/nar/gkr1025", "pmc": "PMC3244998", "pubmed": "22102574", "title": "TopFIND 2.0--linking protein termini with proteolytic processing and modifications altering protein function", "year": 2011 }, { "doi": "10.1038/nmeth.1669", "pubmed": "21822272", "title": "TopFIND, a knowledgebase linking protein termini with function", "year": 2011 } ], "uri_format": "http://clipserve.clip.ubc.ca/topfind/proteins/$1" }, "toxoplasma": { "description": "ToxoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", "example": "TGME49_053730", "homepage": "http://toxodb.org/toxo/", "mappings": { "biocontext": "TOXOPLASMA", "miriam": "toxoplasma", "n2t": "toxoplasma" }, "name": "ToxoDB", "pattern": "^\\w+$", "preferred_prefix": "toxoplasma", "uri_format": "http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1" }, "trans": { "contact": { "email": "lynn.schriml@gmail.com", "github": "lschriml", "name": "Lynn Schriml", "orcid": "0000-0001-8910-9851" }, "description": "The Pathogen Transmission Ontology describes the tranmission methods of human disease pathogens describing how a pathogen is transmitted from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles.", "download_obo": "http://purl.obolibrary.org/obo/trans.obo", "download_owl": "http://purl.obolibrary.org/obo/trans.owl", "example": "0000024", "homepage": "https://github.com/DiseaseOntology/PathogenTransmissionOntology", "keywords": [ "health science", "obo", "ontology", "pathogen" ], "license": "CC0-1.0", "mappings": { "aberowl": "TRANS", "biocontext": "TRANS", "bioportal": "TRANS", "fairsharing": "FAIRsharing.nygmp7", "obofoundry": "trans", "ols": "trans", "ontobee": "TRANS", "prefixcommons": "pt" }, "name": "Pathogen Transmission Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "TRANS", "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/pt:$1" } ], "publications": [ { "doi": "10.1093/nar/gkab1063", "pmc": "PMC8728220", "pubmed": "34755882", "title": "The Human Disease Ontology 2022 update", "year": 2022 }, { "doi": "10.1093/nar/gkp832", "pmc": "PMC2808878", "pubmed": "19850722", "title": "GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database", "year": 2009 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/TRANS_$1", "repository": "https://github.com/DiseaseOntology/PathogenTransmissionOntology", "uri_format": "http://purl.obolibrary.org/obo/TRANS_$1", "version": "2022-10-10" }, "transportdb": { "description": "TransportDB is a relational database describing the predicted cytoplasmic membrane transport protein complement for organisms whose complete genome sequence are available.", "example": "MMP0523", "homepage": "http://www.membranetransport.org", "keywords": [ "protein" ], "mappings": { "pathguide": "105", "prefixcommons": "transportdb" }, "name": "TransportDB", "preferred_prefix": "transportdb", "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/tred:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=geneInfo&gid=$1" }, "treebase": { "contact": { "email": "rutgeraldo@gmail.com", "github": "rvosa", "name": "Rutger Vos", "orcid": "0000-0001-9254-7318" }, "description": "TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships. It includes phylogenetic trees and data matrices, together with information about the relevant publication, taxa, morphological and sequence-based characters, and published analyses. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, etc.", "example": "TB2:S1000", "homepage": "http://treebase.org/", "keywords": [ "classification", "phylogenetics", "phylogenomics" ], "mappings": { "biocontext": "TREEBASE", "fairsharing": "FAIRsharing.zcn4w4", "integbio": "nbdc01882", "miriam": "treebase", "n2t": "treebase", "prefixcommons": "treebase", "re3data": "r3d100010170" }, "name": "TreeBASE", "pattern": "^TB[1,2]?:[A-Z][a-z]?\\d+$", "preferred_prefix": "treebase", "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/treebase:$1" } ], "publications": [ { "doi": "10.1186/1471-2148-9-93", "pmc": "PMC2685121", "pubmed": "19426482", "title": "Improved data retrieval from TreeBASE via taxonomic and linguistic data enrichment", "year": 2009 } ], "repository": "https://github.com/TreeBASE/treebase/issues", "twitter": "treebase", "uri_format": "http://purl.org/phylo/treebase/phylows/study/$1?format=html" }, "treefam": { "contact": { "email": "Fab.Schreiber@gmail.com", "github": "fabsta", "name": "Fabian Schreiber", "orcid": "0000-0001-9150-5706" }, "description": "TreeFam is a database of phylogenetic trees of gene families found in animals. Automatically generated trees are curated, to create a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments.", "example": "TF101014", "homepage": "http://www.treefam.org/", "keywords": [ "classification", "gene" ], "mappings": { "biocontext": "TREEFAM", "integbio": "nbdc01596", "miriam": "treefam", "n2t": "treefam", "prefixcommons": "treefam", "uniprot": "DB-0185" }, "name": "TreeFam", "pattern": "^\\w{1,2}\\d+$", "preferred_prefix": "treefam", "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/treefam:$1" } ], "publications": [ { "doi": "10.1093/nar/gkt1055", "pmc": "PMC3965059", "pubmed": "24194607", "title": "TreeFam v9: a new website, more species and orthology-on-the-fly", "year": 2013 } ], "uri_format": "http://www.treefam.org/family/$1" }, "tricdb": { "description": "Tri©DB is a newly developed integrated platform functioning as a knowledge base and reporting system for cancer precision medicine. This platform harmonizes and mines cancer-related data from various aspects, presenting them on a centralized platform with enhanced accessibility, rich annotations, and robust analysis capabilities. The development of Tri©DB is aimed at meeting the needs of a broad range of researchers, thereby propelling both foundational and translational research in cancer precision medicine.", "example": "1eec8393-e598-41ed-9d8b-6d5b0db94470", "homepage": "http://www.biomeddb.org/", "mappings": { "miriam": "tricdb" }, "name": "tricdb", "pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$", "preferred_prefix": "tricdb", "uri_format": "http://biomeddb.org/Disease/Details?DISEASEID=$1" }, "trichdb": { "contact": { "email": "oharb@pcbi.upenn.edu", "name": "Omar Harb", "orcid": "0000-0003-4446-6200" }, "description": "TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", "example": "TVAG_386080", "homepage": "http://trichdb.org/trichdb/", "keywords": [ "genomics" ], "mappings": { "biocontext": "TRICHDB", "fairsharing": "FAIRsharing.pv0ezt", "integbio": "nbdc01785", "miriam": "trichdb", "n2t": "trichdb", "re3data": "r3d100012461" }, "name": "TrichDB", "pattern": "^\\w+$", "preferred_prefix": "trichdb", "publications": [ { "doi": "10.1093/nar/gkn631", "pmc": "PMC2686445", "pubmed": "18824479", "title": "GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis", "year": 2008 } ], "twitter": "eupathdb", "uri_format": "http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1" }, "tritrypdb": { "contact": { "email": "oharb@pcbi.upenn.edu", "name": "Omar Harb", "orcid": "0000-0003-4446-6200" }, "description": "TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", "example": "Tb927.8.620", "homepage": "http://tritrypdb.org/tritrypdb/", "keywords": [ "comparative genomics", "genomics", "infectious disease medicine" ], "mappings": { "biocontext": "TRITRYPDB", "fairsharing": "FAIRsharing.fs1z27", "go": "TriTrypDB", "integbio": "nbdc01786", "miriam": "tritrypdb", "n2t": "tritrypdb", "re3data": "r3d100011479" }, "name": "TriTrypDB", "pattern": "^\\w+(\\.)?\\w+(\\.)?\\w+$", "preferred_prefix": "tritrypdb", "publications": [ { "doi": "10.1093/nar/gkp851", "pmc": "PMC2808979", "pubmed": "19843604", "title": "TriTrypDB: a functional genomic resource for the Trypanosomatidae", "year": 2009 } ], "twitter": "VEuPathDB", "uri_format": "http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1" }, "trnadbce": { "comment": "requires authentication to access", "description": "The tRNA Gene DataBase Curated by Experts \"tRNADB-CE\" was constructed by analyzing 927 complete and 1301 draft genomes of Bacteria and Archaea, 171 complete virus genomes, 121 complete chloroplast genomes, 12 complete eukaryote (Plant and Fungi) genomes and approximately 230 million DNA sequence entries that originated from environmental metagenomic clones.", "example": "265912", "homepage": "http://trna.nagahama-i-bio.ac.jp", "keywords": [ "dna", "gene", "genome", "rna" ], "mappings": { "integbio": "nbdc00720", "prefixcommons": "trnadbce" }, "name": "tRNA Gene Database", "preferred_prefix": "trnadbce", "proprietary": true, "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/trnadbce:$1" } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/whole_detail.cgi?SID=$1" }, "tsc": { "description": "Centralized repository and distribution site for variety of Tetrahymena strains and species. Maintains diverse array of wild type, mutant, and genetically engineered strains of T. thermophila, the most commonly used laboratory species, and variety of other species derived from both laboratory maintained stocks and wild isolates. All stocks are stored in liquid nitrogen to maintain genetic integrity and prevent senescence. In addition to providing worldwide access to strains currently in collection, TSC continually upgrades collection by accepting deposition of newly developed laboratory strains and well characterized wild isolates collected from clearly defined natural sites. [from RRID]", "example": "SD00043", "homepage": "https://tetrahymena.vet.cornell.edu/", "keywords": [ "biology", "cell", "cellular", "culture", "eukaryota", "genetics", "model", "molecular", "protozoan", "repository", "research", "tetrahymena thermophila" ], "mappings": { "rrid": "TSC" }, "name": "Tetrahymena Stock Center", "pattern": "^SD\\d+$", "preferred_prefix": "tsc", "uri_format": "https://tetrahymena.vet.cornell.edu/display.php?stockid=$1" }, "ttd.drug": { "description": "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target.", "example": "DAP000773", "homepage": "http://bidd.nus.edu.sg/group/ttd/ttd.asp", "mappings": { "biocontext": "TTD.DRUG", "edam": "2653", "miriam": "ttd.drug", "n2t": "ttd.drug" }, "name": "TTD Drug", "pattern": "^DAP\\d+$", "preferred_prefix": "ttd.drug", "uri_format": "http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$1" }, "ttd.target": { "description": "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target.", "example": "TTDS00056", "homepage": "http://bidd.nus.edu.sg/group/ttd/ttd.asp", "mappings": { "biocontext": "TTD.TARGET", "edam": "2654", "miriam": "ttd.target", "n2t": "ttd.target" }, "name": "TTD Target", "pattern": "^TTDS\\d+$", "preferred_prefix": "ttd.target", "uri_format": "http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$1" }, "tto": { "contact": { "email": "balhoff@renci.org", "github": "balhoff", "name": "Jim Balhoff", "orcid": "0000-0002-8688-6599" }, "description": "An ontology covering the taxonomy of teleosts (bony fish)", "download_obo": "http://purl.obolibrary.org/obo/tto.obo", "download_owl": "http://purl.obolibrary.org/obo/tto.owl", "example": "1058367", "homepage": "https://github.com/phenoscape/teleost-taxonomy-ontology", "keywords": [ "fish", "life science", "obo", "ontology", "phenotype", "taxonomic classification" ], "license": "CC0-1.0", "mappings": { "aberowl": "TTO", "biocontext": "TTO", "bioportal": "TTO", "fairsharing": "FAIRsharing.1rj558", "obofoundry": "tto", "ols": "tto", "ontobee": "TTO", "prefixcommons": "tto" }, "name": "Teleost taxonomy ontology", "pattern": "^\\d+$", "preferred_prefix": "TTO", "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/tto:$1" } ], "publications": [ { "doi": "10.1038/npre.2010.4629.1", "title": "The Teleost Taxonomy Ontology", "year": 2010 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/TTO_$1", "repository": "https://github.com/phenoscape/teleost-taxonomy-ontology", "uri_format": "http://purl.obolibrary.org/obo/TTO_$1" }, "txpo": { "contact": { "email": "yuki.yamagata@riken.jp", "github": "yuki-yamagata", "name": "Yuki Yamagata", "orcid": "0000-0002-9673-1283" }, "description": "Elucidating the mechanism of toxicity is crucial in drug safety evaluations. TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity.\n\nThe TXPO contains an is-a hierarchy that is organized into three layers: the top layer contains general terms, mostly derived from the Basic Formal Ontology. The intermediate layer contains biomedical terms in OBO foundry from UBERON, Cell Ontology, NCBI Taxon, ChEBI, Gene Ontology, PATO, OGG, INOH, HINO, NCIT, DOID and Relational ontology (RO). The lower layer contains toxicological terms.