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ebi_ontologies.json
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ebi_ontologies.json
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{
"ontologies": [
{
"id": "upheno",
"ontology_purl": "https://github.com/obophenotype/upheno-dev/releases/latest/download/upheno.owl"
},
{
"id": "uniprotrdfs",
"ontology_purl": "https://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/core.owl"
},
{
"id": "hra",
"ontology_purl": "https://cdn.humanatlas.io/digital-objects/collection/hra-ols/latest/graph.ttl",
"hierarchical_property": [
"http://purl.org/ccf/ccf_part_of"
],
"label_property": [
"http://purl.org/ccf/ccf_pref_label"
]
},
{
"id": "dcat",
"ontology_purl": "https://www.w3.org/ns/dcat.ttl"
},
{
"id": "biolink",
"ontology_purl": "https://github.com/biolink/biolink-model/raw/master/project/owl/biolink_model.owl.ttl",
"homepage": "https://biolink.github.io/biolink-model/"
},
{
"id": "addicto",
"is_foundary": "true",
"preferredPrefix": "ADDICTO",
"title": "Addiction Ontology",
"uri": "http://addictovocab.org/addicto.owl",
"description": "The Addiction Ontology (AddictO) is an ontology being developed all aspects of addiction research.",
"homepage": "https://addictovocab.org",
"label_property": ["http://www.w3.org/2000/01/rdf-schema#label"],
"definition_property": ["http://purl.obolibrary.org/obo/IAO_0000115"],
"synonym_property": ["http://purl.obolibrary.org/obo/IAO_0000118"],
"hierarchical_property": ["http://purl.obolibrary.org/obo/BFO_0000050"],
"hidden_property": null,
"base_uri": ["http://addictovocab.org/ADDICTO_"],
"oboSlims": "false",
"ontology_purl": "http://addictovocab.org/addicto.owl"
},
{
"id": "dhba",
"creator": [
"David Osumi-Sutherland",
"Huseyin Kir"
],
"preferredPrefix": "DHBA",
"title": "Developing Human Brain Atlas Ontology",
"uri": "https://purl.brain-bican.org/ontology/dhbao",
"description": "An application ontology built by combining ontologised versions of the Allen Institute Developing Human Brain Atlas (DHBA) Structure Graph mapped to Uberon.",
"homepage": "https://purl.brain-bican.org/ontology/dhbao",
"label_property": [
"rdfs:label",
"IAO:0000589",
"http://www.w3.org/2004/02/skos/core#prefLabel"
],
"definition_property": [
"http://purl.obolibrary.org/obo/IAO_0000115"
],
"synonym_property": [
"http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"
],
"hierarchical_property": [
"http://purl.obolibrary.org/obo/BFO_0000050"
],
"base_uri": [
"https://purl.brain-bican.org/ontology/dhbao/DHBA_"
],
"reasoner": "OWL2",
"oboSlims": false,
"ontology_purl": "https://purl.brain-bican.org/ontology/dhbao/dhbao.owl"
},
{
"id": "hba",
"creator": [
"David Osumi-Sutherland",
"Huseyin Kir"
],
"preferredPrefix": "HBA",
"title": "Human Brain Atlas Ontology",
"uri": "https://purl.brain-bican.org/ontology/hbao",
"description": "An application ontology built by combining ontologised versions of the Allen Institute Human Brain Atlas (HBA) Structure Graph mapped to Uberon.",
"homepage": "https://purl.brain-bican.org/ontology/hbao",
"label_property": [
"rdfs:label",
"IAO:0000589",
"http://www.w3.org/2004/02/skos/core#prefLabel"
],
"definition_property": [
"http://purl.obolibrary.org/obo/IAO_0000115"
],
"synonym_property": [
"http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"
],
"hierarchical_property": [
"http://purl.obolibrary.org/obo/BFO_0000050"
],
"base_uri": [
"https://purl.brain-bican.org/ontology/hbao/HBA_"
],
"reasoner": "OWL2",
"oboSlims": false,
"ontology_purl": "https://purl.brain-bican.org/ontology/hbao/hbao.owl"
},
{
"id": "semapv",
"title": "Semantic Mapping Vocabulary",
"description": "The Semantic Mapping Vocabulary (SEMAPV) captures concepts and relations related to semantic matching, including types of matching (e.g. lexical, manually curated), preprocessing methods and specialised mapping relations.",
"ontology_purl": "https://raw.githubusercontent.com/mapping-commons/semantic-mapping-vocabulary/main/semapv.owl",
"homepage": "https://mapping-commons.github.io/semantic-mapping-vocabulary/",
"preferredPrefix": "semapv",
"label_property": "http://www.w3.org/2004/02/skos/core#prefLabel",
"synonym_property": [
"http://www.w3.org/2004/02/skos/core#altLabel"
],
"base_uri": [
"https://w3id.org/semapv/vocab/"
]
},
{
"id": "slm",
"title": "SwissLipids",
"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.",
"ontology_purl": "file:///nfs/production/parkinso/spot/ols4/prod/local_ontologies/swisslipids.ttl",
"preferredPrefix": "SLM",
