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Sometimes NIFSTD prefixed identifiers appear undifferentiated, but usually if it shows up it means that another prefix definition is missing when serializing.", "pattern": "^BAMSC\\d+$", "uri_format": "http://uri.neuinfo.org/nif/nifstd/$1", "homepage": "https://github.com/SciCrunch/NIF-Ontology", "repository": "https://github.com/SciCrunch/NIF-Ontology", "contact": {"name": "Tom Gillespie", "orcid": "0000-0002-7509-4801", "email": "tgbugs@gmail.com", "github": "tgbugs"}, "example": "BAMSC981", "license": "CC BY-4.0", "part_of": "nif", "download_owl": "http://aber-owl.net/media/ontologies/NIFSTD/23/nifstd.owl", "mappings": {"aberowl": "NIFSTD", "bioportal": "NIFSTD", "fairsharing": "FAIRsharing.vgw1m6"}, "synonyms": ["NIFSTD"], "publications": [{"pubmed": "18975148", "doi": "10.1007/s12021-008-9032-z", "pmc": "PMC2743139", "title": "The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience.", "year": 2008}], "contributor": {"name": "Tom Gillespie", "orcid": "0000-0002-7509-4801", "email": "tgbugs@gmail.com", "github": "tgbugs"}, "reviewer": {"name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370", "email": "cthoyt@gmail.com", "github": "cthoyt"}, "preferred_prefix": "nif.std", "twitter": "SciCrunch"}, "oae": {"name": "Ontology of Adverse Events", "description": "The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning.  OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc.", "pattern": "^\\d{7}$", "uri_format": "http://purl.obolibrary.org/obo/OAE_$1", "homepage": "https://github.com/OAE-ontology/OAE/", "repository": "https://github.com/OAE-ontology/OAE", "contact": {"name": "Yongqunh He", "orcid": "0000-0001-9189-9661", "email": "yongqunh@med.umich.edu", "github": "yongqunh"}, "example": "0002959", "license": "CC-BY-3.0", "version": "1.2.44", "download_owl": "http://purl.obolibrary.org/obo/oae.owl", "mappings": {"aberowl": "OAE", "biocontext": "OAE", "bioportal": "OAE", "fairsharing": "FAIRsharing.tw4q8x", "obofoundry": "oae", "ols": "oae", "ontobee": "OAE"}, "publications": [{"pubmed": "25093068", "doi": "10.1186/2041-1480-5-29", "pmc": "PMC4120740", "title": "OAE: The Ontology of Adverse Events.", "year": 2014}], "preferred_prefix": "OAE"}, "obcs": {"name": "Ontology of Biological and Clinical Statistics", "description": "OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). OBCS imports all possible biostatistics terms in OBI and includes many additional biostatistics terms, some of which were proposed and discussed in the OBI face-to-face workshop in Ann Arbor in 2012.  ", "pattern": "^\\d{7}$", "uri_format": "http://purl.obolibrary.org/obo/OBCS_$1", "homepage": "https://github.com/obcs/obcs", "repository": "https://github.com/obcs/obcs", "contact": {"name": "Jie Zheng", "orcid": "0000-0002-2999-0103", "email": "jiezheng@pennmedicine.upenn.edu", "github": "zhengj2007"}, "example": "0000121", "license": "CC-BY-3.0", "version": "101", "download_owl": "http://purl.obolibrary.org/obo/obcs.owl", "mappings": {"aberowl": "OBCS", "biocontext": "OBCS", "bioportal": "OBCS", "fairsharing": "FAIRsharing.5p12xh", "obofoundry": "obcs", "ols": "obcs", "ontobee": "OBCS"}, "publications": [{"pubmed": "27627881", "doi": "10.1186/s13326-016-0100-2", "pmc": "PMC5024438", "title": "The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis.", "year": 2016}], "preferred_prefix": "OBCS"}, "obi": {"name": "Ontology for Biomedical Investigations", "description": "The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO).", "pattern": "^\\d{7}$", "uri_format": "http://purl.obolibrary.org/obo/OBI_$1", "homepage": "http://obi-ontology.org", "repository": "https://github.com/obi-ontology/obi", "contact": {"name": "Bjoern