\n\nIn applied work, we have developed a prototype of TOXPILOT, a TOXic Process InterpretabLe knOwledge sysTem. TOXPILOT provides visualization maps of the toxic course, which facilitates capturing the comprehensive picture for understanding toxicity mechanisms. A prototype of TOXPILOT is available: https://toxpilot.nibiohn.go.jp", "download_owl": "http://purl.obolibrary.org/obo/txpo.owl", "example": "0002066", "homepage": "https://toxpilot.nibiohn.go.jp/", "keywords": [ "obo", "ontology" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "TXPO", "bioportal": "TXPO", "obofoundry": "txpo", "ols": "txpo", "ontobee": "TXPO" }, "name": "Toxic Process Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "TXPO", "publications": [ { "doi": "10.1038/s41598-020-71370-7", "pmc": "PMC7471325", "pubmed": "32883995", "title": "Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management", "year": 2020 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/TXPO_$1", "repository": "https://github.com/txpo-ontology/TXPO", "uri_format": "http://purl.obolibrary.org/obo/TXPO_$1", "version": "2022-12-07" }, "uberon": { "appears_in": [ "aism", "amphx", "chiro", "cl", "clo", "clyh", "colao", "cteno", "ecao", "ecocore", "ecto", "envo", "foodon", "fovt", "genepio", "go", "hso", "lepao", "maxo", "mco", "mfmo", "ons", "pcl", "plana", "poro", "zp" ], "banana": "UBERON", "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "depends_on": [ "bfo", "bspo", "chebi", "cl", "envo", "go", "nbo", "ncbitaxon", "omo", "pato", "pr", "ro" ], "description": "Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.", "download_json": "http://purl.obolibrary.org/obo/uberon.json", "download_obo": "http://purl.obolibrary.org/obo/uberon/basic.obo", "download_owl": "http://purl.obolibrary.org/obo/uberon.owl", "example": "2005080", "homepage": "http://uberon.org", "keywords": [ "anatomy", "developmental biology", "life science", "obo", "ontology", "taxonomy" ], "license": "CC-BY-3.0", "logo": "https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/uberon-logos/uberon_logo_black-banner.png", "mappings": { "aberowl": "UBERON", "biocontext": "UBERON", "bioportal": "UBERON", "cellosaurus": "UBERON", "fairsharing": "FAIRsharing.4c0b6b", "go": "UBERON", "miriam": "uberon", "n2t": "uberon", "obofoundry": "uberon", "ols": "uberon", "ontobee": "UBERON", "togoid": "Uberon", "wikidata": "P1554" }, "name": "Uber Anatomy Ontology", "namespace_in_lui": true, "pattern": "^\\d+$", "preferred_prefix": "UBERON", "providers": [ { "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/tissues/UBERON_$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/UBERON/UBERON:$1" } ], "publications": [ { "doi": "10.1186/2041-1480-5-21", "pmc": "PMC4089931", "pubmed": "25009735", "title": "Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon", "year": 2014 }, { "doi": "10.1186/gb-2012-13-1-r5", "pmc": "PMC3334586", "pubmed": "22293552", "title": "Uberon, an integrative multi-species anatomy ontology", "year": 2012 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/UBERON_$1", "repository": "https://github.com/obophenotype/uberon", "synonyms": [ "UBERON", "Uber-anatomy ontology", "Uberon" ], "twitter": "uberanat", "uri_format": "http://purl.obolibrary.org/obo/UBERON_$1", "version": "2025-01-15" }, "ubio.namebank": { "description": "NameBank is a \"biological name server\" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context.", "example": "2555646", "homepage": "http://www.ubio.org", "mappings": { "biocontext": "UBIO.NAMEBANK", "miriam": "ubio.namebank", "n2t": "ubio.namebank" }, "name": "uBio NameBank", "pattern": "^\\d+$", "preferred_prefix": "ubio.namebank", "uri_format": "http://www.ubio.org/browser/details.php?namebankID=$1" }, "ubprop": { "comment": "All of these are typedefs in uberon now", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "name": "Uberon Property", "preferred_prefix": "ubprop", "synonyms": [ "UBPROP", "UBREL" ] }, "ucas": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An identifier for institutions in the United Kingdom, used in GRID and ROR.", "example": "N21", "homepage": "https://www.ucas.com", "keywords": [ "bibliometrics", "institution" ], "name": "UK Universities and Colleges Admissions Service", "pattern": "^\\w\\d+$", "preferred_prefix": "ucas" }, "ucsc": { "contact": { "email": "max@soe.ucsc.edu", "github": "maximilianh", "name": "Maximilian Haeussler", "orcid": "0000-0001-8721-8253" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The UCSC Genome Browser is an on-line, and downloadable, genome browser hosted by the University of California, Santa Cruz (UCSC).[2][3][4] It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations.", "example": "uc001rvw.5", "homepage": "https://genome.ucsc.edu/", "mappings": { "biocontext": "UCSC", "uniprot": "DB-0139", "wikidata": "P2576" }, "name": "UCSC Genome Browser", "preferred_prefix": "ucsc", "publications": [ { "doi": "10.1093/nar/gky1095", "pmc": "PMC6323953", "pubmed": "30407534", "title": "The UCSC Genome Browser database: 2019 update", "year": 2019 } ], "uri_format": "ftp://hgdownload.cse.ucsc.edu/goldenPath/$1" }, "ucum": { "contact": { "email": "dr.shorthair@pm.me", "github": "dr-shorthair", "name": "Simon Cox", "orcid": "0000-0002-3884-3420" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Unified Code for Units of Measure (UCUM) is a code system intended to include all units of measures being contemporarily used in international science, engineering, and business.", "example": "aBq", "example_extras": [ "%", "/A/s3/cg3/T3", "/g", "/m3", "Cel.d-1", "Em.s-2", "K2", "Wb", "dL/g", "dlm", "dlx", "g.cm-3", "kW/h", "m.s-2", "m/s", "m/s/d", "mmol.mL-1", "mol.L-1", "mol.um", "ng-1", "pA", "ug.mL-1", "umol.L-1", "us" ], "homepage": "https://ucum.org", "keywords": [ "data identity and mapping", "general & upper", "measurement", "subject agnostic", "unit" ], "mappings": { "bartoc": "1895", "fairsharing": "FAIRsharing.27w8k0", "hl7": "2.16.840.1.113883.6.8", "lov": "ucum" }, "name": "Unified Code for Units of Measure", "preferred_prefix": "ucum", "publications": [ { "doi": "10.1136/jamia.1999.0060151", "pmc": "PMC61354", "pubmed": "10094068", "title": "Units of measure in clinical information systems", "year": 1999 } ], "references": [ "https://units-of-measurement.org/" ], "repository": "https://github.com/ucum-org/ucum", "uri_format": "https://units-of-measurement.org/$1" }, "ukprn": { "comment": "Added because of appearance in ROR", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "identifier for an educational organization issued by the UK Register of Learning Providers", "example": "10007835", "homepage": "https://www.ukrlp.co.uk", "mappings": { "wikidata": "P4971" }, "name": "UK Provider Reference Number", "pattern": "^[1-9]\\d*$", "preferred_prefix": "ukprn", "synonyms": [ "ukprns" ], "uri_format": "https://www.ukrlp.co.uk/ukrlp/ukrlp_provider.page_pls_provDetails?x=&pn_p_id=$1&pv_status=VERIFIED&pv_vis_code=L" }, "umbbd.compound": { "description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to compound information.", "example": "c0001", "homepage": "http://umbbd.ethz.ch/", "mappings": { "biocontext": "UMBBD.COMPOUND", "miriam": "umbbd.compound", "n2t": "umbbd.compound", "wikidata": "P8121" }, "name": "UM-BBD compound", "part_of": "umbbd", "pattern": "^c\\d+$", "preferred_prefix": "umbbd.compound", "synonyms": [ "UM-BBD_compID" ], "uri_format": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1" }, "umbbd.enzyme": { "description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to enzyme information.", "example": "e0333", "homepage": "http://umbbd.ethz.ch/", "mappings": { "biocontext": "UMBBD.ENZYME", "go": "UM-BBD_enzymeID", "miriam": "umbbd.enzyme", "n2t": "umbbd.enzyme" }, "name": "EAWAG Biocatalysis/Biodegradation Database", "part_of": "umbbd", "pattern": "^e\\d+$", "preferred_prefix": "umbbd.enzyme", "synonyms": [ "UM-BBD_enzymeID" ], "uri_format": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1" }, "umbbd.pathway": { "description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to pathway information.", "example": "ala", "homepage": "http://umbbd.ethz.ch/", "mappings": { "biocontext": "UMBBD.PATHWAY", "go": "UM-BBD_pathwayID", "miriam": "umbbd.pathway", "n2t": "umbbd.pathway" }, "name": "EAWAG Biocatalysis/Biodegradation Database", "part_of": "umbbd", "pattern": "^\\w+$", "preferred_prefix": "umbbd.pathway", "providers": [ { "code": "eawag", "description": "Graphical depiction of pathway", "homepage": "http://eawag-bbd.ethz.ch", "name": "Pathway map diagram", "uri_format": "http://eawag-bbd.ethz.ch/$1/$1_map.html" } ], "synonyms": [ "UM-BBD_pathwayID" ], "uri_format": "http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr=$1" }, "umbbd.reaction": { "description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to reaction information.", "example": "r0001", "homepage": "http://umbbd.ethz.ch/", "mappings": { "biocontext": "UMBBD.REACTION", "go": "UM-BBD_reactionID", "miriam": "umbbd.reaction", "n2t": "umbbd.reaction" }, "name": "EAWAG Biocatalysis/Biodegradation Database", "part_of": "umbbd", "pattern": "^r\\d+$", "preferred_prefix": "umbbd.reaction", "synonyms": [ "UM-BBD_reactionID" ], "uri_format": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1" }, "umbbd.rule": { "description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction System (PPS) predicts microbial catabolic reactions using substructure searching, a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional groups found in a compound and predicts transformations based on biotransformation rules. These rules are based on reactions found in the UM-BBD database. This collection references those rules.", "example": "bt0001", "homepage": "http://umbbd.ethz.ch/servlets/pageservlet?ptype=allrules", "mappings": { "biocontext": "UMBBD.RULE", "go": "UM-BBD_ruleID", "miriam": "umbbd.rule", "n2t": "umbbd.rule" }, "name": "EAWAG Biocatalysis/Biodegradation Database", "part_of": "umbbd", "pattern": "^bt\\d+$", "preferred_prefix": "umbbd.rule", "synonyms": [ "UM-BBD_ruleID" ], "uri_format": "http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=$1" }, "uminctr": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An additional Japanese clinical trial registry", "example": "UMIN000049383", "homepage": "https://www.umin.ac.jp/ctr/index.htm", "mappings": { "integbio": "nbdc01470" }, "name": "University hospital Medical Information Network Clinical Trial Registry", "pattern": "^UMIN\\d+$|^C\\d+$", "preferred_prefix": "uminctr", "references": [ "https://center6.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000056224" ] }, "umls": { "description": "The Unified Medical Language System is a repository of biomedical vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank.", "example": "C2584994", "homepage": "https://www.nlm.nih.gov/research/umls", "license": "https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/license_agreement.html", "logo": "https://uts.nlm.nih.gov/uts/assets/images/umls_tree_sm.jpg", "mappings": { "bartoc": "20052", "biocontext": "UMLS", "edam": "1181", "hl7": "2.16.840.1.113883.6.86", "miriam": "umls", "n2t": "umls", "wikidata": "P2892" }, "name": "Unified Medical Language System Concept Unique Identifier", "pattern": "^C\\d+$", "preferred_prefix": "umls", "synonyms": [ "UMLS", "UMLS CUI", "UMLS_CUI", "umls.cui" ], "uri_format": "https://uts.nlm.nih.gov/uts/umls/concept/$1" }, "umls.aui": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An identifier for an atom; the smallest unit of naming in a source, viz, a specific string with specific code values and identifiers from a specific source. As such, they can be thought of as representing a single meaning with a source Atoms are the units of terminology that come from sources and form the building blocks of the concepts in the Metathesaurus.", "example": "A0118748", "homepage": "https://www.nlm.nih.gov/research/umls", "name": "Unified Medical Language System Atomic Unique Identifier", "pattern": "^A\\d+$", "preferred_prefix": "umls.aui", "synonyms": [ "UMLS_ICD9CM_2005_AUI" ] }, "unicarbdb": { "contact": { "email": "niclas.karlsson@medkem.gu.se", "name": "Niclas Karlsson", "orcid": "0000-0002-3045-2628" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "UniCarb-DB stores structural and mass spectrometry (MS) glycomic data, and has now grown to be one of the largest experimental glycomic MS databases. Identifiers correspond to individual glycan structures and corresponding MS spectra.", "example": "91", "github_request_issue": 1509, "homepage": "https://unicarb-db.expasy.org", "license": "CC-BY-4.0", "name": "UniCarb-DB", "pattern": "^\\d+$", "preferred_prefix": "unicarbdb", "publications": [ { "doi": "10.1016/j.bbapap.2013.04.018", "pubmed": "23624262", "title": "Validation of the curation pipeline of UniCarb-DB: building a global glycan reference MS/MS repository", "year": 2014 } ], "reviewer": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "uri_format": "https://unicarb-db.expasy.org/msData/$1" }, "unichem": { "description": "identifier of a compound in the UniChem database", "example": "161671", "homepage": "https://chembl.gitbook.io/unichem/downloads", "mappings": { "wikidata": "P11089" }, "name": "UniChem compound", "pattern": "^\\d+$", "preferred_prefix": "unichem", "uri_format": "https://www.ebi.ac.uk/unichem/compoundsources?type=uci&compound=$1" }, "unigene": { "deprecated": true, "description": "A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.", "example": "4900", "homepage": "http://www.ncbi.nlm.nih.gov/unigene", "keywords": [ "dna", "gene", "gene expression", "life science", "protein" ], "mappings": { "biocontext": "UNIGENE", "fairsharing": "FAIRsharing.ge1c3p", "integbio": "nbdc00220", "miriam": "unigene", "n2t": "unigene", "prefixcommons": "unigene", "re3data": "r3d100010774" }, "name": "UniGene", "pattern": "^\\d+$", "preferred_prefix": "unigene", "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/unigene:$1" } ], "publications": [ { "doi": "10.1093/nar/gkg033", "pmc": "PMC165480", "pubmed": "12519941", "title": "Database resources of the National Center for Biotechnology", "year": 2003 } ], "uri_format": "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$1" }, "unii": { "description": "The purpose of the joint FDA/USP Substance Registration System (SRS) is to support health information technology initiatives by generating unique ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric identifier based on a substance’s molecular structure and/or descriptive information.", "example": "3G6A5W338E", "homepage": "https://precision.fda.gov/uniisearch", "mappings": { "biocontext": "UNII", "cheminf": "000563", "miriam": "unii", "n2t": "unii", "wikidata": "P652" }, "name": "Unique Ingredient Identifier", "pattern": "^[A-Z0-9]+$", "preferred_prefix": "unii", "uri_format": "https://precision.fda.gov/uniisearch/srs/unii/$1" }, "unimod": { "contact": { "email": "jcottrell@matrixscience.com", "name": "John Cottrell", "orcid": "0000-0003-3843-0818" }, "description": "Unimod is a public domain database created to provide a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide).", "download_owl": "https://raw.githubusercontent.com/PRIDE-Utilities/pride-ontology/master/unimod.owl", "example": "1200", "homepage": "http://www.unimod.org/", "keywords": [ "bioinformatics", "ontology" ], "mappings": { "biocontext": "UNIMOD", "edam": "3757", "fairsharing": "FAIRsharing.zZHCUQ", "miriam": "unimod", "n2t": "unimod", "ols": "unimod" }, "name": "Unimod protein modification database for mass spectrometry", "pattern": "^\\d+$", "preferred_prefix": "unimod", "publications": [ { "doi": "10.1002/pmic.200300744", "pubmed": "15174123", "title": "Unimod: Protein modifications for mass spectrometry", "year": 2004 } ], "uri_format": "http://www.unimod.org/modifications_view.php?editid1=$1" }, "uniparc": { "contact": { "email": "agb@ebi.ac.uk", "github": "bateman-research", "name": "Alex Bateman", "orcid": "0000-0002-6982-4660" }, "description": "The UniProt Archive (UniParc) is a database containing non-redundant protein sequence information from many sources. Each unique sequence is given a stable and unique identifier (UPI) making it possible to identify the same protein from different source databases.", "example": "UPI000000000A", "homepage": "http://www.uniprot.org/uniparc/", "keywords": [ "protein", "structure" ], "mappings": { "biocontext": "UNIPARC", "edam": "2392", "go": "UniParc", "miriam": "uniparc", "n2t": "uniparc", "prefixcommons": "uniparc", "re3data": "r3d100011519" }, "name": "UniProt Archive", "pattern": "^UPI[A-F0-9]{10}$", "preferred_prefix": "uniparc", "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/uniparc:$1" } ], "publications": [ { "doi": "10.1093/nar/gkh131", "pmc": "PMC308865", "pubmed": "14681372", "title": "UniProt: the Universal Protein knowledgebase", "year": 2004 } ], "uri_format": "https://www.uniprot.org/uniparc/$1" }, "unipathway.compound": { "description": "UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references compounds.", "example": "UPC04349", "homepage": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway", "mappings": { "biocontext": "UNIPATHWAY.COMPOUND", "miriam": "unipathway.compound", "n2t": "unipathway.compound" }, "name": "UniPathway Compound", "pattern": "^UPC\\d{5}$", "preferred_prefix": "unipathway.compound", "uri_format": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid=$1" }, "unipathway.reaction": { "description": "UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references individual reactions.", "example": "UCR00226", "homepage": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway", "mappings": { "biocontext": "UNIPATHWAY.REACTION", "miriam": "unipathway.reaction", "n2t": "unipathway.reaction" }, "name": "UniPathway Reaction", "pattern": "^UCR\\d{5}$", "preferred_prefix": "unipathway.reaction", "uri_format": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid=$1" }, "uniprot": { "contact": { "email": "agb@ebi.ac.uk", "github": "bateman-research", "name": "Alex Bateman", "orcid": "0000-0002-6982-4660" }, "contributor_extras": [ { "email": "m.naguthana@hotmail.com", "github": "nagutm", "name": "Mufaddal Naguthanawala", "orcid": "0009-0009-5240-7463" } ], "description": "The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. 