"base_uri": [
"https://swisslipids.org/rdf/SLM_"
]
},
{
"id": "lipidmaps",
"title": "LIPID MAPS",
"ontology_purl": "https://lipidmaps.org/files/?file=sparql_lipids&ext=ttl",
"preferredPrefix": "LIPIDMAPS",
"homepage": "https://lipidmaps.org",
"base_uri": [
"https://www.lipidmaps.org/rdf/"
]
},
{
"id": "oio",
"ontology_purl": "https://raw.githubusercontent.com/geneontology/go-ontology/master/contrib/oboInOwl",
"base_uri": [
"http://www.geneontology.org/formats/oboInOwl#"
]
},
{
"id": "cao",
"ontology_purl": "https://champ.stuchalk.domains.unf.edu/images/ontology/cao.owl",
"base_uri": [
"http://champ-project.org/images/ontology/cao.owl#CAO_"
],
"homepage": "https://champ.stuchalk.domains.unf.edu/cao",
"mailing_list": "[email protected]",
"title": "The Chemical Analysis Ontology",
"preferredPrefix": "CAO",
"creator": [
"Stuart Chalk"
]
},
{
"id": "rdfs",
"ontology_purl": "https://www.w3.org/2000/01/rdf-schema",
"base_uri": [
"http://www.w3.org/2000/01/rdf-schema#"
]
},
{
"id": "owl",
"ontology_purl": "https://www.w3.org/2002/07/owl",
"base_uri": [
"http://www.w3.org/2002/07/owl#"
]
},
{
"id": "skos",
"ontology_purl": "http://www.w3.org/TR/skos-reference/skos.rdf",
"base_uri": [
"http://www.w3.org/2004/02/skos/core#"
]
},
{
"id": "dcterms",
"ontology_purl": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/dublin_core_terms.rdf",
"base_uri": [
"http://purl.org/dc/terms/"
]
},
{
"id": "dc",
"ontology_purl": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/dublin_core_elements.rdf",
"base_uri": [
"http://purl.org/dc/elements/1.1/"
]
},
{
"id": "schemaorg_http",
"ontology_purl": "https://schema.org/version/latest/schemaorg-all-http.rdf",
"base_uri": [
"http://schema.org/"
]
},
{
"id": "schemaorg_https",
"ontology_purl": "https://schema.org/version/latest/schemaorg-all-https.rdf",
"base_uri": [
"https://schema.org/"
]
},
{
"id": "uberon",
"preferred_root_term": [
"http://purl.obolibrary.org/obo/UBERON_0000104",
"http://purl.obolibrary.org/obo/UBERON_0001062"
]
},
{
"id": "phi",
"preferredPrefix": "PHI",
"title": "PHI-base Ontology",
"description": "Pathogen-Host Interaction database Ontology used by Ensembl",
"definition_property": [
"http://purl.obolibrary.org/obo/IAO_0000115"
],
"synonym_property": [
"http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"
],
"base_uri": [
"http://purl.obolibrary.org/obo/PHI_"
],
"ontology_purl": "file:///nfs/production/parkinso/spot/ols4/prod/local_ontologies/phi.owl"
},
{
"id": "msio",
"preferredPrefix": "MSIO",
"title": "Metabolomics Standards Initiative Ontology",
"uri": "http://purl.obolibrary.org/obo/msio.owl",
"description": "an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies.",
"homepage": "https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO",
"mailing_list": "https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO/issues",
"definition_property": [
"http://purl.obolibrary.org/obo/IAO_0000115"
],
"synonym_property": [
"http://purl.obolibrary.org/obo/IAO_0000118"
],
"base_uri": [
"http://purl.obolibrary.org/obo/MSIO_"
],
"reasoner": "NONE",
"ontology_purl": "https://raw.githubusercontent.com/MSI-Metabolomics-Standards-Initiative/MSIO/master/releases/latest_release/MSIO-merged-reasoned.owl"
},
{
"id": "dicom",
"preferredPrefix": "DICOM",
"title": "DICOM Controlled Terminology",
"uri": "http://dicom.nema.org/resources/ontology/DCM/",
"description": "DICOM Controlled Terminology",
"homepage": "http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_D.html",
"mailing_list": "[email protected]",
"definition_property": [
"http://www.w3.org/2004/02/skos/core#definition"
],
"label_property": "http://www.w3.org/2004/02/skos/core#prefLabel",
"synonym_property": [
"http://www.w3.org/2004/02/skos/core#altLabel"
],
"base_uri": [
"http://dicom.nema.org/resources/ontology/DCM/"
],
"reasoner": "none",
"oboSlims": false,
"ontology_purl": "ftp://medical.nema.org/MEDICAL/Dicom/Resources/Ontology/DCM/dcm.owl"
},
{
"id": "sdgio",
"preferredPrefix": "SDGIO",
"title": "Sustainable Development Goals Interface Ontology",
"uri": "http://purl.unep.org/sdg/sdgio.owl",
"description": "An OBO-compliant ontology representing the entities referenced by the SDGs, their targets, and indicators.",
"homepage": "https://github.com/SDG-InterfaceOntology/sdgio",
"mailing_list": "https://github.com/SDG-InterfaceOntology/sdgio/issues",
"definition_property": [
"http://purl.obolibrary.org/obo/IAO_0000115"
],
"synonym_property": [
"http://www.geneontology.org/formats/oboInOWL#hasExactSynonym"