Peters", "orcid": "0000-0002-8457-6693", "email": "bpeters@lji.org", "github": "bpeters42"}, "example": "0400109", "license": "CC-BY-4.0", "version": "2022-07-11", "download_owl": "http://purl.obolibrary.org/obo/obi.owl", "download_obo": "https://github.com/obi-ontology/obi/raw/master/views/obi.obo", "banana": "OBI", "banana_peel": ":", "mappings": {"aberowl": "OBI", "biocontext": "OBI", "bioportal": "OBI", "fairsharing": "FAIRsharing.284e1z", "go": "OBI", "miriam": "obi", "n2t": "obi", "obofoundry": "obi", "ols": "obi", "ontobee": "OBI", "prefixcommons": "obi"}, "publications": [{"pubmed": "27128319", "doi": "10.1371/journal.pone.0154556", "pmc": "PMC4851331", "title": "The Ontology for Biomedical Investigations.", "year": 2016}, {"pubmed": "25632945", "doi": "10.1093/database/bau132", "pmc": "PMC4309925", "title": "Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach.", "year": 2015}, {"pubmed": "23734660", "doi": "10.1186/2041-1480-4-s1-s6", "pmc": "PMC3633001", "title": "Query enhancement through the practical application of ontology: the IEDB and OBI.", "year": 2013}, {"pubmed": "22180825", "doi": "10.4056/sigs.1994602", "pmc": "PMC3235517", "title": "Minimum Information about a Genotyping Experiment (MIGEN).", "year": 2011}, {"pubmed": "20626927", "doi": "10.1186/2041-1480-1-s1-s7", "pmc": "PMC2903726", "title": "Modeling biomedical experimental processes with OBI.", "year": 2010}], "appears_in": ["foodon"], "namespace_in_lui": true, "preferred_prefix": "OBI"}, "obib": {"name": "Ontology for Biobanking", "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.", "pattern": "^\\d{7}$", "uri_format": "http://purl.obolibrary.org/obo/OBIB_$1", "homepage": "https://github.com/biobanking/biobanking", "repository": "https://github.com/biobanking/biobanking", "contact": {"name": "Jie Zheng", "orcid": "0000-0002-2999-0103", "email": "jiezheng@pennmedicine.upenn.edu", "github": "zhengj2007"}, "example": "0000389", "license": "CC-BY-4.0", "version": "2021-11-12", "download_owl": "http://purl.obolibrary.org/obo/obib.owl", "mappings": {"aberowl": "OBIB", "biocontext": "OBIB", "bioportal": "OBIB", "fairsharing": "FAIRsharing.bxc508", "obofoundry": "obib", "ols": "obib", "ontobee": "OBIB"}, "publications": [{"pubmed": "27148435", "doi": "10.1186/s13326-016-0068-y", "pmc": "PMC4855778", "title": "OBIB-a novel ontology for biobanking.", "year": 2016}], "preferred_prefix": "OBIB"}, "obo": {"name": "Open Biological and Biomedical Ontologies", "description": "The OBO namespace is the top-level namespace used by Open Biological and Biomedical Ontology (OBO) Foundry ontologies.", "uri_format": "http://purl.obolibrary.org/obo/$1", "homepage": "http://www.obofoundry.org/", "mappings": {"biocontext": "OBO", "fairsharing": "FAIRsharing.847069"}, "preferred_prefix": "obo"}, "oboinowl": {"name": "OBO in OWL", "description": "This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties", "uri_format": "http://www.geneontology.org/formats/oboInOwl#$1", "homepage": "https://github.com/geneontology/go-ontology/tree/master/contrib", "repository": "https://github.com/geneontology/go-ontology", "example": "hasDbXref", "download_owl": "https://github.com/geneontology/go-ontology/raw/master/contrib/oboInOwl.owl", "download_obo": "https://github.com/geneontology/go-ontology/raw/master/contrib/oboInOwl.obo", "mappings": {"biocontext": "oboInOwl", "biolink": "oboformat"}, "synonyms": ["oboformat", "oio"], "contributor": {"name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370", "email": "cthoyt@gmail.com", "github": "cthoyt"}, "preferred_prefix": "oboInOwl"}, "ogg": {"name": "The Ontology of Genes and Genomes", "description": "OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets. ", "pattern": "^\\d+$", "uri_format": "http://purl.obolibrary.org/obo/OGG_$1", "homepage": "https://bitbucket.org/hegroup/ogg", "repository": "https://bitbucket.org/hegroup/ogg", "contact": {"name": "Yongqun Oliver He", "orcid": "0000-0001-9189-9661", "email": "yongqunh@med.umich.edu", "github": "yongqunh"}, "example": "3000887619", "license": "CC-BY-3.0", "version": "1.0.59", "download_owl": "http://purl.obolibrary.org/obo/ogg.owl", "mappings": {"aberowl": "OGG", "biocontext": "OGG", "bioportal": "OGG", "fairsharing": "FAIRsharing.zmx7nn", "obofoundry": "ogg", "ols": "ogg", "ontobee": "OGG"}, "preferred_prefix": "OGG"}, "ogms": {"name": "Ontology for General Medical Science", "description": "The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats.\n\nOGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology.", "pattern": "^\\d{7}$", "uri_format": "http://purl.obolibrary.org/obo/OGMS_$1", "homepage": "https://github.com/OGMS/ogms", "repository": "https://github.com/OGMS/ogms", "contact": {"name": "Brian Aevermann", "orcid": "0000-0003-1346-1327", "email": "baeverma@jcvi.org", "github": "BAevermann"}, "example": "0000031", "license": "CC-BY-4.0", "version": "2021-08-19", "download_owl": "http://purl.obolibrary.org/obo/ogms.owl", "download_obo": "http://purl.obolibrary.org/obo/ogms.obo", "mappings": {"aberowl": "OGMS", "bartoc": "216", "biocontext": "OGMS", "bioportal": "OGMS", "fairsharing": "FAIRsharing.rvz0m9", "obofoundry": "ogms", "ols": "ogms", "ontobee": "OGMS"}, "synonyms": ["ogms/OMRE"], "publications": [{"pubmed": "25991121", "doi": null, "pmc": null, "title": "Biomarkers in the Ontology for General Medical Science", "year": null}, {"pubmed": "24314207", "doi": "10.1186/2041-1480-4-42", "pmc": "PMC4028878", "title": "The neurological disease ontology.", "year": 2013}], "preferred_prefix": "OGMS"}, "omiabis": {"name": "Ontologized MIABIS", "description": "An ontological version of MIABIS (Minimum Information About BIobank data Sharing)", "pattern": "^\\d{7}$", "uri_format": "http://purl.obolibrary.org/obo/OMIABIS_$1", "homepage": "https://github.com/OMIABIS/omiabis-dev", "repository": "https://github.com/OMIABIS/omiabis-dev", "contact": {"name": "Mathias Brochhausen", "orcid": "0000-0003-1834-3856", "email": "mbrochhausen@gmail.com", "github": null}, "example": "0001079", "license": "CC-BY-3.0", "version": "2014-05-28", "download_owl": "http://purl.obolibrary.org/obo/omiabis.owl", "deprecated": true, "mappings": {"aberowl": "OMIABIS", "biocontext": "OMIABIS", "bioportal": "OMIABIS", "obofoundry": "omiabis", "ols": "omiabis", "ontobee": "OMIABIS"}, "preferred_prefix": "OMIABIS"}, "omim": {"name": "Online Mendelian Inheritance in Man", "description": "Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders.", "pattern": "^\\d+$", "uri_format": "https://omim.org/MIM:$1", "providers": [{"code": "CURATOR_REVIEW", "name": "OMIM mirror at John Hopkins", "description": "OMIM mirror at John Hopkins", "homepage": "http://mirror.omim.org/", "uri_format": "http://mirror.omim.org/entry/$1"}, {"code": "legacy", "name": "OMIM", "description": "This is the actual endpoint for OMIM entries", "homepage": "https://www.omim.org", "uri_format": "https://www.omim.org/entry/$1"}, {"code": "ncbi.omim", "name": "NCBI", "description": "An NCBI endpoint for OMIM entries", "homepage": "http://www.ncbi.nlm.nih.gov/omim", "uri_format": "http://www.ncbi.nlm.nih.gov/omim/$1"}, {"code": "purl", "name": "OMIM PURL (not in use)", "description": "An extra purl that was registred, but probably won't be used.", "homepage": "https://www.omim.org", "uri_format": "https://purl.org/mim/MIM:$1"}, {"code": "purl2", "name": "OMIM PURL (not in use)", "description": "An extra purl that was registred, but probably won't be used.", "homepage": "https://www.omim.org", "uri_format": "https://omim.org/OMIM:$1"}], "homepage": "https://omim.org/", "contact": {"name": "Ada