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ols-ontologies.yaml
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ols-ontologies.yaml
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"@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