],
"base_uri": [
"http://purl.unep.org/sdg/SDGIO_"
],
"oboSlims": false,
"ontology_purl": "http://purl.unep.org/sdg/sdgio.owl"
},
{
"id": "ensemblglossary",
"preferredPrefix": "ENSGLOSS",
"title": "Ensembl Glossary",
"uri": "http://ensembl.org/glossary",
"description": "The Ensembl glossary lists the terms, data types and file types that are used in Ensembl and describes how they are used.",
"homepage": "http://ensembl.org/glossary",
"definition_property": [
"http://purl.obolibrary.org/obo/IAO_0000115"
],
"synonym_property": [
"http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"
],
"base_uri": [
"http://ensembl.org/glossary/ENSGLOSS_"
],
"reasoner": "NONE",
"ontology_purl": "https://raw.githubusercontent.com/Ensembl/ensembl-glossary/master/ensembl-glossary.owl"
},
{
"id": "efo",
"preferredPrefix": "EFO",
"title": "Experimental Factor Ontology",
"uri": "http://www.ebi.ac.uk/efo",
"description": "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for external projects such as the NHGRI GWAS catalogue. 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 many groups at the EBI and as the core ontology for OpenTargets.org",
"homepage": "http://www.ebi.ac.uk/efo",
"mailing_list": "[email protected]",
"definition_property": [
"http://purl.obolibrary.org/obo/IAO_0000115",
"http://www.ebi.ac.uk/efo/definition"
],
"synonym_property": [
"http://www.ebi.ac.uk/efo/alternative_term",
"http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"
],
"hierarchical_property": [
"http://purl.obolibrary.org/obo/BFO_0000050",
"http://purl.obolibrary.org/obo/RO_0002202"
],
"hidden_property": [
"http://www.ebi.ac.uk/efo/has_flag"
],
"base_uri": [
"http://www.ebi.ac.uk/efo/EFO_"
],
"reasoner": "OWL2",
"oboSlims": false,
"ontology_purl": "http://www.ebi.ac.uk/efo/efo.owl"
},
{
"id": "ordo",
"preferredPrefix": "ORDO",
"description": "The Orphanet Rare Disease ontology (ORDO) is jointly developed by Orphanet and the EBI to provide 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. It derived from the Orphanet database (www.orpha.net ) , a multilingual database dedicated to rare diseases populated from literature and validated by international experts. It 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) or classifications (ICD10).",
"title": "Orphanet Rare Disease Ontology",
"uri": "http://www.orpha.net/ontology/orphanet.owl",
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{
"id": "teddy",
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"id": "edam",
"preferredPrefix": "EDAM",
"title": "Ontology of bioinformatics topics, operations, identifiers, and formats",
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{
"id": "cco",
"preferredPrefix": "CCO",
"title": "Cell Cycle Ontology",
"uri": "http://purl.obolibrary.org/obo/cco",
"description": "The Cell Cycle Ontology extends existing ontologies for cell cycle knowledge building a resource that integrates and manages knowledge about the cell cycle components and regulatory aspects.",
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{
"id": "rexo",
"preferredPrefix": "ReXO",
"title": "Regulation of Gene Expression Ontology",
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"description": "Regulation of Gene Expression",
"homepage": "http://www.semantic-systems-biology.org/apo",
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{
"id": "reto",
"preferredPrefix": "ReTO",
"title": "Regulation of Transcription Ontology",
"uri": "http://www.bio.ntnu.no/ontology/ReTO/reto.owl",
"description": "Regulation of Transcription",
"homepage": "http://www.semantic-systems-biology.org/apo",
"mailing_list": "[email protected]",
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{
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"preferredPrefix": "GeXO",
"title": "Gene Expression Ontology",
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"description": "Gene Expression Ontology",
"homepage": "http://www.semantic-systems-biology.org/apo",
"mailing_list": "[email protected]",
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{
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"preferredPrefix": "CMPO",
"title": "Cellular Microscopy Phenotype Ontology",
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"mailing_list": "[email protected]",
"definition_property": [
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{
"id": "enm",
"preferredPrefix": "ENM",
"title": "eNanoMapper Ontology",
"uri": "http://enanomapper.github.io/ontologies/enanomapper.owl",