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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/uniprot:$1" }, { "code": "describeprot", "description": "Structural and functional descriptors for proteins at the amino acid level", "homepage": "http://biomine.cs.vcu.edu/servers/DESCRIBEPROT", "name": "DescribePROT", "publications": [ { "doi": "10.1007/978-1-0716-4196-5_10", "pubmed": "39576581", "title": "DescribePROT Database of Residue-Level Protein Structure and Function Annotations", "year": 2024 } ], "uri_format": "http://biomine.cs.vcu.edu/servers/DESCRIBEPROT/result_v2.php?uniprot=$1" }, { "code": "drugbank", "description": "DrugBank PolyPeptide.", "homepage": "https://go.drugbank.com", "name": "DrugBank Polypeptide", "uri_format": "https://go.drugbank.com/polypeptides/$1" }, { "code": "iedb.antigen", "description": "A comprehensive collection of data on immune epitopes, covering experimental data and resources, including antigens", "homepage": "https://www.iedb.org/", "name": "Immune Epitope Database", "uri_format": "https://www.iedb.org/antigen/UNIPROT:$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@UP" }, { "code": "iptmnet", "description": "Protein post translational modification information", "homepage": "https://research.bioinformatics.udel.edu/iptmnet", "name": "iPTMnet", "uri_format": "https://research.bioinformatics.udel.edu/iptmnet/entry/$1" }, { "code": "ncbi", "description": "UniProt through NCBI", "homepage": "https://www.ncbi.nlm.nih.gov/protein/", "name": "UniProt through NCBI", "uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1" }, { "code": "oglcnac", "description": "A comprehensive catalog of O-GlcNAcylated proteins", "homepage": "https://www.oglcnac.mcw.edu", "name": "The O-GlcNAc Database", "publications": [ { "doi": "10.1007/s00216-024-05571-8", "pubmed": "39379619", "title": "The O-GlcNAc database: introducing new features and tools developed from community feedback", "year": 2024 } ], "uri_format": "https://www.oglcnac.mcw.edu/search/?query_protein=$1" }, { "code": "oma", "description": "The OMA project is a method and database for the inference of orthologs among complete genomes.", "homepage": "https://omabrowser.org/oma/home/", "name": "Orthologous Matrix Browser", "uri_format": "http://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p2=orthologs&p1=$1" }, { "code": "omnipath", "description": "Molecular interations endpoint from OmniPathDB", "homepage": "https://omnipathdb.org/", "name": "OmniPathDB", "uri_format": "https://omnipathdb.org/interactions/?fields=sources,references&partners=$1" }, { "code": "pharos", "description": "Part of the Illuminating the Druggable Genome project", "homepage": "https://pharos.nih.gov/idg", "name": "Pharos", "uri_format": "https://pharos.nih.gov/idg/targets/$1" }, { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", "homepage": "https://scholia.toolforge.org/", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/uniprot/$1" } ], "publications": [ { "doi": "10.1007/978-1-0716-4196-5_10", "pubmed": "39576581", "title": "DescribePROT Database of Residue-Level Protein Structure and Function Annotations", "year": 2024 }, { "doi": "10.1093/nar/gkae1119", "pubmed": "39574394", "title": "BFVD-a large repository of predicted viral protein structures", "year": 2024 }, { "doi": "10.1093/nar/gkae1010", "pubmed": "39552041", "title": "UniProt: the Universal Protein Knowledgebase in 2025", "year": 2024 }, { "doi": "10.1007/s00216-024-05571-8", "pubmed": "39379619", "title": "The O-GlcNAc database: introducing new features and tools developed from community feedback", "year": 2024 }, { "doi": "10.1093/database/baae085", "pmc": "PMC11349611", "pubmed": "39192607", "title": "Autoinhibited Protein Database: a curated database of autoinhibitory domains and their autoinhibition mechanisms", "year": 2024 }, { "doi": "10.1093/nar/gkj161", "pmc": "PMC1347523", "pubmed": "16381842", "title": "The Universal Protein Resource (UniProt): an expanding universe of protein information", "year": 2006 } ], "rdf_uri_format": "http://purl.uniprot.org/uniprot/$1", "synonyms": [ "SwissProt", "UP", "UniProt", "UniProtKB", "Uniprot ID", "uniprot/swiss-prot" ], "uri_format": "http://purl.uniprot.org/uniprot/$1" }, "uniprot.arba": { "contributor": { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" }, "description": "Association-Rule-Based Annotator (ARBA), a multiclass, self-training annotation system for automatic classification and annotation of UniProtKB proteins. This replaces the previous rule-based SAAS system.", "example": "ARBA00000001", "github_request_issue": 620, "homepage": "https://www.uniprot.org/arba", "mappings": { "go": "ARBA" }, "name": "Association-Rule-Based Annotator", "pattern": "^ARBA\\d+$", "preferred_prefix": "uniprot.arba", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "synonyms": [ "arba" ], "uri_format": "https://www.uniprot.org/arba/$1" }, "uniprot.chain": { "description": "This collection is a subset of UniProtKB that provides a means to reference the proteolytic cleavage products of a precursor protein.", "example": "PRO_0000016681", "homepage": "https://www.uniprot.org", "mappings": { "miriam": "uniprot.chain" }, "name": "UniProt Chain", "part_of": "uniprot", "pattern": "^PRO_[0-9]{10}$", "preferred_prefix": "uniprot.chain", "synonyms": [ "UPPRO" ], "uri_format": "http://purl.uniprot.org/annotation/$1" }, "uniprot.core": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Properties and classes used for protein annotation", "download_owl": "https://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/core.owl", "example": "certain", "homepage": "http://purl.uniprot.org/core/", "keywords": [ "biology", "ontology" ], "mappings": { "lov": "uniprot" }, "name": "Uniprot Core Ontology", "preferred_prefix": "uniprot.core", "uri_format": "http://purl.uniprot.org/core/$1" }, "uniprot.disease": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The human diseases in which proteins are involved are described in UniProtKB entries with a controlled vocabulary.", "download_obo": "https://rest.uniprot.org/diseases/stream?compressed=false&format=obo&query=%28%2A%29", "example": "DI-04240", "homepage": "https://www.uniprot.org/diseases/", "keywords": [ "ontology" ], "mappings": { "biolink": "SPDI", "wikidata": "P11430" }, "name": "UniProt Diseases", "part_of": "uniprot", "pattern": "^DI-\\d{5}$", "preferred_prefix": "uniprot.disease", "synonyms": [ "DI", "SP_DI" ], "uri_format": "https://www.uniprot.org/diseases/$1" }, "uniprot.isoform": { "description": "The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. This collection is a subset of UniProtKB, and provides a means to reference isoform information.", "example": "Q5BJF6-3", "homepage": "http://www.uniprot.org/", "mappings": { "biocontext": "UNIPROT.ISOFORM", "biolink": "UNIPROT.ISOFORM", "miriam": "uniprot.isoform", "n2t": "uniprot.isoform" }, "name": "UniProt Isoform", "part_of": "uniprot", "pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\-\\d+)$", "preferred_prefix": "uniprot.isoform", "providers": [ { "code": "CURATOR_REVIEW", "description": "UniProt Isoform through Universal Protein Resource using Persistent URL system", "homepage": "http://purl.uniprot.org/", "name": "UniProt Isoform through Universal Protein Resource using Persistent URL system", "uri_format": "http://purl.uniprot.org/uniprot/$1" }, { "code": "CURATOR_REVIEW", "description": "UniProt Isoform through UniParc", "homepage": "http://www.uniprot.org/uniparc/", "name": "UniProt Isoform through UniParc", "uri_format": "http://www.uniprot.org/uniparc/?query=$1" }, { "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/UniProtKB_$1" } ], "synonyms": [ "UPISO" ], "uri_format": "http://purl.uniprot.org/isoforms/$1" }, "uniprot.journal": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "identifier for a scientific journal, in the UniProt database", "example": "3546", "homepage": "https://www.uniprot.org/journals", "mappings": { "wikidata": "P4616" }, "name": "UniProt journal", "pattern": "^\\d{4}$", "preferred_prefix": "uniprot.journal", "rdf_uri_format": "http://purl.uniprot.org/journals/$1", "uri_format": "https://www.uniprot.org/journals/$1" }, "uniprot.keyword": { "description": "UniProtKB entries are tagged with keywords that can be used to retrieve particular subsets of entries.", "download_obo": "https://rest.uniprot.org/keywords/stream?compressed=false&fields=id%2Cname%2Ccategory%2Cgene_ontologies&format=tsv&query=%28%2A%29", "example": "KW-1273", "homepage": "http://www.uniprot.org/keywords/", "keywords": [ "classification", "ontology" ], "mappings": { "go": "UniProtKB-KW", "prefixcommons": "uniprot.kw" }, "name": "UniProt Keywords", "part_of": "uniprot", "pattern": "^KW-\\d{4}$", "preferred_prefix": "uniprot.keyword", "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/uniprot.kw:$1" } ], "synonyms": [ "SP_KW", "UniProtKB-KW", "uniprot.keyword", "uniprot.kw" ], "uri_format": "https://www.uniprot.org/keywords/$1" }, "uniprot.location": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The subcellular locations in which a protein is found are described in UniProtKB entries with a controlled vocabulary, which includes also membrane topology and orientation terms.", "download_obo": "https://rest.uniprot.org/locations/stream?compressed=false&format=obo&query=%28%2A%29", "example": "SL-0002", "homepage": "https://www.uniprot.org/locations/", "keywords": [ "ontology" ], "mappings": { "go": "UniProtKB-SubCell" }, "name": "UniProt Subcellular Locations", "part_of": "uniprot", "pattern": "^SL-\\d+$", "preferred_prefix": "uniprot.location", "synonyms": [ "SP_SL", "UPLOC", "UniProtKB-SubCell" ], "uri_format": "https://www.uniprot.org/locations/$1" }, "uniprot.mnemonic": { "contributor": { "email": "b.gyori@northeastern.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information. This entry represents UniProt mnemonics which combine an alphanumeric representation the protein name and a species identification code representing the biological source of the protein.", "example": "BRAF_HUMAN", "github_request_issue": 1110, "homepage": "https://www.uniprot.org/", "mappings": { "togoid": "UniprotMnemonic" }, "name": "UniProt", "pattern": "^[A-Z0-9]{1,10}_[A-Z0-9]{1,5}$", "preferred_prefix": "uniprot.mnemonic", "publications": [ { "doi": "10.1093/nar/gkj161", "pmc": "PMC1347523", "pubmed": "16381842", "title": "The Universal Protein Resource (UniProt): an expanding universe of protein information", "year": 2006 } ], "reviewer": { "email": "tiago.lubiana.alves@usp.br", "github": "lubianat", "name": "Tiago Lubiana", "orcid": "0000-0003-2473-2313" }, "uri_format": "https://www.uniprot.org/uniprotkb/$1" }, "uniprot.proteome": { "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "UniProt provides proteome sets of proteins whose genomes have been completely sequenced.", "example": "UP000005640", "github_request_issue": 604, "homepage": "https://www.uniprot.org/proteomes", "mappings": { "togoid": "UniprotProteome" }, "name": "UniProt Proteomes", "part_of": "uniprot", "pattern": "^UP\\d{9}$", "preferred_prefix": "uniprot.proteome", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.uniprot.org/proteomes/$1" }, "uniprot.ptm": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "contributor_extras": [ { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" } ], "description": "The post-translational modifications used in the UniProt knowledgebase (Swiss-Prot and TrEMBL). The definition of the post-translational modifications usage as well as other information is provided in the following format", "example": "PTM-0450", "homepage": "https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/docs/ptmlist", "keywords": [ "biochemistry", "post-translational modification", "structural biology" ], "license": "CC-BY-4.0", "name": "UniProt Post-Translational Modification", "part_of": "uniprot", "pattern": "^PTM-\\d{4}$", "preferred_prefix": "uniprot.ptm", "references": [ "https://twitter.com/cthoyt/status/1510570256619778053", "https://www.uniprot.org/docs/ptmlist.txt" ], "synonyms": [ "PTM" ], "uri_format": "https://biopragmatics.github.io/providers/uniprot.ptm/$1" }, "uniprot.resource": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources.", "example": "DB-0174", "homepage": "https://www.uniprot.org/database/", "name": "UniProt Resource", "part_of": "uniprot", "pattern": "^DB-\\d{4}$", "preferred_prefix": "uniprot.resource", "synonyms": [ "uniprot.database", "uniprot.db" ], "uri_format": "https://www.uniprot.org/database/$1" }, "uniprot.tissue": { "description": "The UniProt Tissue List is a controlled vocabulary of terms used to annotate biological tissues. It also contains cross-references to other ontologies where tissue types are