"@context": ontologies: ## DOID override - id: doid reasoner: EL ## GO override - id: go reasoner: EL ## MONDO override - id: mondo reasoner: EL ## CL override - id: cl reasoner: EL ## UBERON override - id: uberon reasoner: EL ## PHI - 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/panda/ensembl/production/ensprod/ontologies/phi/PHI.obo ## MSIO - 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 ## DICOM - 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: dclunie@dclunie.com 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 ## SGDIO - 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 ## Ensembl glossary - 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 ## EFO - 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: efo-users@lists.sourceforge.net 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 ## ORDO - 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 definition_property: - http://www.ebi.ac.uk/efo/definition synonym_property: - http://www.ebi.ac.uk/efo/alternative_term hidden_property: - http://www.ebi.ac.uk/efo/has_flag hierarchical_property: - http://purl.obolibrary.org/obo/BFO_0000050 base_uri: - http://www.orpha.net/ORDO/Orphanet_ reasoner: OWL2 oboSlims: false ontology_purl : http://www.orphadata.org/data/ORDO/ordo_orphanet.owl ## TEDDY - id: teddy preferredPrefix: TEDDY description: "TEDDY is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems and Synthetic Biology." title: "Terminology for Description of Dynamics" uri: http://identifiers.org/teddy/ definition_property: - http://www.w3.org/2004/02/skos/core#definition synonym_property: - http://www.w3.org/2004/02/skos/core#altLabel base_uri: - http://identifiers.org/teddy/TEDDY_ oboSlims: false ontology_purl : http://www.biomodels.net/teddy/TEDDY ## EDAM - id: edam preferredPrefix: EDAM title: Ontology of bioinformatics topics, operations, identifiers, and formats uri: http://edamontology.org description: "EDAM is a simple ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM provides a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use." homepage: http://edamontology.org mailing_list: edam@elixir-dk.org definition_property: - http://www.geneontology.org/formats/oboInOwl#hasDefinition synonym_property: - http://www.geneontology.org/formats/oboInOwl#hasExactSynonym - http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym base_uri: - http://edamontology.org/data_ - http://edamontology.org/topic_ - http://edamontology.org/format_ - http://edamontology.org/identifier_ oboSlims: false ontology_purl : https://raw.githubusercontent.com/edamontology/edamontology/master/releases/EDAM.owl ## CCO - 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." homepage: http://www.semantic-systems-biology.org/apo mailing_list: vladimir.n.mironov@gmail.com label_property: http://www.w3.org/2004/02/skos/core#prefLabel definition_property: - http://www.w3.org/2004/02/skos/core#definition synonym_property: - http://www.geneontology.org/formats/oboInOwl#hasExactSynonym base_uri: - http://purl.obolibrary.org/obo/CCO_ oboSlims: true ontology_purl : http://www.bio.ntnu.no/ontology/CCO/cco.owl ### This is the download URL ## ReXo - id: rexo preferredPrefix: ReXO title: Regulation of Gene Expression Ontology uri: http://www.bio.ntnu.no/ontology/ReXO/rexo.owl description: "Regulation of Gene Expression" homepage: http://www.semantic-systems-biology.org/apo mailing_list: vladimir.n.mironov@gmail.com label_property: http://www.w3.org/2004/02/skos/core#prefLabel definition_property: - http://www.w3.org/2004/02/skos/core#definition synonym_property: - http://www.geneontology.org/formats/oboInOwl#hasExactSynonym base_uri: - http://purl.obolibrary.org/obo/ReXO_ oboSlims: true ontology_purl : http://www.bio.ntnu.no/ontology/ReXO/rexo.rdf ### This is the download URL ## ReTo - 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: vladimir.n.mironov@gmail.com label_property: http://www.w3.org/2004/02/skos/core#prefLabel definition_property: - http://www.w3.org/2004/02/skos/core#definition synonym_property: - http://www.geneontology.org/formats/oboInOwl#hasExactSynonym base_uri: - http://purl.obolibrary.org/obo/ReTO_ oboSlims: true ontology_purl : http://www.bio.ntnu.no/ontology/ReTO/reto.rdf ### This is the download URL ## GeXo - id: gexo preferredPrefix: GeXO title: Gene Expression Ontology uri: http://www.bio.ntnu.no/ontology/GeXO/gexo.owl description: "Gene Expression Ontology" homepage: http://www.semantic-systems-biology.org/apo mailing_list: vladimir.n.mironov@gmail.com label_property: http://www.w3.org/2004/02/skos/core#prefLabel definition_property: - http://www.w3.org/2004/02/skos/core#definition synonym_property: - http://www.geneontology.org/formats/oboInOwl#hasExactSynonym base_uri: - http://purl.obolibrary.org/obo/GeXO_ oboSlims: true ontology_purl : http://www.bio.ntnu.no/ontology/GeXO/gexo.rdf ### This is the download URL ## CMPO - id: cmpo preferredPrefix: CMPO title: Cellular Microscopy Phenotype Ontology uri: http://www.ebi.ac.uk/cmpo description: "CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations." homepage: http://www.ebi.ac.uk/cmpo mailing_list: jupp@ebi.ac.uk definition_property: - http://purl.obolibrary.org/obo/IAO_0000115 synonym_property: - http://www.geneontology.org/formats/oboInOwl#hasExactSynonym base_uri: - http://www.ebi.ac.uk/cmpo/CMPO_ oboSlims: true reasoner: EL ontology_purl : http://www.ebi.ac.uk/cmpo/cmpo.owl ### This is the download URL ## eNanoMapper - 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. > This ontology is an application ontology targeting the f\ ull domain of nanomaterial safety assessment. It re-uses several other ontologies including the NPO, CHEMINF, ChEBI, and ENVO. " homepage: http://www.enanomapper.net/ mailing_list: https://github.com/enanomapper/ontologies definition_property: - http://www.ebi.ac.uk/efo/definition - http://purl.obolibrary.org/obo/IAO_0000115 - http://purl.bioontology.org/ontology/npo#definition - http://purl.obolibrary.org/obo#Definition - http://purl.org/dc/elements/1.1/description synonym_property: - http://www.ebi.ac.uk/efo/alternative_term - http://purl.obolibrary.org/obo/IAO_0000118 hierarchical_property: - http://www.bioassayontology.org/bao#BAO_0090002 - http://purl.bioontology.org/ontology/npo#part_of base_uri: - http://purl.enanomapper.org/onto/ENM_ oboSlims: false ontology_purl : http://enanomapper.github.io/ontologies/enanomapper.owl ## ATOL - id: atol preferredPrefix: ATOL title: Animal Trait Ontology for Livestock uri: file:/C:/Lea/ontologies/versions%20ATOL/atol_v3.0.obo 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 scientific\ and 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." homepage: http://www.atol-ontology.com mailing_list: pylebail@rennes.inra.fr definition_property: - "file:/C:/Lea/ontologies/versions%20ATOL/atol_v3.0.obo#definition" synonym_property: - "file:/C:/Lea/ontologies/versions%20ATOL/atol_v3.0.obo#synonymExact" base_uri: - http://purl.org/obo/owlATOL_ oboSlims: false ontology_purl : http://www.atol-ontology.com/public/telechargement/atol.owl ## EOL - 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" homepage: http://www.atol-ontology.com mailing_list: pylebail@rennes.inra.fr definition_property: - "file:/C:/Lea/ontologies/environnement/leo.obo#definition" synonym_property: - "file:/C:/Lea/ontologies/environnement/leo.obo#synonymExact" base_uri: - http://purl.org/obo/owlEOL_ ontology_purl : http://www.atol-ontology.com/public/telechargement/eol.owl ## LBO - id: lbo preferredPrefix: LBO title: Livestock Breed Ontology uri: http://bioportal.bioontology.org/ontologies/LBO description: "A vocabulary for cattle, chicken, horse, pig, and sheep breeds." homepage: http://bioportal.bioontology.org/ontologies/LBO mailing_list: jreecy@iastate.edu 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/LBO_ oboSlims: false ontology_purl : http://data.bioontology.org/ontologies/LBO/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb ## GAZ overide - id: gaz is_foundry: true ontology_purl: http://purl.obolibrary.org/obo/gaz.obo hierarchical_property: - http://purl.obolibrary.org/obo/BFO_0000050 - http://purl.obolibrary.org/obo/RO_0001025 - http://purl.obolibrary.org/obo/RO_0002151 - http://purl.obolibrary.org/obo/RO_0002376 - http://purl.obolibrary.org/obo/RO_0002377 - http://purl.obolibrary.org/obo/UBREL_0000001 - http://purl.obolibrary.org/obo/RO_0002219 - http://purl.obolibrary.org/obo/RO_0002379 - http://purl.obolibrary.org/obo/RO_0002378 - http://purl.obolibrary.org/obo/RO_0002090 - http://purl.obolibrary.org/obo/TEMP#proper_partof - http://purl.obolibrary.org/obo/TEMP#overlapped_by - http://purl.obolibrary.org/obo/RO_0002131 - http://purl.obolibrary.org/obo/RO_0002220 ## BTO overide - id: bto is_foundry: true ontology_purl: http://purl.obolibrary.org/obo/bto.owl hierarchical_property: - http://purl.obolibrary.org/obo/BFO_0000050 - http://purl.obolibrary.org/obo/RO_0002202 - http://purl.obolibrary.org/obo/bto#develops_from - http://purl.obolibrary.org/obo/bto#related_to ## ProbOnto - 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: probonto.dev@gmail.com definition_property: - http://www.probonto.org/core#0000028 base_uri: - http://www.probonto.org/core oboSlims: false ontology_purl : https://raw.githubusercontent.com/probonto/ontology/master/probonto4ols.owl ## PRIDE ontology - 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: - http://purl.obolibrary.org/obo/def synonym_property: - http://www.geneontology.org/formats/oboInOWL#hasExactSynonym base_uri: - http://purl.obolibrary.org/obo/PRIDE_ hierarchical_property: - http://purl.obolibrary.org/obo/pride_cv.obo#part_of oboSlims: false ontology_purl : https://raw.githubusercontent.com/PRIDE-Utilities/pride-ontology/master/pride_cv.obo ## Cheminf overide - id: cheminf title: Chemical Information Ontology ## MF overide - id: mf title: Mental Functioning Ontology ## MAMO overide - id: mamo title: Mathematical Modelling Ontology label_property: http://www.w3.org/2004/02/skos/core#prefLabel synonym_property: - http://www.w3.org/2004/02/skos/core#altLabel ## MFOEM overide - id: mfoem title: Emotion Ontology ## bao - 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." homepage: http://bioassayontology.org mailing_list: http://bioassayontology.org/wp/contact-us/ definition_property: - http://purl.obolibrary.org/obo/IAO_0000115 - http://www.ebi.ac.uk/efo/definition synonym_property: - http://www.geneontology.org/formats/oboInOwl#hasExactSynonym - http://purl.obolibrary.org/obo/IAO_0000118 - http://www.ebi.ac.uk/efo/alternative_term hierarchical_property: - http://purl.obolibrary.org/obo/BFO_0000050 base_uri: - http://www.bioassayontology.org/bao# oboSlims: false reasoner: OWL2 ontology_purl : http://www.bioassayontology.org/bao/ ## sio - id: sio 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: sio-ontology@googlegroups.com definition_property: - http://purl.org/dc/terms/description synonym_property: - http://purl.org/dc/terms/alternative - http://purl.org/dc/elements/1.1/alternativeName - http://purl.org/dc/terms/alternativeName hierarchical_property: - http://purl.obolibrary.org/obo/BFO_0000050 base_uri: - http://semanticscience.org/resource/SIO_ oboSlims: false reasoner: OWL2 ontology_purl : https://raw.githubusercontent.com/micheldumontier/semanticscience/master/ontology/sio/release/sio-release.owl ## unimod - 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: psidev-ms-vocab@lists.sourceforge.net base_uri: - http://purl.obolibrary.org/obo/UNIMOD_ oboSlims: false reasoner: NONE ontology_purl : http://www.unimod.org/obo/unimod.obo ## scdo #- id: scdo #preferredPrefix: SCDO #title: Sickle Cell Disease Ontology #uri: http://scdontology.h3abionet.org/ontology/scdo.owl #description: "The Sickle Cell Disease Ontology (SCDO) project is a collaboration between H3ABioNet (Pan African Bioinformatics Network) and SPAN (Sickle Cell Disease Pan African Network). The SCDO is currently under development and its purpose is to 1) establish community standardized SCD terms and descriptions, 2) establish canonical and hierarchical representation of knowledge on SCD and 3) link to other ontologies and bodies of work such as DO, PhenX MeSH, ICD, NCI’s thesaurus, SNOMED and OMIM." #homepage: http://scdontology.h3abionet.org/ #mailing_list: https://github.com/scdodev/scdo-ontology/issues #base_uri: #- http://scdontology.h3abionet.org/ontology/SCDO_ #oboSlims: false #reasoner: NONE #ontology_purl : https://raw.githubusercontent.com/scdodev/scdo-ontology/master/scdo.owl ## overide for mondo # - id: mondo # ontology_purl: http://purl.obolibrary.org/obo/mondo.obo ## overide for mi - todo remove after obo lib updates - id: mi ontology_purl: https://raw.githubusercontent.com/HUPO-PSI/psi-mi-CV/master/psi-mi.owl definition_property: - http://purl.obolibrary.org/obo/IAO_0000115 ## nmrCV - id: nmrCV preferredPrefix: NMR title: nuclear magnetic resonance CV uri: http://nmrML.org/nmrCV description: "This artefact is an MSI-approved controlled vocabulary primarily developed under COSMOS EU and PhenoMeNal EU governance. The nmrCV is supporting the nmrML XML format with standardized terms. nmrML is a vendor agnostic open access NMR raw data standard. Its primaly role is analogous to the mzCV for the PSI-approved mzML XML format. It uses BFO2.0 as its Top level. This CV was derived from two predecessors (The NMR CV from the David Wishart Group, developed by Joseph Cruz) and the MSI nmr CV developed by Daniel Schober at the EBI. This simple taxonomy of terms (no DL semantics used) serves the nuclear magnetic resonance markup language (nmrML) with meaningful descriptors to amend the nmrML xml file with CV terms. Metabolomics scientists are encouraged to use this CV to annotrate their raw and experimental context data, i.e. within nmrML. The approach to have an exchange syntax mixed of an xsd and CV stems from the PSI mzML effort. The reason to branch out from an xsd into a CV is, that in areas where the terminology is likely to change faster than the nmrML xsd could be updated and aligned, an externally and decentrallised maintained CV can accompensate for such dynamics in a more flexible way. A second reason for this set-up is that semantic validity of CV terms used in an nmrML XML instance (allowed CV terms, position/relation to each other, cardinality) can be validated by rule-based proprietary validators: By means of cardinality specifications and XPath expressions defined in an XML mapping file (an instances of the CvMappingRules.xsd ), one can define what ontology terms are allowed in a specific location of the data model." homepage: http://nmrml.org/cv/ mailing_list: https://groups.google.com/forum/?hl=en#!forum/nmrml/join definition_property: - http://purl.obolibrary.org/obo/IAO_0000115 - http://www.w3.org/2004/02/skos/core#definition - http://www.w3.org/2000/01/rdf-schema#comment synonym_property: - http://www.geneontology.org/formats/oboInOwl#hasExactSynonym hierarchical_property: - http://purl.obolibrary.org/obo/BFO_0000050 base_uri: - http://nmrML.org/nmrCV#NMR reasoner: NONE ontology_purl : http://nmrml.org/cv/stable/nmrCV.owl ## SBO - id: sbo title: Systems Biology Ontology definition_property: - http://www.w3.org/2000/01/rdf-schema#comment base_uri: - http://biomodels.net/SBO/SBO_ # add BFO part_of as local term in RO ## Relations Ontology - id: ro base_uri: - http://purl.obolibrary.org/obo/BFO_0000050 - http://purl.obolibrary.org/obo/RO_ # set the base URI for NCBI taxon ## NCBI taxonomy - id: ncbitaxon base_uri: - http://purl.obolibrary.org/obo/NCBITaxon_ ## AFO - id: afo preferredPrefix: AFO title: Allotrope Merged Ontology Suite description: Allotrope Merged Ontology Suite uri: http://purl.allotrope.org/voc/afo/merged/REC/2018/11 base_uri: - http://purl.allotrope.org/ontologies label_property: http://www.w3.org/2004/02/skos/core#prefLabel synonym_property: - http://www.w3.org/2004/02/skos/core#altLabel definition_property: - http://www.w3.org/2004/02/skos/core#definition - http://purl.obolibrary.org/obo/IAO_0000115 reasoner: EL oboSlims: false ontology_purl : http://afo-ols.semanticsfirst.com/ontologies/afo #hpath - 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 mailing_list: https://github.com/Novartis/hpath definition_property: - http://www.geneontology.org/formats/oboInOwl#hasDefinition synonym_property: - http://www.geneontology.org/formats/oboInOwl#hasExactSynonym hierarchical_property: - http://purl.obolibrary.org/obo/BFO_0000050 base_uri: - http://purl.obolibrary.org/obo/MC_ oboSlims: false reasoner: None ontology_purl: https://raw.githubusercontent.com/Novartis/hpath/master/src/hpath.obo ## DUO override - id: duo ontology_purl: http://purl.obolibrary.org/obo/duo.owl preferred_root_term: - http://purl.obolibrary.org/obo/DUO_0000001 - http://purl.obolibrary.org/obo/DUO_0000017 - http://purl.obolibrary.org/obo/OBI_0000066 ## SRAO - 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: contact@fairsharing.