"description": "The eNanoMapper project (www.enanomapper.net) is creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. \u003e This ontology is an application ontology targeting the full domain of nanomaterial safety assessment. It re-uses several other ontologies including the NPO, CHEMINF, ChEBI, and ENVO. ",
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"mailing_list": "https://github.com/enanomapper/ontologies",
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{
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"preferredPrefix": "ATOL",
"title": "Animal Trait Ontology for Livestock",
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"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.",
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"mailing_list": "[email protected]",
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{
"id": "eol",
"preferredPrefix": "EOL",
"title": "Environment Ontology for Livestock",
"uri": "file:/C:/Lea/ontologies/environnement/leo.obo",
"description": "L'ontologie EOL décrit les conditions d'environnement des élevages d'animaux domestiques. Elle décrit plus particulièrement les modalités de l'alimentation, de l'environnement, de la structure des élevages et des systèmes d'élevage",
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{
"id": "lbo",
"preferredPrefix": "LBO",
"title": "Livestock Breed Ontology",
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"description": "A vocabulary for cattle, chicken, horse, pig, and sheep breeds.",
"homepage": "http://bioportal.bioontology.org/ontologies/LBO",
"mailing_list": "[email protected]",
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{
"id": "probonto",
"preferredPrefix": "PROBONTO",
"title": "Probability Distribution Ontology",
"uri": "http://www.probonto.org/ontology",
"description": "ProbOnto, is an ontology-based knowledge base of probability distributions, featuring more than eighty uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulas.",
"homepage": "http://probonto.org",
"mailing_list": "[email protected]",
"definition_property": [
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{
"id": "pride",
"preferredPrefix": "PRIDE",
"title": "PRIDE Controlled Vocabulary",
"uri": "http://purl.obolibrary.org/obo/pride_cv.obo",
"description": "The PRIDE PRoteomics IDEntifications (PRIDE) database is a centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence.",
"homepage": "https://github.com/PRIDE-Utilities/pride-ontology",
"mailing_list": "https://github.com/PRIDE-Utilities/pride-ontology/issues",
"definition_property": [
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"id": "bao",
"preferredPrefix": "BAO",
"title": "BioAssay Ontology",
"uri": "http://www.bioassayontology.org/bao/bao_complete.owl",
"description": "The BioAssay Ontology (BAO) describes biological screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. BAO is an extensible, knowledge-based, highly expressive (currently SHOIQ(D)) description of biological assays making use of descriptive logic based features of the Web Ontology Language (OWL). BAO currently has over 700 classes and also makes use of several other ontologies. It describes several concepts related to biological screening, including Perturbagen, Format, Meta Target, Design, Detection Technology, and Endpoint. Perturbagens are perturbing agents that are screened in an assay; they are mostly small molecules. Assay Meta Target describes what is known about the biological system and / or its components interrogated in the assay (and influenced by the Perturbagen). Meta target can be directly described as a molecular entity (e.g. a purified protein or a protein complex), or indirectly by a biological process or event (e.g. phosphorylation). Format describes the biological or chemical features common to each test condition in the assay and includes biochemical, cell-based, organism-based, and variations thereof. The assay Design describes the assay methodology and implementation of how the perturbation of the biological system is translated into a detectable signal. Detection Technology relates to the physical method and technical details to detect and record a signal. Endpoints are the final HTS results as they are usually published (such as IC50, percent inhibition, etc). BAO has been designed to accommodate multiplexed assays. All main BAO components include multiple levels of sub-categories and specification classes, which are linked via object property relationships forming an expressive knowledge-based representation.",