specified.", "example": "TS-0285", "homepage": "https://www.uniprot.org/docs/tisslist.txt", "mappings": { "biocontext": "TISSUELIST", "miriam": "tissuelist", "n2t": "tissuelist" }, "name": "Tissue List", "part_of": "uniprot", "pattern": "^TS-\\d{4}$", "preferred_prefix": "uniprot.tissue", "uri_format": "https://www.uniprot.org/tissues/$1" }, "uniprot.var": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The purpose of the UniProtKB/Swiss-Prot variant pages is: to display the variant related information extracted from UniProtKB/Swiss-Prot, and to provide useful additional information such as the conservation of the modified residues across orthologous species.", "example": "068078", "homepage": "https://web.expasy.org/variant_pages", "name": "UniProt Variants", "part_of": "uniprot", "pattern": "^\\d+$", "preferred_prefix": "uniprot.var", "providers": [ { "code": "expasy", "description": "Expasy external page for protein variant", "homepage": "https://web.expasy.org/variant_pages", "name": "ExPaSy", "uri_format": "https://web.expasy.org/variant_pages/VAR_$1.html" } ], "synonyms": [ "SP_VAR", "UPVAR", "UniProtKB_VAR" ], "uri_format": "http://purl.uniprot.org/annotation/VAR_$1" }, "uniref": { "description": "The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc records in order to obtain complete coverage of the sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view.", "example": "UniRef90_P00750", "homepage": "https://www.uniprot.org/", "mappings": { "edam": "2346", "miriam": "uniref", "re3data": "r3d100011518" }, "name": "UniRef", "pattern": "^UniRef(100|90|50)_([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}|UPI[A-F0-9]{10})$", "preferred_prefix": "uniref", "uri_format": "https://www.uniprot.org/uniref/$1" }, "unirule": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Rules are devised and tested by experienced curators using experimental data from manually annotated entries as templates. UniRule rules can annotate protein properties such as the protein name, function, catalytic activity, pathway membership, and subcellular location, along with sequence specific information, such as the positions of post-translational modifications and active sites.", "example": "UR000124451", "homepage": "https://www.uniprot.org/unirule/", "mappings": { "go": "UniRule" }, "name": "UniRule", "preferred_prefix": "unirule", "uri_format": "https://www.uniprot.org/unirule/$1" }, "unists": { "deprecated": true, "description": "UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences.", "example": "456789", "homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=unists", "keywords": [ "gene", "protein" ], "mappings": { "biocontext": "UNISTS", "edam": "2389", "miriam": "unists", "n2t": "unists", "ncbi": "UniSTS", "prefixcommons": "unists" }, "name": "Database of Sequence Tagged Sites", "pattern": "^\\d+$", "preferred_prefix": "unists", "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/unists:$1" } ], "uri_format": "https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$1" }, "unite": { "contact": { "email": "urmas.koljalg@ut.ee", "name": "Urmas Kõljalg", "orcid": "0000-0002-5171-1668" }, "description": "UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database. It focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. Entries may be supplemented with metadata on describing locality, habitat, soil, climate, and interacting taxa.", "example": "UDB000691", "homepage": "http://unite.ut.ee/", "keywords": [ "biodiversity", "bioinformatics", "dna", "ecology", "genomics", "metagenomics", "taxonomy" ], "mappings": { "biocontext": "UNITE", "edam": "2390", "fairsharing": "FAIRsharing.cnwx8c", "integbio": "nbdc01905", "miriam": "unite", "n2t": "unite", "ncbi": "UNITE", "prefixcommons": "unite", "re3data": "r3d100011316" }, "name": "Molecular database for the identification of fungi", "pattern": "^UDB\\d{6}$", "preferred_prefix": "unite", "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/unite:$1" } ], "publications": [ { "doi": "10.1111/j.1469-8137.2009.03160.x", "pubmed": "20409185", "title": "The UNITE database for molecular identification of fungi--recent updates and future perspectives", "year": 2010 } ], "uri_format": "http://unite.ut.ee/bl_forw.php?nimi=$1" }, "unpd": { "comment": "The website is dead, there are no places to get the source information except inside https://oolonek.github.io/ISDB/.", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "homepage": "http://pkuxxj.pku.edu.cn/UNPD/", "name": "Universal Natural Products Database", "preferred_prefix": "unpd", "publications": [ { "doi": "10.1021/acs.jnatprod.6b01093", "pubmed": "28616931", "title": "Database for Rapid Dereplication of Known Natural Products Using Data from MS and Fast NMR Experiments", "year": 2017 }, { "doi": "10.1371/journal.pone.0062839", "pmc": "PMC3636197", "pubmed": "23638153", "title": "Use of natural products as chemical library for drug discovery and network pharmacology", "year": 2013 } ], "references": [ "http://bioinf-applied.charite.de/supernatural_new/index.php?site=vendor_info&id=Universal%20Natural%20Products%20Database", "https://pharmacognosy.in/the-universal-natural-products-database-unpd/", "https://oolonek.github.io/ISDB/" ] }, "uo": { "appears_in": [ "agro", "ms", "rbo", "scdo" ], "banana": "UO", "contact": { "email": "g.gkoutos@gmail.com", "github": "gkoutos", "name": "George Gkoutos", "orcid": "0000-0002-2061-091X" }, "description": "Ontology of standardized units", "download_obo": "http://purl.obolibrary.org/obo/uo.obo", "download_owl": "http://purl.obolibrary.org/obo/uo.owl", "example": "0000080", "homepage": "https://github.com/bio-ontology-research-group/unit-ontology", "keywords": [ "life science", "mathematics", "measurement", "obo", "ontology", "unit" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "UO", "agroportal": "UO", "biocontext": "UO", "bioportal": "UO", "fairsharing": "FAIRsharing.mjnypw", "miriam": "uo", "n2t": "uo", "obofoundry": "uo", "ols": "uo", "ontobee": "UO", "prefixcommons": "uo" }, "name": "Units of measurement ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "UO", "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/uo:$1" } ], "publications": [ { "doi": "10.1093/database/bas033", "pmc": "PMC3468815", "pubmed": "23060432", "title": "The Units Ontology: a tool for integrating units of measurement in science", "year": 2012 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/UO_$1", "repository": "https://github.com/bio-ontology-research-group/unit-ontology", "uri_format": "http://purl.obolibrary.org/obo/UO_$1", "version": "2023-05-25" }, "upa": { "contact": { "email": "Anne.Morgat@sib.swiss", "github": "amorgat", "name": "Anne Morgat", "orcid": "0000-0002-1216-2969" }, "depends_on": [ "ro" ], "deprecated": true, "description": "A manually curated resource for the representation and annotation of metabolic pathways", "download_obo": "https://raw.githubusercontent.com/geneontology/unipathway/master/upa.obo", "download_owl": "http://purl.obolibrary.org/obo/upa.owl", "example": "UCR00513", "homepage": "https://github.com/geneontology/unipathway", "keywords": [ "obo", "ontology", "pathway" ], "license": "CC-BY-3.0", "mappings": { "aberowl": "UPA", "biocontext": "UNIPATHWAY", "bioportal": "UPA", "edam": "2645", "go": "UniPathway", "obofoundry": "upa", "ols": "upa", "ontobee": "UPA", "pathguide": "414", "prefixcommons": "unipathway" }, "name": "Unipathway", "pattern": "^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\\d{5}$", "preferred_prefix": "UPA", "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/unipathway:$1" } ], "publications": [ { "doi": "10.1093/nar/gkr1023", "pmc": "PMC3245108", "pubmed": "22102589", "title": "UniPathway: a resource for the exploration and annotation of metabolic pathways", "year": 2011 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/UPA_$1", "repository": "https://github.com/geneontology/unipathway", "synonyms": [ "UPa", "unipathway", "unipathway.pathway" ], "uri_format": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1", "version": "2024-03-06" }, "upheno": { "contact": { "email": "jmcl@ebi.ac.uk", "github": "jamesamcl", "name": "James McLaughlin", "orcid": "0000-0002-8361-2795" }, "description": "The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.", "download_owl": "http://purl.obolibrary.org/obo/upheno.owl", "homepage": "https://github.com/obophenotype/upheno", "keywords": [ "evolutionary biology", "expression data", "obo", "omics", "omics data analysis", "ontology", "phenomics", "phenotype" ], "license": "CC0-1.0", "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBa01CIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--3f5258d2bcf30a7e127b5a9fe209b27e25e88883/up.png?disposition=inline", "mappings": { "aberowl": "UPHENO", "biocontext": "UPHENO", "bioportal": "UPHENO", "fairsharing": "FAIRsharing.r41qhx", "obofoundry": "upheno", "ols": "upheno", "ontobee": "UPHENO" }, "name": "Unified Phenotype Ontology", "no_own_terms": true, "preferred_prefix": "UPHENO", "publications": [ { "doi": "10.1093/genetics/iyaf027", "pubmed": "40048704", "title": "The Unified Phenotype Ontology : a framework for cross-species integrative phenomics", "year": 2025 }, { "doi": "10.1101/2024.09.18.613276", "title": "The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/UPHENO_$1", "repository": "https://github.com/obophenotype/upheno", "uri_format": "http://purl.obolibrary.org/obo/UPHENO_$1", "version": "2025-01-11" }, "urdbms.syndromefinder": { "appears_in": [ "nando" ], "contact": { "email": "naritomi@med.u-ryukyu.ac.jp", "name": "Kenji Naritomi" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "example": "3567", "github_request_issue": 1320, "mappings": { "integbio": "nbdc00728" }, "name": "UR-DBMS Syndrome Finder", "pattern": "^\\d+$", "preferred_prefix": "urdbms.syndromefinder", "publications": [ { "doi": "10.1038/s10038-024-01277-y", "pubmed": "39085458", "title": "An application supporting diagnosis for rare genetic diseases - UR-DBMS and Syndrome Finder", "year": 2024 } ], "uri_format": "http://syndromefinder.ncchd.go.jp/UR-DBMS/SyndromeDetail.php?winid=1&recid=$1" }, "uspto": { "comment": "Information about the regular expression was derived from examples at https://patft.uspto.gov/netahtml/PTO/srchnum.htm. TODO, make the regular expression work for '100000000'", "contributor_extras": [ { "github": "dhimmel", "name": "Daniel Himmelstein", "orcid": "0000-0002-3012-7446" } ], "description": "The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement.", "example": "4145692", "example_extras": [ "0000001", "10,000,000", "6923014", "AI00007", "D000152", "H001234", "PP07514", "RE12345", "RX00001", "T855019", "X000001" ], "homepage": "http://patft.uspto.gov/netahtml/PTO/index.html", "mappings": { "biocontext": "USPTO", "miriam": "uspto", "n2t": "uspto" }, "name": "United States Patent and Trademark Office", "pattern": "^(\\d{1,2},?\\d{3},?\\d{3}|(PP|RE|AI|RX)\\d{2},?\\d{3}|(D|T|H|X)\\d{3},?\\d{3})$", "preferred_prefix": "uspto", "references": [ "https://github.com/biopragmatics/bioregistry/issues/253" ], "uri_format": "http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/$1" }, "utrdb": { "description": "A curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs. In the current update, the UTR entries are organized in a gene-centric structure to better visualize and retrieve 5' and 3'UTR variants generated by alternative initiation and termination of transcription and alternative splicing. Experimentally validated miRNA targets and conserved sequence elements are also annotated. The integration of UTRdb with genomic data has allowed the implementation of an efficient annotation system and a powerful retrieval resource for the selection and extraction of specific UTR subsets. ", "example": "5UTR_107_ENST00000517291.2", "homepage": "https://utrdb.cloud.ba.infn.it/utrdb/index_107.html", "mappings": { "integbio": "nbdc00730", "miriam": "utrdb" }, "name": "UTRdb", "pattern": "^([3-5][A-Z])\\w+[^A-Z][0-9]$", "preferred_prefix": "utrdb", "uri_format": "https://utrdb.cloud.ba.infn.it/cgi-bin/utrdb/utrdb?e=$1" }, "vac": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Vaccine Adjuvant Compendium (VAC) was established in 2020 by the NIAID Division of Allergy, Immunology, and Transplantation to foster collaborations between NIAID-supported adjuvant researchers and the broader scientific community. The VAC displays adjuvant characteristics or metadata defined through NIAID-supported adjuvant studies to help vaccine developers identify suitable adjuvants for various vaccine indications, including immune-mediated and infectious diseases. In addition, the VAC welcomes the inclusion of adjuvant metadata generated by other research programs.", "example": "15", "homepage": "https://vac.niaid.nih.gov", "keywords": [ "biology", "immunology", "vaccines" ], "name": "Vaccine Adjuvant Compendium", "pattern": "^\\d+$", "preferred_prefix": "vac", "uri_format": "https://vac.niaid.nih.gov/view?id=$1" }, "validatordb": { "contact": { "email": "david.sehnal@gmail.com", "name": "David Sehnal", "orcid": "0000-0002-0682-3089" }, "description": "Database of validation results for ligands and non-standard residues in the Protein Data Bank.", "example": "2h6o", "homepage": "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/", "keywords": [ "life science" ], "mappings": { "biocontext": "VALIDATORDB", "fairsharing": "FAIRsharing.c9psgb", "integbio": "nbdc02174", "miriam": "validatordb", "n2t": "validatordb" }, "name": "ValidatorDB", "pattern": "^[A-Za-z0-9\\/]+$", "preferred_prefix": "validatordb", "provides": "pdb", "publications": [ { "doi": "10.1093/nar/gku1118", "pmc": "PMC4383933", "pubmed": "25392418", "title": "ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank", "year": 2014 } ], "uri_format": "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/$1" }, "vandf": { "contact": { "email": "michael.lincoln@med.va.gov", "name": "Michael Lincoln" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The National Drug File (NDF) is produced by the U.S. Department of Veterans Affairs, Veterans Health Administration (VHA). NDF is a centrally maintained electronic drug list used by the VHA hospitals and clinics. Facilities use the NDF to check drug interactions, to manage orders, and to send outpatient prescriptions to regional automated mail-out pharmacies. NDF includes information on clinical drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes. ", "example": "4019477", "homepage": "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF", "keywords": [ "biomedical science", "drug", "drug interaction", "ontology", "pharmacology" ], "mappings": { "aberowl": "VANDF", "biolink": "VANDF", "bioportal": "VANDF", "fairsharing": "FAIRsharing.xn3pb3", "hl7": "2.16.840.1.113883.6.229" }, "name": "Veterans Administration National Drug File", "pattern": "^\\d+$", "preferred_prefix": "vandf", "publications": [ { "pmc": "PMC2244318", "pubmed": "12463886", "title": "A semantic normal form for clinical drugs in the UMLS: early experiences with the VANDF", "year": 2002 } ], "uri_format": "http://purl.bioontology.org/ontology/VANDF/$1" }, "vann": { "contact": { "email": "nospam@iandavis.com", "github": "iand", "name": "Ian Davis" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "This document describes a vocabulary for annotating descriptions of vocabularies with examples and usage notes.", "example": "usageNote", "homepage": "https://vocab.org/vann/", "keywords": [ "metadata" ], "mappings": { "lov": "vann", "zazuko": "vann" }, "name": "A vocabulary for annotating vocabulary descriptions", "preferred_prefix": "vann", "uri_format": "https://vocab.org/vann/#$1" }, "vario": { "banana": "VariO", "contact": { "email": "mauno.vihinen@med.lu.se", "github": "maunov", "name": "Mauno Vihinen", "orcid": "0000-0002-9614-7976" }, "deprecated": true, "description": "The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level.", "download_obo": "http://purl.obolibrary.org/obo/vario.obo", "download_owl": "http://purl.obolibrary.org/obo/vario.owl", "example": "0376", "homepage": "http://variationontology.org", "keywords": [ "deoxyribonucleic acid", "dna structural variation", "genetics", "obo", "ontology", "protein", "ribonucleic acid", "sequence variant" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "VARIO", "agroportal": "VARIO", "biocontext": "VARIO", "bioportal": "VARIO", "fairsharing": "FAIRsharing.65xkbs", "miriam": "vario", "n2t": "vario", "obofoundry": "vario", "ols": "vario", "ontobee": "VariO" }, "name": "Variation Ontology", "namespace_in_lui": true, "pattern": "^\\d+$", "preferred_prefix": "VariO", "providers": [ { "code": "CURATOR_REVIEW", "description": "VariO at Lund University", "homepage": "http://www.variationontology.org/", "name": "VariO at Lund University", "uri_format": "http://www.ontobee.org/search?ontology=VariO&keywords=VariO_$1&submit=Search+terms" } ], "publications": [ { "doi": "10.1186/s12864-018-5262-0", "pmc": "PMC6309100", "pubmed": "30591019", "title": "Systematics for types and effects of DNA variations", "year": 2018 }, { "doi": "10.1002/humu.22954", "pubmed": "26773573", "title": "VariOtator, a Software Tool for Variation Annotation with the Variation Ontology", "year": 2016 }, { "doi": "10.1007/s00439-015-1529-6", "pubmed": "25616435", "title": "Types and effects of protein variations", "year": 2015 }, { "doi": "10.1186/2041-1480-5-9", "pmc": "PMC3931275", "pubmed": "24533660", "title": "Variation ontology: annotator guide", "year": 2014 }, { "doi": "10.1101/gr.157495.113", "pmc": "PMC3912426", "pubmed": "24162187", "title": "Variation Ontology for annotation of variation effects and mechanisms", "year": 2013 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/VariO_$1", "uri_format": "http://purl.obolibrary.org/obo/VariO_$1", "version": "2018-11-09" }, "vbase2": { "contact": { "email": "wmueller@gbf.de", "name": "Werner Müller", "orcid": "0000-0002-1297-9725" }, "description": "The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes.", "example": "humIGHV025", "homepage": "http://www.vbase2.org/vbase2.php", "keywords": [ "gene", "life science" ], "mappings": { "biocontext": "VBASE2", "fairsharing": "FAIRsharing.qvxhb1", "integbio": "nbdc01897", "miriam": "vbase2", "n2t": "vbase2", "ncbi": "VBASE2", "prefixcommons": "vbase2" }, "name": "Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse", "pattern": "^\\w+$", "preferred_prefix": "vbase2", "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/vbase2:$1" } ], "publications": [ { "doi": "10.1093/nar/gki088", "pmc": "PMC540042", "pubmed": "15608286", "title": "VBASE2, an integrative V gene database", "year": 2005 } ], "uri_format": "http://www.vbase2.org/vgene.php?id=$1" }, "vbo": { "contact": { "email": "Sabrina@tislab.org", "github": "sabrinatoro", "name": "Sabrina Toro", "orcid": "0000-0002-4142-7153" }, "depends_on": [ "ncbitaxon" ], "description": "Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names.", "download_json": "http://purl.obolibrary.org/obo/vbo.json", "download_obo": "http://purl.obolibrary.org/obo/vbo.obo", "download_owl": "http://purl.obolibrary.org/obo/vbo.owl", "example": "0000038", "homepage": "https://github.com/monarch-initiative/vertebrate-breed-ontology", "keywords": [ "obo", "ontology" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "VBO", "bioportal": "VBO", "cellosaurus": "VBO", "obofoundry": "vbo", "ols": "vbo", "ontobee": "VBO" }, "name": "Vertebrate Breed Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "VBO", "rdf_uri_format": "http://purl.obolibrary.org/obo/VBO_$1", "repository": "https://github.com/monarch-initiative/vertebrate-breed-ontology", "uri_format": "http://purl.obolibrary.org/obo/VBO_$1", "version": "2025-02-12" }, "vbrc": { "description": "The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis.", "example": "35742", "homepage": "http://vbrc.org/", "mappings": { "biocontext": "VBRC", "miriam": "vbrc", "n2t": "vbrc", "prefixcommons": "vbrc" }, "name": "Viral Bioinformatics Resource Center", "pattern": "^\\d+$", "preferred_prefix": "vbrc", "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/vbrc:$1" } ], "uri_format": "http://vbrc.org/gene_detail.asp?gene_id=$1" }, "vcard": { "contact": { "email": "r@iannel.la", "github": "riannella", "name": "Renato Iannella", "orcid": "0000-0001-5547-3508" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "vCard is a specification developed by the Internet Engineering Task Force (IETF) for the description of people and organisations", "download_rdf": "https://www.w3.org/2006/vcard/ns", "example": "Agent", "github_request_issue": 1317, "homepage": "https://www.w3.org/TR/vcard-rdf/", "keywords": [ "people" ], "mappings": { "lov": "vcard", "zazuko": "vcard" }, "name": "Virtual Contact File", "preferred_prefix": "vcard", "uri_format": "http://www.w3.org/2006/vcard/ns#$1" }, "vcell": { "description": "Models developed with the Virtual Cell (VCell) software prorgam.", "example": "201022999", "homepage": "https://health.uconn.edu/", "mappings": { "miriam": "vcell" }, "name": "VCell Published Models", "pattern": "^\\d{5,}$", "preferred_prefix": "vcell", "uri_format": "https://vcell.org/biomodel-$1" }, "vdrc": { "description": "Biomaterial supply resource which collects, maintains, and distributes independent transgenic fly lines. Most of the 38,000 fly lines are RNAi lines, but VDRC also maintains a collection of enhancer-GAL4 driver lines. Nearly all lines are in duplicate. Users can search for the stocks or DNA constructs for the gene of interest by entering CG number, synonym, or Transformant ID. [from RRID]", "example": "100291", "homepage": "http://stockcenter.vdrc.at/control/main", "keywords": [ "biomaterial supply resource", "drosophila", "fly lines" ], "mappings": { "rrid": "VDRC" }, "name": "Vienna Drosophila Resource Center", "pattern": "^\\d+$", "preferred_prefix": "vdrc", "uri_format": "https://shop.vbc.ac.at/vdrc_store/$1.html" }, "vectorbase": { "contact": { "email": "d.e.starns@liv.ac.uk", "github": "obsidian83", "name": "David Starns", "orcid": "0000-0001-6583-9067" }, "description": "VectorBase is part of the VEuPathDB, a NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens and related species of interest. Currently, VectorBase contains genome information for approximately 80 organisms: mosquitoes, bed bugs, biting midges, ticks, tsetse flies, mites, sand flies, house flies, body lice, stable flies, kissing bugs, and a snail which is an intermediate host.", "example": "ISCW007415", "homepage": "https://www.vectorbase.org/", "keywords": [ "comparative genomics", "functional genomics", "gene", "genome", "genomics", "population dynamics", "population genetics", "protein" ], "mappings": { "biocontext": "VECTORBASE", "fairsharing": "FAIRsharing.3etvdn", "integbio": "nbdc01909", "miriam": "vectorbase", "n2t": "vectorbase", "ncbi": "VectorBase", "prefixcommons": "vectorbase", "re3data": "r3d100010880" }, "name": "Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens", "pattern": "^\\D{4}\\d{6}(\\-\\D{2})?$", "preferred_prefix": "vectorbase", "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/vectorbase:$1" }, { "code": "vectorbase.alt1", "description": "An alternate provider based on the search functionality", "homepage": "https://www.vectorbase.org", "name": "Vectorbase Alt. 1", "uri_format": "https://www.vectorbase.org/search/site/$1?&site=\"Genome\"" }, { "code": "vectorbase.alt2", "description": "An alternate provider based on the app structure", "homepage": "https://www.vectorbase.org", "name": "Vectorbase Alt. 2", "uri_format": "https://vectorbase.org/vectorbase/app/record/gene/$1" } ], "publications": [ { "doi": "10.1093/nar/gku1117", "pmc": "PMC4383932", "pubmed": "25510499", "title": "VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases", "year": 2014 }, { "doi": "10.1093/nar/gkn857", "pmc": "PMC2686483", "pubmed": "19028744", "title": "VectorBase: a data resource for invertebrate vector genomics", "year": 2008 } ], "twitter": "VectorBase", "uri_format": "https://vectorbase.org/gene/$1" }, "vega": { "contact": { "email": "jla1@sanger.ac.uk", "name": "Jennifer L Harrow", "orcid": "0000-0003-0338-3070" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A repository for high-quality gene models produced by the manual annotation of vertebrate genomes.", "example": "OTTHUMG00000169812", "homepage": "https://vega.archive.ensembl.org/index.html", "keywords": [ "genome", "life science" ], "mappings": { "fairsharing": "FAIRsharing.mr293q", "prefixcommons": "vega", "re3data": "r3d100012575" }, "name": "Vertebrate Genome Annotation Database", "preferred_prefix": "vega", "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/vega:$1" } ], "publications": [ { "doi": "10.1093/nar/gkt1241", "pmc": "PMC3964964", "pubmed": "24316575", "title": "The Vertebrate Genome Annotation browser 10 years on", "year": 2013 }, { "doi": "10.1093/nar/gkm987", "pmc": "PMC2238886", "pubmed": "18003653", "title": "The vertebrate genome annotation (Vega) database", "year": 2007 } ], "synonyms": [ "VEGA" ], "uri_format": "http://vega.sanger.ac.uk/[?species_name]/Gene/Summary?g=$1" }, "vegbank": { "description": "VegBank is the vegetation plot database of the Ecological Society of America's Panel on Vegetation Classification. VegBank consists of three linked databases that contain (1) vegetation plot records, (2) vegetation types recognized in the U.S. National Vegetation Classification and other vegetation types submitted by users, and (3) all plant taxa recognized by ITIS/USDA as well as all other plant taxa recorded in plot records. Vegetation records, community types and plant taxa may be submitted to VegBank and may be subsequently searched, viewed, annotated, revised, interpreted, downloaded, and cited. ", "example": "VB.Ob.3736.GRSM125", "homepage": "http://vegbank.org/", "mappings": { "miriam": "vegbank", "re3data": "r3d100010153" }, "name": "VegBank", "pattern": "^VB\\.[A-Za-z][A-Za-z]\\..*$", "preferred_prefix": "vegbank", "uri_format": "http://vegbank.org/cite/$1" }, "venom": { "appears_in": [ "vbo" ], "contact": { "email": "DBrodbelt@RVC.AC.UK", "name": "David Brodbelt", "orcid": "0000-0001-5628-4194" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Veterinary Nomenclature (VeNom) is a standard set of clinical veterinary terms for use in referral veterinary hospital electronic patient records and first opinion veterinary practice management systems.", "example": "12969", "homepage": "https://venomcoding.org/", "name": "Veterinary Nomenclature", "pattern": "^\\d+$", "preferred_prefix": "VeNom", "proprietary": true, "references": [ "https://github.com/biopragmatics/bioregistry/pull/724" ] }, "vfb": { "contact": { "email": "r.court@ed.ac.uk", "name": "Robert Court", "orcid": "0000-0002-0173-9080" }, "description": "An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster.", "example": "00000001", "homepage": "https://VirtualFlyBrain.org", "keywords": [ "life science", "neurobiology" ], "mappings": { "fairsharing": "FAIRsharing.nzaz6z", "miriam": "vfb", "n2t": "vfb", "re3data": "r3d100011373" }, "name": "Virtual Fly Brain", "pattern": "^[0-9a-zA-Z]{8}$", "preferred_prefix": "vfb", "publications": [ { "doi": "10.1186/1471-2105-13-122", "pmc": "PMC3412715", "pubmed": "22676296", "title": "Web tools for large-scale 3D biological images and atlases", "year": 2012 }, { "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": "doi:10.1186/1471-2105-13-122", "title": "Web tools for large-scale 3D biological images and atlases" } ], "uri_format": "http://virtualflybrain.org/reports/$1" }, "vfdb.gene": { "description": "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes.", "example": "VFG2154", "homepage": "http://www.mgc.ac.cn/VFs/", "mappings": { "biocontext": "VFDB.GENE", "miriam": "vfdb.gene", "n2t": "vfdb.gene" }, "name": "VFDB Gene", "pattern": "^\\w+$", "preferred_prefix": "vfdb.gene", "uri_format": "http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$1" }, "vfdb.genus": { "description": "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus.", "example": "Chlamydia", "homepage": "http://www.mgc.ac.cn/VFs/", "mappings": { "biocontext": "VFDB.GENUS", "miriam": "vfdb.genus", "n2t": "vfdb.genus" }, "name": "VFDB Genus", "pattern": "^\\w+$", "preferred_prefix": "vfdb.genus", "uri_format": "http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=$1" }, "vgnc": { "contact": { "email": "stweedie@ebi.ac.uk", "name": "Susan Tweedie", "orcid": "0000-0003-1818-8243" }, "description": "The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of the established HGNC (HUGO Gene Nomenclature Committee) project that names human genes. VGNC is responsible for assigning standardized names to genes in vertebrate species that currently lack a nomenclature committee.", "example": "3792", "homepage": "https://vertebrate.genenames.org", "keywords": [ "life science" ], "mappings": { "cellosaurus": "VGNC", "fairsharing": "FAIRsharing.5NhJFK", "integbio": "nbdc02624", "miriam": "vgnc", "ncbi": "VGNC", "togoid": "Vgnc", "uniprot": "DB-0226" }, "name": "Vertebrate Gene Nomenclature