Hamosh", "orcid": "0000-0002-1780-5230", "email": "ahamosh@jhmi.edu", "github": "ahamosh"}, "example": "603903", "mappings": {"aberowl": "OMIM", "biocontext": "OMIM", "bioportal": "OMIM", "edam": "1153", "fairsharing": "FAIRsharing.b084yh", "go": "OMIM", "hl7": "2.16.840.1.113883.6.174", "miriam": "mim", "n2t": "mim", "ncbi": "MIM", "prefixcommons": "omim", "uniprot": "DB-0062", "wikidata": "P492"}, "synonyms": ["OMIM", "mim"], "references": ["https://github.com/biopragmatics/bioregistry/issues/497"], "publications": [{"pubmed": "25428349", "doi": "10.1093/nar/gku1205", "pmc": "PMC4383985", "title": "OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders.", "year": 2014}, {"pubmed": "15608251", "doi": "10.1093/nar/gki033", "pmc": "PMC539987", "title": "Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders.", "year": 2005}], "preferred_prefix": "omim"}, "omrse": {"name": "Ontology of Medically Related Social Entities", "description": "This ontology covers the domain of social entities that are related to health care, such as demographic information and the roles of various individuals and organizations.", "pattern": "^\\d{8}$", "uri_format": "http://purl.obolibrary.org/obo/OMRSE_$1", "homepage": "https://github.com/ufbmi/OMRSE/wiki/OMRSE-Overview", "repository": "https://github.com/ufbmi/OMRSE", "contact": {"name": "Bill Hogan", "orcid": "0000-0002-9881-1017", "email": "hoganwr@gmail.com", "github": "hoganwr"}, "example": "00000022", "license": "CC-BY-4.0", "version": "2022-04-06", "download_owl": "http://purl.obolibrary.org/obo/omrse.owl", "download_obo": "https://github.com/ufbmi/OMRSE/raw/master/omrse-full.obo", "download_json": "http://purl.obolibrary.org/obo/omrse.json", "mappings": {"aberowl": "OMRSE", "biocontext": "OMRSE", "bioportal": "OMRSE", "fairsharing": "FAIRsharing.z0p37e", "obofoundry": "omrse", "ols": "omrse", "ontobee": "OMRSE"}, "publications": [{"pubmed": "27406187", "doi": "10.1186/s13326-016-0087-8", "pmc": "PMC4942889", "title": "The ontology of medically related social entities: recent developments.", "year": 2016}], "preferred_prefix": "OMRSE"}, "opmi": {"name": "Ontology of Precision Medicine and Investigation", "description": "OPMI is a biomedical ontology in the area of precision medicine and its related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles.", "pattern": "^\\d{7}$", "uri_format": "http://purl.obolibrary.org/obo/OPMI_$1", "homepage": "https://github.com/OPMI/opmi", "repository": "https://github.com/OPMI/opmi", "contact": {"name": "Yongqun Oliver He", "orcid": "0000-0001-9189-9661", "email": "yongqunh@med.umich.edu", "github": "yongqunh"}, "example": "0000101", "license": "CC-BY-4.0", "version": "1.0.158", "download_owl": "http://purl.obolibrary.org/obo/opmi.owl", "mappings": {"aberowl": "OPMI", "bioportal": "OPMI", "obofoundry": "opmi", "ols": "opmi", "ontobee": "OPMI"}, "preferred_prefix": "OPMI"}, "orphanet.ordo": {"name": "Orphanet Rare Disease Ontology", "description": "The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases.\r\nIt integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10).", "pattern": "^C?\\d+$", "uri_format": "http://www.orpha.net/ORDO/Orphanet_$1", "homepage": "https://www.ebi.ac.uk/ols/ontologies/ordo", "contact": {"name": "Ana Rath", "orcid": null, "email": "ordo.orphanet@inserm.fr", "github": null}, "example": "C023", "example_extras": ["478"], "version": "4.1", "download_owl": "http://www.orphadata.org/data/ORDO/ordo_orphanet.owl", "banana": "Orphanet", "banana_peel": "_", "mappings": {"aberowl": "ordo", "biocontext": "ORPHANET.ORDO", "biolink": "ORPHA", "bioportal": "ORDO", "cellosaurus": "ORDO", "fairsharing": "FAIRsharing.pbbnwa", "miriam": "orphanet.ordo", "n2t": "orphanet.ordo", "ols": "ordo"}, "synonyms": ["ordo"], "publications": [{"pubmed": "22874158", "doi": null, "pmc": null, "title": "Rare diseases knowledge management: the contribution of proximity measurements in OntoOrpha and OMIM.", "year": 2012}], "preferred_prefix": "orphanet.ordo"}, "ovae": {"name": "Ontology of Vaccine Adverse Events", "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). 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