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"mailing_list": "http://bioassayontology.org/wp/contact-us/",
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{
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"preferredPrefix": "SIO",
"title": "Semanticscience Integrated Ontology",
"uri": "http://semanticscience.org/ontology/sio.owl",
"description": "The Semanticscience Integrated Ontology (SIO) provides a simple, integrated ontology of types and relations for rich description of objects, processes and their attributes.",
"homepage": "https://github.com/micheldumontier/semanticscience",
"mailing_list": "[email protected]",
"definition_property": [
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},
{
"id": "unimod",
"preferredPrefix": "UNIMOD",
"title": "Unimod protein modification database for mass spectrometry",
"uri": "http://www.unimod.org/obo/unimod.obo",
"description": "Unimod is 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, an d site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide).",
"homepage": "http://www.unimod.org/",
"mailing_list": "[email protected]",
"base_uri": [
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"oboSlims": false,
"reasoner": "NONE",
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{
"id": "nmrCV",
"preferredPrefix": "NMR",
"title": "nuclear magnetic resonance CV",
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"mailing_list": "https://groups.google.com/forum/?hl=en#!forum/nmrml/join",
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"ontology_purl": "http://nmrml.org/cv/stable/nmrCV.owl"
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{
"id": "sbo",
"title": "Systems Biology Ontology",
"definition_property": [
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{
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{
"id": "afo",
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"title": "Allotrope Merged Ontology Suite",
"description": "Allotrope Merged Ontology Suite",
"uri": "http://purl.allotrope.org/voc/afo/merged/REC/2018/11",
"base_uri": [
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"ontology_purl": "http://purl.allotrope.org/voc/afo/latest.xml"
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{
"id": "hpath",
"preferredPrefix": "MC",
"title": "Histopathology Ontology",
"uri": "https://github.com/Novartis/hpath",
"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.",
"homepage": "https://github.com/Novartis/hpath",
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{
"id": "srao",
"preferredPrefix": "SRAO",
"title": "FAIRsharing Subject Ontology (SRAO)",
"uri": "http://www.fairsharing.org/ontology/subject/SRAO.owl",
"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.",
"homepage": "https://github.com/FAIRsharing/subject-ontology",
"mailing_list": "[email protected]",
"label_property": "http://www.w3.org/2000/01/rdf-schema#label",
"definition_property": [
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{
"id": "hcao",
"preferredPrefix": "HCAO",
"title": "Human Cell Atlas Ontology",
"uri": "https://ontology.archive.data.humancellatlas.org/ontologies/hcao",
"base_uri": [
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"description": "Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas.",
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{
"id": "amphx",
"preferredPrefix": "AMPHX",
"title": "Amphioxus Development and Anatomy Ontology",
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{
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{
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{
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},
{
"id": "bcio",
"preferredPrefix": "BCIO",
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{
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"title": "COVID-19 Vocabulary Ontology",
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"ontology_purl": "https://github.com/EBISPOT/covoc/releases/download/current/covoc.owl"
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"id": "om",
"preferredPrefix": "OM",
"title": "Ontology of units of Measure (OM)",
"uri": "http://www.wurvoc.org/vocabularies/om-2.0/",
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"homepage": "https://github.com/HajoRijgersberg/OM",
"mailing_list": "[email protected]",
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