Committee", "pattern": "^\\d{1,9}$", "preferred_prefix": "vgnc", "publications": [ { "doi": "10.1093/nar/gkaa980", "pmc": "PMC7779007", "pubmed": "33152070", "title": "Genenames.org: the HGNC and VGNC resources in 2021", "year": 2021 } ], "uri_format": "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1" }, "vhog": { "contact": { "email": "bgee@isb-sib.ch", "name": "Bgee team" }, "deprecated": true, "description": "vHOG is a multi-species anatomical ontology for the vertebrate lineage, developed as part of the Bgee project. The mapping to species-specific anatomical ontologies is provided as a separated file: http://bgee.unil.ch/download/organ_association_vHOG.txt This mapping represents homology-strict relationships, in the sense of HOM:0000007 \"historical homology\". Each mapping has been manually reviewed, and we provide confidence codes and references when available.", "download_obo": "ftp://ftp.bgee.org/general/ontologies/vHOG.obo", "download_owl": "http://purl.obolibrary.org/obo/vhog.owl", "example": "0000411", "homepage": "http://bgee.unil.ch", "keywords": [ "anatomy", "development", "obo", "ontology" ], "logo": "http://bgee.org/img/logo/bgee13_logo.png", "mappings": { "aberowl": "VHOG", "biocontext": "VHOG", "bioportal": "VHOG", "obofoundry": "vhog", "prefixcommons": "vhog" }, "name": "Vertebrate Homologous Organ Group Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "VHOG", "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/vhog:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/VHOG_$1", "synonyms": [ "VHOG_RETIRED" ], "uri_format": "http://purl.obolibrary.org/obo/VHOG_$1" }, "viaf": { "description": "The VIAF® (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service. The goal of the service is to lower the cost and increase the utility of library authority files by matching and linking widely-used authority files and making that information available on the Web.", "example": "75121530", "homepage": "http://viaf.org", "keywords": [ "centrally registered identifier", "knowledge and information systems" ], "mappings": { "bartoc": "2053", "fairsharing": "FAIRsharing.a15ac6", "miriam": "viaf", "n2t": "viaf", "wikidata": "P214" }, "name": "VIAF ID", "pattern": "^\\d+$", "preferred_prefix": "viaf", "providers": [ { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", "homepage": "https://scholia.toolforge.org/", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/viaf/$1" }, { "code": "viaf.https", "description": "A duplicate endpoint over HTTPS", "first_party": true, "homepage": "http://viaf.org", "name": "VIAF (https)", "uri_format": "https://viaf.org/$1" } ], "rdf_uri_format": "http://viaf.org/viaf/$1", "uri_format": "http://viaf.org/viaf/$1" }, "vibso": { "contact": { "email": "philip.stroemert@tib.eu", "github": "StroemPhi", "name": "Philip Strömert", "orcid": "0000-0002-1595-3213" }, "contributor": { "email": "philip.stroemert@tib.eu", "github": "StroemPhi", "name": "Philip Strömert", "orcid": "0000-0002-1595-3213" }, "description": "The Vibration Spectroscopy Ontology defines technical terms with which research data produced in vibrational spectroscopy experiments can be semantically enriched, made machine readable and FAIR.", "example": "0000008", "github_request_issue": 1278, "homepage": "https://nfdi4chem.github.io/VibrationalSpectroscopyOntology/", "license": "CC-BY-4.0", "name": "Vibrational Spectroscopy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "vibso", "repository": "https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://purl.obolibrary.org/obo/VIBSO_$1" }, "vido": { "contact": { "email": "johnbeverley2021@u.northwestern.edu", "github": "johnbeve", "name": "John Beverly", "orcid": "0000-0002-1118-1738" }, "description": "The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used by Virologists, i.e. virus, prion, satellite, viroid, etc.", "download_owl": "https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-virus/master/ontology/vido.owl", "example": "0001114", "homepage": "https://github.com/infectious-disease-ontology-extensions/ido-virus", "keywords": [ "ontology" ], "mappings": { "aberowl": "VIDO", "bioportal": "VIDO", "ols": "vido", "ontobee": "VIDO" }, "name": "The Virus Infectious Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "vido", "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/VIDO_$1" } ], "repository": "https://github.com/infectious-disease-ontology-extensions/ido-virus", "uri_format": "http://purl.obolibrary.org/obo/VIDO_$1", "version": "2020-08-25" }, "violinnet": { "appears_in": [ "oae" ], "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "deprecated": true, "description": "Defunct vaccine information source from the He Lab", "example": "4140", "mappings": { "wikidata": "P1925" }, "name": "ViolinNet", "pattern": "^\\d+$", "preferred_prefix": "violinnet", "synonyms": [ "violinID", "violinId" ], "uri_format": "http://www.violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=$1" }, "viperdb": { "description": "VIPERdb is a database for icosahedral virus capsid structures . The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration.", "example": "2c6s", "homepage": "http://viperdb.scripps.edu/", "keywords": [ "small molecule", "structure" ], "mappings": { "integbio": "nbdc00835", "prefixcommons": "viperdb", "re3data": "r3d100012362" }, "name": "VIPERdb", "preferred_prefix": "viperdb", "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/viperdb:$1" } ], "provides": "pdb", "uri_format": "https://viperdb.org/Info_Page.php?VDB=$1" }, "vipr": { "contact": { "email": "rscheuermann@jcvi.org", "name": "Richard Scheuermann", "orcid": "0000-0003-1355-892X" }, "description": "The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses. It provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, and host factor data. This collection references viral strain information.", "example": "BeAn 70563", "homepage": "http://www.viprbrc.org/brc/home.do?decorator=vipr", "keywords": [ "biomedical science", "epidemiology", "genomics", "immunology", "life science", "proteomics", "virology" ], "mappings": { "biocontext": "VIPR", "fairsharing": "FAIRsharing.2qx8n8", "miriam": "vipr", "n2t": "vipr", "ncbi": "ViPR", "re3data": "r3d100011931" }, "name": "Virus Pathogen Resource", "pattern": "^[A-Za-z 0-9]+$", "preferred_prefix": "vipr", "publications": [ { "doi": "10.3390/v4113209", "pmc": "PMC3509690", "pubmed": "23202522", "title": "Virus pathogen database and analysis resource (ViPR): a comprehensive bioinformatics database and analysis resource for the coronavirus research community", "year": 2012 }, { "doi": "10.1093/nar/gkr859", "pmc": "PMC3245011", "pubmed": "22006842", "title": "ViPR: an open bioinformatics database and analysis resource for virology research", "year": 2011 }, { "doi": "10.1016/b978-0-12-809633-8.20995-3", "pmc": "PMC7173540", "title": "Database and Analytical Resources for Viral Research Community", "year": 2021 }, { "doi": "10.1016/b978-0-12-801238-3.95728-3", "pmc": "PMC7157461", "title": "Virus Databases ☆", "year": 2017 } ], "repository": "https://github.com/VirusBRC", "uri_format": "http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$1&decorator=arena" }, "viralzone": { "contact": { "email": "Philippe.Lemercier@sib.swiss", "name": "Philippe Le Mercier", "orcid": "0000-0001-8528-090X" }, "description": "ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures.", "example": "992", "homepage": "http://www.expasy.org/viralzone/", "keywords": [ "epidemiology", "life science", "molecular biology", "virology", "virus" ], "mappings": { "biocontext": "VIRALZONE", "fairsharing": "FAIRsharing.tppk10", "go": "VZ", "integbio": "nbdc02226", "miriam": "viralzone", "n2t": "viralzone", "prefixcommons": "vz", "re3data": "r3d100013314" }, "name": "ViralZone", "pattern": "^\\d+$", "preferred_prefix": "viralzone", "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/vz:$1" }, { "code": "viralzone.alt1", "description": "Alternate view", "homepage": "http://viralzone.expasy.org", "name": "Viralzone Alt 1.", "uri_format": "http://viralzone.expasy.org/all_by_protein/$1" } ], "publications": [ { "doi": "10.1093/nar/gks1220", "pmc": "PMC3531065", "pubmed": "23193299", "title": "ViralZone: recent updates to the virus knowledge resource", "year": 2012 }, { "doi": "10.1093/nar/gkq901", "pmc": "PMC3013774", "pubmed": "20947564", "title": "ViralZone: a knowledge resource to understand virus diversity", "year": 2010 } ], "synonyms": [ "vz" ], "uri_format": "https://viralzone.expasy.org/$1" }, "virgen": { "description": "VirGen a comprehensive viral genome resource, which organizes the ‘sequence space’ of viral genomes in a structured fashion. It has been developed with an objective to serve as an annotated and curated database for complete viral genome sequences.", "example": "AY321118", "homepage": "http://bioinfo.ernet.in/virgen/virgen.html", "keywords": [ "genome" ], "mappings": { "prefixcommons": "virgen" }, "name": "VirGen", "preferred_prefix": "virgen", "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/virgen:$1" } ] }, "virmirdb": { "description": "A database containing predicted viral miRNA candidate hairpins.", "example": "11002", "homepage": "http://alk.ibms.sinica.edu.tw", "keywords": [ "rna", "structure" ], "mappings": { "prefixcommons": "virmirdb" }, "name": "Vir-Mir db", "preferred_prefix": "virmirdb", "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/virmirdb:$1" } ], "provides": "ncbitaxon", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/virus.cgi?tax_id=$1" }, "viroligo": { "description": "The VirOligo database (1) is part of an effort to provide methods suitable for assessing what viruses are present in samples. Such methods should faciliate studies of the spatial and temporal distribution of viruses and their diversity at any one time and place.", "example": "BM0456", "homepage": "http://viroligo.okstate.edu", "keywords": [ "small molecule" ], "mappings": { "prefixcommons": "viroligo" }, "name": "VirOligo", "preferred_prefix": "viroligo", "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/viroligo:$1" } ], "uri_format": "http://viroligo.okstate.edu/main.php?vid=$1" }, "virsirna": { "description": "The VIRsiRNA database contains details of siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region.", "example": "virsi1909", "homepage": "http://crdd.osdd.net/servers/virsirnadb", "mappings": { "biocontext": "VIRSIRNA", "miriam": "virsirna", "n2t": "virsirna" }, "name": "VIRsiRNA", "pattern": "^virsi\\d+$", "preferred_prefix": "virsirna", "uri_format": "http://crdd.osdd.net/servers/virsirnadb/record.php?details=$1" }, "virushostdb": { "contact": { "email": "ogata@kuicr.kyoto-u.ac.jp", "name": "Hiroyuki Ogata", "orcid": "0000-0001-6594-377X" }, "description": "Virus-Host DB organizes data about the relationships between viruses and their hosts, represented in the form of pairs of NCBI taxonomy IDs for viruses and their hosts. Virus-Host DB covers viruses with complete genomes stored in 1) NCBI/RefSeq and 2) GenBank whose accession numbers are listed in EBI Genomes. The host information is collected from RefSeq, GenBank (in free text format), UniProt, ViralZone, and manually curated with additional information obtained by literature surveys.", "example": "438782", "homepage": "https://www.genome.jp/virushostdb/", "keywords": [ "virus" ], "mappings": { "integbio": "nbdc02395", "prefixcommons": "virushostdb" }, "name": "Virus-HostDB", "preferred_prefix": "virushostdb", "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/virushostdb:$1" } ], "provides": "ncbitaxon", "publications": [ { "doi": "10.3390/v8030066", "pmc": "PMC4810256", "pubmed": "26938550", "title": "Linking Virus Genomes with Host Taxonomy", "year": 2016 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://www.genome.jp/virushostdb/$1" }, "vita": { "description": "ViTa is a database which collects virus data from miRBase and ICTV, VirGne, VBRC.., etc, including known miRNAs on virus and supporting predicted host miRNA targets by miRanda and TargetScan. ViTa also rovide effective annotations, including human miRNA expression, virus infected tissues, annotation of virus and comparisons.", "example": "AB016785", "homepage": "http://vita.mbc.nctu.edu.tw/", "keywords": [ "gene expression", "rna", "structure" ], "mappings": { "prefixcommons": "vita" }, "name": "Virus' miRNA target", "preferred_prefix": "vita", "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/vita:$1" } ], "uri_format": "http://vita.mbc.nctu.edu.tw/search.php?acc=$1" }, "vitro": { "appears_in": [ "fabio", "foaf" ], "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Vitro is a full stack framework for building semantic web applications. It is not domain specific.", "download_owl": "https://raw.githubusercontent.com/vivo-archive/Linked-Data-Indexer/refs/heads/master/src/main/resources/vitro-0.7.owl", "example": "descriptionAnnot", "github_request_issue": 1317, "homepage": "https://github.com/vivo-project/Vitro", "keywords": [ "ontology" ], "name": "Vitro Application Ontology", "preferred_prefix": "vitro", "repository": "https://github.com/vivo-project/Vitro", "uri_format": "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#$1" }, "vivo": { "contact": { "email": "christian.hauschke@tib.eu", "github": "hauschke", "name": "Christian Hauschke", "orcid": "0000-0003-2499-7741" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology about scholarship", "download_owl": "https://raw.githubusercontent.com/vivo-ontologies/vivo-ontology/master/vivo.owl", "example": "Laboratory", "github_request_issue": 1317, "homepage": "https://vivoweb.org", "keywords": [ "academy", "natural science", "ontology", "protocol", "researcher data", "resource metadata", "study design" ], "license": "unlicense", "mappings": { "aberowl": "VIVO", "biocontext": "VIVO", "bioportal": "VIVO", "fairsharing": "FAIRsharing.6xfgaq", "lov": "vivo" }, "name": "VIVO Ontology", "preferred_prefix": "vivo", "repository": "https://github.com/vivo-ontologies/vivo-ontology", "uri_format": "http://vivoweb.org/ontology/core#$1" }, "vmc": { "deprecated": true, "mappings": { "biolink": "VMC" }, "name": "Variation Modelling Collaboration", "preferred_prefix": "vmc", "references": [ "https://docs.google.com/document/d/12E8WbQlvfZWk5NrxwLytmympPby6vsv60RxCeD5wc1E/edit#heading=h.67hbe76b6a4z", "https://github.com/ga4gh/vr-spec" ] }, "vmhgene": { "description": "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.", "example": "8639.1", "homepage": "https://www.vmh.life/", "mappings": { "miriam": "vmhgene" }, "name": "VMH Gene", "pattern": "^[0-9]+\\.