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 - http://www.fairsharing.org/ontology/subject/SRAO_0000279 - http://www.fairsharing.org/ontology/subject/SRAO_0000278 - http://www.fairsharing.org/ontology/subject/SRAO_0000269 - http://www.fairsharing.org/ontology/domain/DRAO_0000001 - http://www.fairsharing.org/ontology/subject/SRAO_0000276 - http://www.fairsharing.org/ontology/subject/SRAO_0000317 - http://www.fairsharing.org/ontology/subject/SRAO_0000272 - http://www.fairsharing.org/ontology/subject/SRAO_0000292 - http://www.fairsharing.org/ontology/subject/SRAO_0000268 base_uri: - http://www.fairsharing.org/ontology/subject reasoner: OWL2 oboSlims: false ontology_purl : https://github.com/FAIRsharing/subject-ontology/raw/master/releases/SRAO.owl ## HCAO - id: hcao preferredPrefix: HCAO title: Human Cell Atlas Ontology uri: http://ontology.data.humancellatlas.org/ontologies/hcao base_uri: - http://ontology.data.humancellatlas.org/ontologies/HCA_ description: "Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas." definition_property: - http://purl.obolibrary.org/obo/IAO_0000115 synonym_property: - http://www.geneontology.org/formats/oboInOwl#hasExactSynonym reasoner: EL oboSlims: false ontology_purl : https://raw.githubusercontent.com/ebi-ait/ontology/master/hcao.owl - id: amphx preferredPrefix: AMPHX title: Amphioxus Development and Anatomy Ontology 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/AMPHX_ ontology_purl: https://raw.githubusercontent.com/EBISPOT/amphx_ontology/master/amphx.owl - id: clyh preferredPrefix: CLYH title: Clytia hemisphaerica Development and Anatomy Ontology 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/CLYH_ ontology_purl: https://raw.githubusercontent.com/EBISPOT/clyh_ontology/master/clyh.owl # Plana override - id: plana is_foundry: true ontology_purl: http://purl.obolibrary.org/obo/plana.owl synonym_property: - http://www.geneontology.org/formats/oboInOwl#hasExactSynonym - id: idocovid19 preferredPrefix: IDO-COVID-19 title: The COVID-19 Infectious Disease Ontology uri: https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-covid-19/master/ontology/ido%20covid-19 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." homepage: https://github.com/infectious-disease-ontology-extensions/ido-covid-19 mailing_list: johnbeverley2021@u.northwestern.edu 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: - http://purl.obolibrary.org/obo/IDO-COVID-19 oboSlims: false reasoner: OWL2 ontology_purl : https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-covid-19/master/ontology/ido%20covid-19 - id: vido preferredPrefix: VIDO title: The Virus Infectious Disease Ontology uri: https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-virus/master/ontology/vido.owl 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." homepage: https://github.com/infectious-disease-ontology-extensions/ido-virus mailing_list: johnbeverley2021@u.northwestern.edu 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: - http://purl.obolibrary.org/obo/VIDO_ oboSlims: false reasoner: OWL2 ontology_purl : https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-virus/master/ontology/vido.owl - id: bcio preferredPrefix: BCIO title: The Behaviour Change Intervention Ontology uri: http://humanbehaviourchange.org/ontology/bcio.owl description: "The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation." homepage: https://www.humanbehaviourchange.org/ 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 base_uri: - http://humanbehaviourchange.org/ontology oboSlims: false reasoner: OWL2 ontology_purl : http://humanbehaviourchange.org/ontology/bcio.owl - id: covoc preferredPrefix: COVOC title: COVID-19 Vocabulary Ontology uri: http://purl.obolibrary.org/obo/covoc.owl description: "The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more." homepage: https://github.com/EBISPOT/covoc 