[0-9]+$", "preferred_prefix": "vmhgene", "uri_format": "https://www.vmh.life/#gene/$1" }, "vmhmetabolite": { "description": "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.", "example": "h2o", "homepage": "https://www.vmh.life/", "mappings": { "biocontext": "VMHMETABOLITE", "miriam": "vmhmetabolite", "n2t": "vmhmetabolite" }, "name": "VMH metabolite", "pattern": "^[a-zA-Z0-9_\\(\\_\\)\\[\\]]+$", "preferred_prefix": "vmhmetabolite", "uri_format": "https://www.vmh.life/#metabolite/$1" }, "vmhreaction": { "description": "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.", "example": "HEX1", "homepage": "https://www.vmh.life/", "mappings": { "biocontext": "VMHREACTION", "miriam": "vmhreaction", "n2t": "vmhreaction" }, "name": "VMH reaction", "pattern": "^[a-zA-Z0-9_\\(\\_\\)\\[\\]]+$", "preferred_prefix": "vmhreaction", "uri_format": "https://www.vmh.life/#reaction/$1" }, "vo": { "appears_in": [ "scdo" ], "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", "name": "Yongqunh He", "orcid": "0000-0001-9189-9661" }, "description": "The Vaccine Ontology (VO) is a community-based biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine types and annotations, integrate various vaccine data, and support computer-assisted reasoning. The VO supports basic vaccine R&D and clincal vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities.", "download_owl": "http://purl.obolibrary.org/obo/vo.owl", "example": "0000093", "homepage": "https://violinet.org/vaccineontology", "keywords": [ "biological process", "biomedical science", "immunology", "obo", "ontology", "pathobiochemistry", "pathogen", "small molecule", "vaccination", "vaccine" ], "license": "CC-BY-4.0", "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaUFDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--0d3898a5618b34c0bc948bb0d101e906f212f05f/vo_banner.png?disposition=inline", "mappings": { "aberowl": "VO", "biocontext": "VO", "bioportal": "VO", "fairsharing": "FAIRsharing.zwtww5", "obofoundry": "vo", "ols": "vo", "ontobee": "VO", "prefixcommons": "vo", "wikidata": "P1928" }, "name": "Vaccine Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "VO", "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/vo:$1" } ], "publications": [ { "doi": "10.2174/1381612826666201125112131", "pubmed": "33238868", "title": "Ontology-based Precision Vaccinology for Deep Mechanism Understanding and Precision Vaccine Development", "year": 2021 }, { "doi": "10.1186/2041-1480-3-17", "pmc": "PMC3639077", "pubmed": "23256535", "title": "Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses", "year": 2012 }, { "doi": "10.1186/2041-1480-2-s2-s8", "pmc": "PMC3102897", "pubmed": "21624163", "title": "Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology", "year": 2011 }, { "doi": "10.1186/1745-7580-6-s1-s5", "pmc": "PMC2946783", "pubmed": "20875156", "title": "Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN", "year": 2010 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/VO_$1", "repository": "https://github.com/vaccineontology/VO", "uri_format": "http://purl.obolibrary.org/obo/VO_$1", "version": "2025-02-26" }, "voc4cat": { "comment": "The most current version of a concept can be accessed so * https://w3id.org/nfdi4cat/voc4cat_0000123 other/older versions from releases like so * https://w3id.org/nfdi4cat/voc4cat/v2023-08-17/voc4cat_0000123. This is pretty unique and isn't tracked by the Bioregistry currently.", "contact": { "email": "nikolaos.moustakas@catalysis.de", "github": "nmoust", "name": "Nikolaos Moustakas", "orcid": "0000-0002-6242-2167" }, "contributor": { "email": "David.Linke@catalysis.de", "github": "dalito", "name": "David Linke", "orcid": "0000-0002-5898-1820" }, "description": "Voc4Cat is a [SKOS](https://www.w3.org/TR/2009/REC-skos-reference-20090818/) vocabulary for the catalysis disciplines. The vocabulary was created in the [NFDI4Cat](http://www.nfdi4cat.org/) initiative. The first collection of terms was published in June 2023 with a focus on photo catalysis. Our goal is to continuously extend the vocabulary to other areas of catalysis and related disciplines like chemical engineering or materials science.", "example": "0000123", "github_request_issue": 957, "homepage": "https://nfdi4cat.github.io/voc4cat/", "license": "CC0-1.0", "name": "A vocabulary for the catalysis disciplines", "pattern": "^\\d{7,}$", "preferred_prefix": "voc4cat", "repository": "https://github.com/nfdi4cat/voc4cat", "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://w3id.org/nfdi4cat/voc4cat_$1" }, "void": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary for expressing metadata about RDF datasets. It is intended as a bridge between the publishers and users of RDF data, with applications ranging from data discovery to cataloging and archiving of datasets. This document provides a formal definition of the new RDF classes and properties introduced for VoID. It is a companion to the main specification document for VoID, Describing Linked Datasets with the VoID Vocabulary.", "example": "feature", "homepage": "http://vocab.deri.ie/void", "keywords": [ "metadata" ], "mappings": { "biocontext": "void", "lov": "void", "zazuko": "void" }, "name": "Vocabulary of Interlinked Datasets", "preferred_prefix": "void", "uri_format": "http://rdfs.org/ns/void#$1" }, "vsao": { "contact": { "email": "wasila.dahdul@usd.edu", "name": "Wasila Dahdul", "orcid": "0000-0003-3162-7490" }, "deprecated": true, "description": "Vertebrate skeletal anatomy ontology.", "download_obo": "http://aber-owl.net/media/ontologies/VSAO/20/vsao.obo", "download_owl": "http://purl.obolibrary.org/obo/vsao.owl", "example": "0000183", "homepage": "https://www.nescent.org/phenoscape/Main_Page", "keywords": [ "anatomy", "obo", "ontology", "vertebrate" ], "mappings": { "aberowl": "VSAO", "biocontext": "VSAO", "bioportal": "VSAO", "obofoundry": "vsao", "ols": "vsao", "prefixcommons": "vao" }, "name": "Vertebrate Skeletal Anatomy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "VSAO", "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/vao:$1" } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/VSAO_$1", "synonyms": [ "VSAO_RETIRED" ], "uri_format": "http://purl.obolibrary.org/obo/VSAO_$1", "version": "2012-11-06" }, "vsdb": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Veterinary pharmaceuticals are biologically active and potentially persistent substances which are recognised as a continuing threat to environmental quality. Whilst the environmental risk of agricultural pesticides has had considerable attention in recent decades, risks assessments for veterinary pharmaceuticals have only relatively recently began to be addressed. Risk assessments and risk modelling tend to be inherently data hungry processes and one of the main obstacles to consistent, accurate and efficient assessments is the need for a reliable, quality and comprehensive data source.", "example": "1868", "homepage": "https://sitem.herts.ac.uk/aeru/vsdb", "name": "Veterinary Substances DataBase", "pattern": "^\\d+$", "preferred_prefix": "vsdb", "uri_format": "https://sitem.herts.ac.uk/aeru/vsdb/Reports/$1.htm" }, "vsmo": { "contact": { "email": "lars.eisen@colostate.edu", "name": "Lars Eisen", "orcid": "0000-0002-0094-3186" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "an ontology for vector surveillance and management, focusing on arthropod vectors and vector-borne pathogens with relevance to humans or domestic animals, and with special emphasis on content to support operational activities through inclusion in databases, data management systems, or decision support systems.", "download_json": "https://raw.githubusercontent.com/cthoyt/vsmo/main/vsmo.json", "download_obo": "https://raw.githubusercontent.com/cthoyt/vsmo/main/vsmo.obo", "download_owl": "https://raw.githubusercontent.com/cthoyt/vsmo/main/vsmo.owl", "example": "0000000", "homepage": "https://code.google.com/archive/p/vector-surveillance-and-management-ontology/", "keywords": [ "ontology" ], "license": "New BSD License", "name": "Ontology for vector surveillance and management", "preferred_prefix": "vsmo", "publications": [ { "doi": "10.1603/me12169", "pmc": "PMC3695545", "pubmed": "23427646", "title": "Ontology for vector surveillance and management", "year": 2013 } ], "uri_format": "http://purl.obolibrary.org/obo/VSMO_$1" }, "vso": { "contact": { "email": "albertgoldfain@gmail.com", "name": "Albert Goldfain" }, "description": "The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements. ", "download_owl": "http://aber-owl.net/media/ontologies/VSO/1/vso.owl", "example": "0000041", "homepage": "https://bioportal.bioontology.org/ontologies/VSO", "keywords": [ "biomedical science", "blood", "experimental measurement", "health", "health science", "ontology", "owl" ], "mappings": { "aberowl": "VSO", "bioportal": "VSO", "fairsharing": "FAIRsharing.jjb2p2", "prefixcommons": "vso", "zazuko": "vso" }, "name": "Vital Sign Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "vso", "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/vso:$1" } ], "uri_format": "https://bioportal.bioontology.org/ontologies/VSO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVSO_$1" }, "vt": { "appears_in": [ "scdo" ], "contact": { "email": "caripark@iastate.edu", "github": "caripark", "name": "Carissa Park", "orcid": "0000-0002-2346-5201" }, "description": "The Vertebrate Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms.", "download_obo": "https://github.com/AnimalGenome/vertebrate-trait-ontology/raw/master/current_release/vt.obo", "download_owl": "http://purl.obolibrary.org/obo/vt.owl", "example": "0000685", "homepage": "https://github.com/AnimalGenome/vertebrate-trait-ontology", "keywords": [ "animal physiology", "biology", "developmental biology", "morphology", "obo", "ontology", "phenotype", "physiology", "trait", "vertebrate" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "VT", "agroportal": "VT", "biocontext": "VT", "bioportal": "VT", "fairsharing": "FAIRsharing.10gr18", "obofoundry": "vt", "ols": "vt", "ontobee": "VT", "prefixcommons": "vt" }, "name": "Vertebrate trait ontology", "pattern": "^\\d{7}$", "preferred_prefix": "VT", "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/vt:$1" } ], "publications": [ { "doi": "10.1186/2041-1480-4-13", "pmc": "PMC3851175", "pubmed": "23937709", "title": "The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species", "year": 2013 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/VT_$1", "repository": "https://github.com/AnimalGenome/vertebrate-trait-ontology", "uri_format": "http://purl.obolibrary.org/obo/VT_$1", "version": "2025-03-25" }, "vto": { "contact": { "email": "balhoff@renci.org", "github": "balhoff", "name": "Jim Balhoff", "orcid": "0000-0002-8688-6599" }, "description": "Comprehensive hierarchy of extinct and extant vertebrate taxa.", "download_obo": "http://purl.obolibrary.org/obo/vto.obo", "download_owl": "http://purl.obolibrary.org/obo/vto.owl", "example": "9008500", "homepage": "https://github.com/phenoscape/vertebrate-taxonomy-ontology", "keywords": [ "bone", "obo", "ontology", "taxonomy" ], "license": "CC0-1.0", "mappings": { "aberowl": "VTO", "biocontext": "VTO", "bioportal": "VTO", "fairsharing": "FAIRsharing.akmeb9", "obofoundry": "vto", "ols": "vto", "ontobee": "VTO" }, "name": "Vertebrate Taxonomy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "VTO", "publications": [ { "doi": "10.1186/2041-1480-4-34", "pmc": "PMC4177199", "pubmed": "24267744", "title": "The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes", "year": 2013 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/VTO_$1", "repository": "https://github.com/phenoscape/vertebrate-taxonomy-ontology", "uri_format": "http://purl.obolibrary.org/obo/VTO_$1", "version": "2020-11-13" }, "vuid": { "comment": "The example corresponds to acetaminophen", "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "The Veterans Health Administration is America’s largest integrated health care system, providing care at 1,293 health care facilities, including 171 medical centers and 1,112 outpatient sites of care of varying complexity (VHA outpatient clinics), serving 9 million enrolled Veterans each year.", "example": "4007166", "homepage": "https://www.va.gov/health", "name": "Veterans Health Administration (VHA) unique identifier", "pattern": "^\\d+$", "preferred_prefix": "vuid", "references": [ "https://academic.oup.com/jamia/article/17/4/432/866953" ] }, "wb.rnai": { "description": "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes.", "example": "WBRNAi00086878", "homepage": "https://www.wormbase.org/", "mappings": { "biocontext": "WB.RNAI", "miriam": "wb.rnai", "n2t": "wb.rnai" }, "name": "WormBase RNAi", "pattern": "^WBRNAi\\d{8}$", "preferred_prefix": "wb.rnai", "uri_format": "https://www.wormbase.org/species/c_elegans/rnai/$1" }, "wbbt": { "contact": { "email": "raymond@caltech.edu", "github": "raymond91125", "name": "Raymond Lee", "orcid": "0000-0002-8151-7479" }, "description": "Ontology about the gross anatomy of the C. elegans", "download_obo": "http://purl.obolibrary.org/obo/wbbt.obo", "download_owl": "http://purl.obolibrary.org/obo/wbbt.owl", "example": "0001290", "homepage": "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology", "keywords": [ "anatomy", "cell", "life science", "obo", "ontology", "worm" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "WBBT", "biocontext": "WBbt", "biolink": "WBbt", "bioportal": "WB-BT", "fairsharing": "FAIRsharing.phk7dd", "go": "WBbt", "obofoundry": "wbbt", "ols": "wbbt", "ontobee": "WBbt", "prefixcommons": "wbbt" }, "name": "C. elegans Gross Anatomy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "WBbt", "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/wbbt:$1" } ], "publications": [ { "doi": "10.1002/cfg.248", "pmc": "PMC2447384", "pubmed": "18629098", "title": "Building a cell and anatomy ontology of Caenorhabditis elegans", "year": 2003 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/WBbt_$1", "repository": "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology", "synonyms": [ "WBbt" ], "uri_format": "http://purl.obolibrary.org/obo/WBbt_$1", "version": "2025-03-26" }, "wbls": { "contact": { "email": "cgrove@caltech.edu", "github": "chris-grove", "name": "Chris Grove", "orcid": "0000-0001-9076-6015" }, "description": "Ontology about the development and life stages of the C. elegans", "download_obo": "http://purl.obolibrary.org/obo/wbls.obo", "download_owl": "http://purl.obolibrary.org/obo/wbls.owl", "example": "0000690", "homepage": "https://github.com/obophenotype/c-elegans-development-ontology", "keywords": [ "development", "developmental biology", "life cycle", "life cycle stage", "life science", "obo", "ontology", "worm" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "WBLS", "biocontext": "WBLS", "biolink": "WBls", "bioportal": "WB-LS", "fairsharing": "FAIRsharing.sm90nh", "go": "WBls", "obofoundry": "wbls", "ols": "wbls", "ontobee": "WBls", "prefixcommons": "wbls" }, "name": "C. elegans development ontology", "pattern": "^\\d{7}$", "preferred_prefix": "WBls", "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/wbls:$1" } ], "publications": [ { "doi": "10.1093/nar/gkz920", "pmc": "PMC7145598", "pubmed": "31642470", "title": "WormBase: a modern Model Organism Information Resource", "year": 2020 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/WBls_$1", "repository": "https://github.com/obophenotype/c-elegans-development-ontology", "synonyms": [ "WBls" ], "uri_format": "http://purl.obolibrary.org/obo/WBls_$1", "version": "2025-01-04" }, "wbphenotype": { "contact": { "email": "cgrove@caltech.edu", "github": "chris-grove", "name": "Chris Grove", "orcid": "0000-0001-9076-6015" }, "description": "Ontology about C. elegans and other nematode phenotypes", "download_obo": "http://purl.obolibrary.org/obo/wbphenotype.obo", "download_owl": "http://purl.obolibrary.org/obo/wbphenotype.owl", "example": "0000983", "homepage": "https://github.com/obophenotype/c-elegans-phenotype-ontology", "keywords": [ "anatomy", "life science", "obo", "omics", "omics data analysis", "ontology", "phenomics", "phenotype", "worm" ], "license": "CC-BY-4.0", "mappings": { "aberowl": "WBPHENOTYPE", "biocontext": "WBPhenotype", "bioportal": "WB-PHENOTYPE", "fairsharing": "FAIRsharing.agvc7y", "go": "WBPhenotype", "obofoundry": "wbphenotype", "ols": "wbphenotype", "ontobee": "WBPhenotype", "prefixcommons": "wbphenotype" }, "name": "C. elegans phenotype", "pattern": "^\\d{7}$", "preferred_prefix": "WBPhenotype", "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/wbphenotype:$1" } ], "publications": [ { "doi": "10.1186/1471-2105-12-32", "pmc": "PMC3039574", "pubmed": "21261995", "title": "Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community", "year": 2011 } ], "rdf_uri_format": "http://purl.obolibrary.org/obo/WBPhenotype_$1", "repository": "https://github.com/obophenotype/c-elegans-phenotype-ontology", "synonyms": [ "WBPhenotype" ], "uri_format": "http://purl.obolibrary.org/obo/WBPhenotype_$1", "version": "2025-01-02" }, "webelements": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Browser for the periodic table of the elements", "example": "chromium", "homepage": "https://www.webelements.com/", "keywords": [ "chemistry" ], "name": "Web Elements", "pattern": "^\\w+$", "preferred_prefix": "webelements", "uri_format": "https://www.webelements.com/$1" }, "wgs84": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A vocabulary for representing latitude, longitude and altitude information in the WGS84 geodetic reference datum", "example": "latitude", "homepage": "https://www.w3.org/2003/01/geo/wgs84_pos", "keywords": [ "geography" ], "mappings": { "biolink": "wgs", "lov": "geo" }, "name": "WGS84 Geo Positioning", "preferred_prefix": "wgs84", "uri_format": "http://www.w3.org/2003/01/geo/wgs84_pos#$1" }, "wicell": { "description": "Cell line collections (Providers)", "example": "ai10e-kctd13b", "homepage": "https://www.wicell.org", "mappings": { "cellosaurus": "WiCell" }, "name": "WiCell Research Institute Cell Collection", "preferred_prefix": "wicell", "uri_format": "https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx?closable=true" }, "wikidata": { "contact": { "email": "vrandecic@gmail.com", "github": "vrandezo", "name": "Denny Vrandečić", "orcid": "0000-0002-9593-2294" }, "description": "Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic.", "example": "Q47475003", "example_extras": [ "L704278", "P675" ], "homepage": "https://www.wikidata.org/", "keywords": [ "chemistry", "genomics", "metabolomics", "proteomics", "subject agnostic" ], "license": "CC0-1.0", "mappings": { "bartoc": "1940", "biocontext": "WIKIDATA", "biolink": "WIKIDATA", "cellosaurus": "Wikidata", "cheminf": "000567", "fairsharing": "FAIRsharing.6s749p", "miriam": "wikidata", "n2t": "wikidata" }, "name": "Wikidata", "pattern": "^(Q|P|E|L)\\d+$", "preferred_prefix": "wikidata", "providers": [ { "code": "scholia", "description": "Scholia can generally resolve many Wikidata entries in the biomedical and bibliometric domains", "homepage": "https://scholia.toolforge.org", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/$1" } ], "publications": [ { "doi": "10.1145/2187980.2188242", "title": "Wikidata", "year": 2012 } ], "synonyms": [ "WD_Entity", "wd", "wdeschema" ], "twitter": "wikidata", "uri_format": "http://www.wikidata.org/entity/$1" }, "wikidata.property": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Wikidata is a free and open knowledge base that can be read and edited by both humans and machines.\nWikidata acts as central storage for the structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others. ", "example": "P4355", "homepage": "https://www.wikidata.org", "license": "CC0-1.0", "mappings": { "biocontext": "WD_Prop", "biolink": "WIKIDATA_PROPERTY" }, "name": "Wikidata Property", "part_of": "wikidata", "pattern": "^P\\d+$", "preferred_prefix": "wikidata.property", "providers": [ { "code": "scholia", "description": "Scholia can generally resolve many Wikidata entries in the biomedical and bibliometric domains", "homepage": "https://scholia.toolforge.org", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/$1" } ], "uri_format": "https://www.wikidata.org/wiki/Property:$1" }, "wikigenes": { "description": "WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide a platform for the scientific community to collect, communicate and evaluate knowledge about genes, chemicals, diseases and other biomedical concepts in a bottom-up process.", "example": "3771877", "homepage": "http://www.wikigenes.org/", "mappings": { "biocontext": "WIKIGENES", "miriam": "wikigenes", "n2t": "wikigenes" }, "name": "WikiGenes", "pattern": "^\\d+$", "preferred_prefix": "wikigenes", "provides": "ncbigene", "uri_format": "http://www.wikigenes.org/e/gene/e/$1.html" }, "wikipathways": { "contact": { "email": "egon.willighagen@gmail.com", "github": "egonw", "name": "Egon Willighagen", "orcid": "0000-0001-7542-0286" }, "contributor_extras": [ { "email": "egon.willighagen@gmail.com", "github": "egonw", "name": "Egon Willighagen", "orcid": "0000-0001-7542-0286" } ], "description": "WikiPathways is a database of biological pathways maintained by and for the scientific community.", "example": "WP732", "homepage": "http://www.wikipathways.org/", "keywords": [ "biological regulation", "drug interaction", "epidemiology", "genetic interaction", "molecular interaction", "pathway", "pathway model", "protein interaction", "reaction data", "signaling", "virology" ], "license": "CC0-1.0", "logo": "https://www.wikipathways.org/assets/img/wikipathways-logo-horizontal.svg", "mappings": { "biocontext": "WIKIPATHWAYS", "edam": "3952", "fairsharing": "FAIRsharing.g7b4rj", "integbio": "nbdc02116", "miriam": "wikipathways", "n2t": "wikipathways", "pathguide": "237", "prefixcommons": "wikipathways", "re3data": "r3d100013316", "togoid": "Wikipathways", "wikidata": "P2410" }, "mastodon": "wikipathways@fosstodon.org", "name": "WikiPathways", "pattern": "^WP\\d{1,5}(\\_r\\d+)?$", "preferred_prefix": "wikipathways", "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/wikipathways:$1" }, { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.\n", "homepage": "https://scholia.toolforge.org/", "name": "Scholia", "uri_format": "https://scholia.toolforge.org/wikipathways/$1" } ], "publications": [ { "doi": "10.1093/nar/gkad960", "pmc": "PMC10767877", "pubmed": "37941138", "title": "WikiPathways 2024: next generation pathway database", "year": 2024 }, { "doi": "10.1093/nar/gkaa1024", "pmc": "PMC7779061", "pubmed": "33211851", "title": "WikiPathways: connecting communities", "year": 2021 }, { "doi": "10.1093/nar/gkx1064", "pmc": "PMC5753270", "pubmed": "29136241", "title": "WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research", "year": 2018 }, { "doi": "10.1093/nar/gkv1024", "pmc": "PMC4702772", "pubmed": "26481357", "title": "WikiPathways: capturing the full diversity of pathway knowledge", "year": 2015 }, { "doi": "10.1093/nar/gkr1074", "pmc": "PMC3245032", "pubmed": "22096230", "title": "WikiPathways: building research communities on biological pathways", "year": 2011 }, { "doi": "10.1371/journal.pbio.0060184", "pmc": "PMC2475545", "pubmed": "18651794", "title": "WikiPathways: pathway editing for the people", "year": 2008 } ], "rdf_uri_format": "http://identifiers.org/wikipathways/$1", "twitter": "WikiPathways", "uri_format": "http://www.wikipathways.org/instance/$1" }, "wikipathways.vocab": { "contact": { "email": "egon.willighagen@gmail.com", "github": "egonw", "name": "Egon Willighagen", "orcid": "0000-0001-7542-0286" }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "An ontology supporting data modeling in WikiPathways", "download_owl": "http://aber-owl.net/media/ontologies/WIKIPATHWAYS/225/wikipathways.owl", "example": "DataNode", "homepage": "http://www.wikipathways.org", "keywords": [ "ontology" ], "mappings": { "aberowl": "WIKIPATHWAYS", "bioportal": "WIKIPATHWAYS" }, "mastodon": "wikipathways@fosstodon.org", "name": "WikiPathways Ontology", "preferred_prefix": "wikipathways.vocab", "references": [ "https://github.com/biopragmatics/bioregistry/issues/818" ], "uri_format": "https://bioportal.bioontology.org/ontologies/WIKIPATHWAYS/?p=classes&conceptid=http%3A%2F%2Fvocabularies.wikipathways.org%2Fwp%23$1" }, "wikipedia.en": { "contributor_extras": [ { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" } ], "description": "Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay.", "example": "SM_UB-81", "example_extras": [ "Pharyngeal_pouch_(embryology)" ], "homepage": "http://en.wikipedia.org/wiki/Main_Page", "mappings": { "biocontext": "WIKIPEDIA.EN", "go": "Wikipedia", "miriam": "wikipedia.en", "n2t": "wikipedia.en", "prefixcommons": "wikipedia" }, "name": "Wikipedia", "pattern": "^\\S+$", "preferred_prefix": "wikipedia.en", "providers": [ { "code": "CURATOR_REVIEW", "description": "Wikipedia structured content through DBpedia", "homepage": "http://wiki.dbpedia.org/", "name": "Wikipedia structured content through DBpedia", "uri_format": "http://dbpedia.org/page/$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/wikipedia:$1" }, { "code": "volupedia", "description": "A mix of wikipedia and 3d", "homepage": "http://en.volupedia.org", "name": "Volupedia", "uri_format": "http://en.volupedia.org/wiki/$1" } ], "references": [ "https://github.com/biopragmatics/bioregistry/issues/794" ], "synonyms": [ "Wikipedia", "wikipedia" ], "uri_format": "http://en.wikipedia.org/wiki/$1" }, "wiktionary": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "A free dictionary", "example": "pharmacist", "github_request_issue": 1310, "homepage": "https://wiktionary.org", "license": "CC BY SA 4.0", "name": "Wiktionary", "preferred_prefix": "wiktionary", "uri_format": "https://en.wiktionary.org/wiki/$1" }, "worfdb": { "description": "WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans. 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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/worfdb:$1" } ], "uri_format": "http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query=$1" }, "world2dpage": { "comment": "This resource doesn't exist on the web anymore", "deprecated": true, "description": "A public repository, standards compliant, for proteomics image data published in the literature. This repository currently contains data from 16 published articles, putting together 22 reference maps for 15 species, totalizing nearly 4'400 identified spots.", "example": "0020", "homepage": "http://world-2dpage.expasy.org/repository/", "keywords": [ "2d-page", "protein", "structure" ], "mappings": { "prefixcommons": "world2dpage", "uniprot": "DB-0121" }, "name": "The World-2DPAGE database", "preferred_prefix": "world2dpage", "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/world2dpage:$1" } ], "publications": [ { "doi": "10.1016/j.jprot.2008.02.005", "pubmed": "18617148", "title": "The World-2DPAGE Constellation to promote and publish gel-based proteomics data through the ExPASy server", "year": 2008 } ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "uri_format": "https://world-2dpage.expasy.org/repository/$1" }, "worldavatar.compchem": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Linked-data framework for connecting species in chemical kinetic reaction mechanisms with quantum calculations. A mechanism can be constructed from thermodynamic, reaction rate, and transport data that has been obtained either experimentally, computationally, or by a combination of both. In order to implement this approach, two existing ontologies, namely OntoKin, for representing chemical kinetic reaction mechanisms, and OntoCompChem, for representing quantum chemistry calculations, are extended. (from https://nfdi4cat.org/services/ontologie-sammlung/)", "download_owl": "http://www.theworldavatar.com/ontology/ontocompchem/ontocompchem.owl", "homepage": "https://como.ceb.cam.ac.uk/preprints/223/", "keywords": [ "ontology" ], "name": "Computational Chemistry Ontology", "no_own_terms": true, "preferred_prefix": "worldavatar.compchem" }, "worldavatar.kin": { "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, "description": "Represents chemical kinetic reaction mechanisms.", "download_owl": "http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl", "example": "ElementNumber", "homepage": "http://www.theworldavatar.com/ontokin/", "keywords": [ "ontology" ], "name": "Ontology for Chemical Kinetic Reaction Mechanisms", "preferred_prefix": "worldavatar.kin", "uri_format": "http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl#$1" }, "wormbase": { "contact": { "email": "todd@wormbase.org", "github": "tharris", "name": "Todd W Harris", "orcid": "0000-0003-3406-163X" }, "contributor_extras": [ { "email": "cjmungall@lbl.gov", "github": "cmungall", "name": "Chris Mungall", "orcid": "0000-0002-6601-2165" } ], "description": "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and other nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. 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