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: - http://purl.obolibrary.org/obo/COVOC_ oboSlims: false reasoner: OWL2 ontology_purl : https://github.com/EBISPOT/covoc/releases/download/current/covoc.owl ## OM - id: om preferredPrefix: OM title: Ontology of units of Measure (OM) uri: http://www.wurvoc.org/vocabularies/om-2.0/ description: "The OM ontology provides classes, instances, and properties that represent the different concepts used for defining and using measures and units. It includes, for instance, common units such as the SI units meter and kilogram, but also units from other systems of units such as the mile or nautical mile. For many application areas it includes more specific units and quantities, such as the unit of the Hubble constant: km/s/Mpc, or the quantity vaselife. OM defines the complete set of concepts in the domain as distinguished in the textual standards. As a result the ontology can answer a wider range of competency questions than the existing approaches do. The following application areas are supported by OM: Geometry; Mechanics; Thermodynamics; Electromagnetism; Fluid mechanics; Chemical physics; Photometry; Radiometry and Radiobiology; Nuclear physics; Astronomy and Astrophysics; Cosmology; Earth science; Meteorology; Material science; Microbiology; Economics; Information technology; Typography; Shipping; Food engineering; Post-harvest; technology; Dynamics of texture and taste; Packaging" homepage: https://github.com/HajoRijgersberg/OM mailing_list: hajo.rijgersberg@wur.nl 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 - http://purl.obolibrary.org/obo/RO_0002202 hidden_property: - http://www.ebi.ac.uk/efo/has_flag base_uri: - http://www.wurvoc.org/vocabularies/om-2.0/ reasoner: EL oboSlims: false ontology_purl : https://raw.githubusercontent.com/HajoRijgersberg/OM/master/om-2.0.rdf ## REPRODUCE-ME - id: reproduceme preferredPrefix: REPR title: REPRODUCE-ME Ontology uri: https://w3id.org/reproduceme/ 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." homepage: https://w3id.org/reproduceme/research mailing_list: sheeba.samuel@uni-jena.de definition_property: - http://www.w3.org/2000/01/rdf-schema#comment - http://www.w3.org/2000/01/rdf-schema#isDefinedBy synonym_property: - http://www.geneontology.org/formats/oboInOwl#hasExactSynonym hierarchical_property: - http://www.w3.org/2000/01/rdf-schema#subClassOf - http://www.w3.org/2000/01/rdf-schema#subPropertyOf hidden_property: - http://www.ebi.ac.uk/efo/has_flag base_uri: - https://w3id.org/reproduceme# reasoner: OWL2 oboSlims: false ontology_purl : https://sheeba-samuel.github.io/REPRODUCE-ME/doc/reproduce-me.xml - id: prov preferredPrefix: PROV title: Provenance Ontology (PROV-O) uri: http://www.w3.org/ns/prov# homepage: https://www.w3.org/TR/prov-o/ definition_property: - http://purl.obolibrary.org/obo/IAO_0000115 synonym_property: - http://www.geneontology.org/formats/oboInOwl#hasExactSynonym - http://purl.obolibrary.org/obo/IAO_0000118 - http://www.ebi.ac.uk/efo/alternative_term hierarchical_property: - http://purl.obolibrary.org/obo/BFO_0000050 base_uri: - http://www.bioassayontology.org/bao# ontology_purl: https://www.w3.org/ns/prov-o - id: orth preferredPrefix: ORTH title: Orthology Ontology uri: http://purl.org/net/orth homepage: http://purl.org/net/orth definition_property: - http://www.w3.org/2004/02/skos/core#definition - http://www.w3.org/2000/01/rdf-schema#comment synonym_property: - http://www.w3.org/2002/07/owl#equivalentClass hierarchical_property: - http://purl.obolibrary.org/obo/BFO_0000050 base_uri: - http://purl.org/net/orth# ontology_purl: http://purl.org/net/orth creator: - Tarcisio Mendes de Farias, Hirokazu Chiba, Dmitry Kuznetsov, Erick Antezana, María del Carmen Legaz-García, Florent Villiers, Christophe Dessimoz, Jesualdo Tomás Fernández-Breis, Ikuo Uchiyama 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." - id: cryoem preferredPrefix: CRYOEM title: Cryo Electron Microscopy ontology uri: https://www.ebi.ac.uk/ols/ontologies/cryoem homepage: http://scipion.i2pc.es/ontology/cryoem 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 base_uri: - http://scipion.i2pc.es/ontology/ ontology_purl: http://scipion.i2pc.es/ontology/cryoem.owl mailing_list: isanchez@cnb.csic.es creator: - Carlos Oscar Sorzano, Irene Sánchez description: "Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles" - id: snomed preferredPrefix: SNOMED title: SNOMED CT (International Edition) description: > SNOMED CT or SNOMED Clinical Terms is a systematically organized computer processable collection of medical terms providing codes, terms, synonyms and definitions used in clinical documentation and reporting. uri: http://snomed.info/sct/900000000000207008 base_uri: - http://snomed.info/id/ synonym_property: - http://www.geneontology.org/formats/oboInOwl#hasExactSynonym definition_property: - http://purl.obolibrary.org/obo/IAO_0000115 # label_property: http://www.w3.org/2004/02/skos/core#prefLabel reasoner: EL oboSlims: false ontology_purl: file:///nfs/spot/data/test/ols/snomed.owl allow_download: false - id: pcl preferredPrefix: PCL title: PCL Ontology description: Cell types that are provisionally defined by experimental techniques such as single cell or single nucleus transcriptomics rather than a straightforward & coherent set of properties. uri: https://raw.githubusercontent.com/obophenotype/provisional_cell_ontology/master/pcl-full.owl base_uri: - http://purl.obolibrary.org/obo/PCL_ synonym_property: - http://www.geneontology.org/formats/oboInOwl#hasExactSynonym definition_property: - http://purl.obolibrary.org/obo/IAO_0000115 preferred_root_term: - http://purl.obolibrary.org/obo/CL_0000000 reasoner: EL oboSlims: false ontology_purl: https://raw.githubusercontent.com/obophenotype/provisional_cell_ontology/master/pcl-full.owl allow_download: false ## SHARELOC - id: shareloc preferredPrefix: SHARELOC title: ShareLoc ontology_purl: https://raw.githubusercontent.com/imodpasteur/ShareLoc.XYZ/ontology/shareloc.owl ## CCF - id: ccf preferredPrefix: CCF title: Human Reference Atlas Common Coordinate Framework Ontology is_foundry: false uri: http://purl.org/ccf/ccf.owl label_property: http://www.w3.org/2000/01/rdf-schema#label definition_property: - http://purl.obolibrary.org/obo/IAO_0000115 hierarchical_property: - http://purl.obolibrary.org/obo/BFO_0000050 synonym_property: - http://purl.org/sig/ont/fma/synonym - http://www.lungmap.net/ontologies/database#synonym - https://www.geneontology.org/formats/oboInOwl#hasExactSynonym preferred_root_term: - http://purl.obolibrary.org/obo/UBERON_0000955 - http://purl.obolibrary.org/obo/UBERON_0000029 - http://purl.obolibrary.org/obo/UBERON_0000970 - http://purl.obolibrary.org/obo/UBERON_0003889 - http://purl.obolibrary.org/obo/UBERON_0000948 - http://purl.obolibrary.org/obo/UBERON_0002113 - http://purl.obolibrary.org/obo/UBERON_0001465 - http://purl.obolibrary.org/obo/UBERON_0002107 - http://purl.obolibrary.org/obo/UBERON_0002048 - http://purl.obolibrary.org/obo/UBERON_0000992 - http://purl.obolibrary.org/obo/UBERON_0001264 - http://purl.obolibrary.org/obo/UBERON_0001270 - http://purl.obolibrary.org/obo/UBERON_0002367 - http://purl.obolibrary.org/obo/UBERON_0002097 - http://purl.obolibrary.org/obo/UBERON_0002108 - http://purl.obolibrary.org/obo/UBERON_0000059 - http://purl.obolibrary.org/obo/UBERON_0002106 - http://purl.obolibrary.org/obo/UBERON_0002370 - http://purl.obolibrary.org/obo/UBERON_0000056 - http://purl.obolibrary.org/obo/UBERON_0001255 - http://purl.obolibrary.org/obo/UBERON_0000995 - http://purl.obolibrary.org/obo/UBERON_0004537 - http://purl.obolibrary.org/obo/UBERON_0000178 - http://purl.obolibrary.org/obo/UBERON_0004536 base_uri: - https://purl.org/ccf/ oboSlims: false ontology_purl: https://purl.org/ccf/2.0/ccf.owl creator: - Aaron Horning (0000-0003-3247-0798), Adel Eskaros (0000-0001-9028-338X), Al Powers (0000-0003-1941-5786), Amy Bernard (0000-0003-2540-1153), Andrea J. Radtke (0000-0003-4379-8967), Angela Kruse (0000-0001-8776-2769), Anna Maria Masci (0000-0003-1940-6740), Ansley Conchola (0000-0002-2385-6712), Avinash Boppana (0000-0003-0834-8274), Ayako Suzuki (0000-0003-1824-1067), Becky Steck (0000-0001-7565-4904), Bernard de Bono (0000-0001-7183-2638), Bertie Gottgens (0000-0001-6302-5705), Birte Steiniger (0000-0002-3602-7331), Blue Lake (0000-0002-8637-9044), Chad Vezina (0000-0001-7058-5399), Christine Curcio (0000-0001-8776-2769; 0000-0001-9769-1538), Clayton Mathews (0000-0002-8817-6355), Clive Wasserfall (0000-0002-3522-8932), David Anderson (0000-0002-3866-0923), David M. Owens, David Osumi-Sutherland (0000-0002-7073-9172), David Rowe (0000-0001-7852-7775), Dhruv Singhal (0000-0002-6300-1647), Diane Saunders (0000-0002-8849-6746), Douglas Strand (0000-0002-0746-927X), Ed Morrisey (0000-0001-5785-1939), Elaine Jaffe (0000-0003-4632-0301), Elisa Laurenti (0000-0002-9917-9092), Elizabeth Tsui (0000-0003-4503-8494), Ellen M. Quardokus (0000-0001-7655-4833), Fiona Ginty (0000-0001-6638-683X), Gloria Pryhuber (0000-0002-9185-3994), Griffin Weber (0000-0002-2597-881X), Hemali Phatnani (0000-0002-6571-3891), Ioannis Vlachos (0000-0002-8849-808X), Jakub Abramson (0000-0002-1745-8996), Jeff Whitsett (0000-0003-1668-5174), Jeffrey Spraggins (0000-0001-9198-5498), Jeremy A. Miller (0000-0003-4549-588X), Joel Sunshine (0000-0001-9987-6712), John Hickey (0000-0001-5675-3974), Jonhan Ho (0000-0002-1134-8585), Josef Hardi (0000-0002-2533-6681), Kalyanam Shivkumar (0000-0002-4121-1766), Kathleen ONeill (0000-0003-1980-6840), Katy Börner (0000-0002-3321-6137), Kevin Schey (0000-0001-9769-1538), Kristin Ardlie (0000-0003-4272-6283), Laura Jardine (0000-0003-4495-8205), Lou Falo (0000-0001-9813-0433), Luke Boulter (0000-0002-7954-6705), M. Todd Valerius (0000-0001-8143-9231), Maigan Brusko (0000-0002-4331-2202), Marc Halushka (0000-0002-7112-7389), Marda Jorgensen (0000-0002-7250-3569), Mark Arends (0000-0002-6826-8770), Martha Campbell-Thompson (0000-0001-6878-1235), Martijn Nawijn (0000-0003-3372-6521), Maxim Itkin (0000-0003-1361-7109), Monica M. Laronda (0000-0001-7840-4695), Muzlifah A. Haniffa (0000-0002-3927-2084), Natalie Rodriguez (0000-0001-6870-0300), Nazanin Ebrahimi (0000-0001-7183-2638), Peter Hanna (0000-0003-3092-5090), Purushotha Tata (0000-0003-4837-0337), Rachel Dull (0000-0002-0864-7007), Rajeev Malhotra (0000-0003-0120-4630), Rebecca T. Beuschel (0000-0002-3882-457X), Richard LeDuc (0000-0002-6951-2923), Robert Seifert (0000-0002-4404-8116), Sanjay Jain (0000-0003-2804-127X), Sarah A. Teichmann (0000-0002-6294-6366), Shin Lin (0000-0003-0118-0413), Song-Lin Ding (0000-0002-7072-5272), Stefania Pittaluga (0000-0001-7688-1439), Sujin Lee (0000-0002-6692-6880), Teri A. Longacre (0000-0002-0935-7300), Tim Kendall (0000-0002-4174-2786), Tom Taghon (000-0002-5781-0288), Xin Sun (0000-0002-9185-3994), Yiing Lin (0000-0002-0317-7608), Yongqun He (0000-0001-9189-9661), Z. Gordon Jiang (0000-0003-0495-9940) 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. homepage: https://hubmapconsortium.github.io/ccf/pages/ccf-ontology.html mailing_list: infoccf@indiana.edu reasoner: NONE ## CPONT - id: cpont preferredPrefix: CPONT title: Critical Path Ontology description: An application ontology for integrating data from the Critical Path Institute's Rare Disease Cures Accelerator Data and Analytica Platform (RDCA-DAP). repository: https://gitlab.c-path.org/c-pathontology/critical-path-ontology/ homepage: https://gitlab.c-path.org/c-pathontology/critical-path-ontology ontology_purl: https://w3id.org/cpont/cpont.owl uri: https://w3id.org/cpont/cpont.owl creator: - James Overton https://orcid.org/0000-0001-5139-5557, Nicole Vasilesvky https://orcid.org/0000-0001-5208-3432, Emily Hartley https://orcid.org/0000-0001-5839-2535, Emani Hunter https://orcid.org/0000-0001-8545-8114, Daniel Olson https://orcid.org/0000-0002-8134-1207, Rebecca Jackson https://orcid.org/0000-0003-4871-5569 is_foundry: false mailing_list: rwalls@c-path.org label_property: http://www.w3.org/2000/01/rdf-schema#label definition_property: - http://purl.obolibrary.org/obo/IAO_0000115 synonym_property: - http://www.w3.org/2004/02/skos/core#closeMatch - http://www.w3.org/2004/02/skos/core#exactMatch - http://www.w3.org/2004/02/skos/core#narrowMatch - http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym base_uri: - https://w3id.org/cpont reasoner: NONE oboSlims: false ## OBA override - id: oba hierarchical_property: - http://purl.obolibrary.org/obo/BFO_0000050