diff --git a/ols-config-importer/foundry-ontologies.yaml b/ols-config-importer/foundry-ontologies.yaml deleted file mode 100644 index 58cd269..0000000 --- a/ols-config-importer/foundry-ontologies.yaml +++ /dev/null @@ -1,206 +0,0 @@ -name: OBO Foundry -title: The OBO Foundry -markdown: kramdown -highlighter: rouge -baseurl: / -imgurl: /images -repo: https://github.com/OBOFoundry/OBOFoundry.github.io/ -repo_src: https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/ -author: - name: OBO Technical WG -ontologies: - -- activity_status: active - browsers: - - {label: BioPortal, title: BioPortal Browser, url: 'http://bioportal.bioontology.org/ontologies/BFO?p=classes'} - contact: {email: phismith@buffalo.edu, github: phismith, label: Barry Smith} - depicted_by: https://avatars2.githubusercontent.com/u/12972134?v=3&s=200 - description: The upper level ontology upon which OBO Foundry ontologies are built. - domain: upper - homepage: http://ifomis.org/bfo/ - id: bfo - in_foundry_order: 1 - layout: ontology_detail - license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png', - url: 'http://creativecommons.org/licenses/by/4.0/'} - mailing_list: https://groups.google.com/forum/#!forum/bfo-discuss - ontology_purl: http://purl.obolibrary.org/obo/bfo.owl - products: - - {id: bfo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/bfo.owl'} - - {id: bfo.obo, ontology_purl: 'http://purl.obolibrary.org/obo/bfo.obo'} - title: Basic Formal Ontology - tracker: https://github.com/BFO-ontology/BFO/issues - usages: - - {description: BFO is imported by multiple OBO ontologies to standardize upper level structure, type: owl_import, user: 'http://obofoundry.org'} - -- activity_status: active - biosharing: https://www.biosharing.org/bsg-000016 - browsers: - - {label: RGD, title: Gene Ontology AmiGO 2 Browser, url: 'http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=UBERON:0001062'} - - {label: AmiGO (SUBSET), title: Gene Ontology AmiGO 2 Browser, url: 'http://amigo.geneontology.org/amigo/term/UBERON:0001062#display-lineage-tab'} - - {label: Bgee (gene expression), title: Bgee gene expression queries, url: 'http://bgee.org/?page=gene'} - - {label: FANTOM5, title: FANTOM5 Data Portal, url: 'http://fantom.gsc.riken.jp/5/sstar/UBERON:0001890'} - - {label: KnowledgeSpace, title: INCF KnowledgeSpace Portal, url: 'https://knowledge-space.org/index.php/pages/view/UBERON:0000061'} - build: {checkout: 'svn --ignore-externals co http://svn.code.sf.net/p/obo/svn/uberon/trunk', - email_cc: cjmungall@lbl.gov, infallible: 1, method: vcs, system: svn} - canonical: uberon.owl - contact: {email: cjmungall@lbl.gov, label: Chris Mungall} - dependencies: - - {id: go, subset: uberon/go_import.owl} - - {id: cl, subset: uberon/cl_import.owl} - - {id: chebi, subset: uberon/chebi_import.owl} - - {id: pr, subset: uberon/pr_import.owl} - depicted_by: http://uberon.github.io/images/u-logo.jpg - description: An integrated cross-species anatomy ontology covering animals and bridging - multiple species-specific ontologies - domain: anatomy - exampleClass: UBERON_0002046 - funded_by: [NIH R24OD011883, NIH R01HG004838, NIH P41HG002273, NSF DEB-0956049] - google_plus: +UberonOrg - homepage: http://uberon.org - id: uberon - label: Uberon - layout: ontology_detail - license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png', - url: 'http://creativecommons.org/licenses/by/3.0/'} - mailing_list: https://lists.sourceforge.net/lists/listinfo/obo-anatomy - ontology_purl: http://purl.obolibrary.org/obo/uberon.owl - page: http://en.wikipedia.org/wiki/Uberon - products: - - {description: core ontology, id: uberon.owl, is_canonical: true, ontology_purl: 'http://purl.obolibrary.org/obo/uberon.owl', - title: Uberon, type: 'owl:Ontology'} - - {description: Axioms defined within Uberon and to be used in imports for other - ontologies, id: uberon/uberon-base.owl, ontology_purl: 'http://purl.obolibrary.org/obo/uberon/uberon-base.owl', - page: 'https://github.com/INCATools/ontology-development-kit/issues/50', title: Uberon - base ontology} - - {description: Uberon extended, id: uberon/ext.owl, mireots_from: ncbitaxon, ontology_purl: 'http://purl.obolibrary.org/obo/uberon/ext.owl', - title: Uberon edition that includes subsets of other ontologies and axioms connecting - to them, type: 'owl:Ontology'} - - {description: Uberon edition that excludes external ontologies and most relations, - format: obo, id: uberon/basic.obo, ontology_purl: 'http://purl.obolibrary.org/obo/uberon/basic.obo', - title: Uberon basic, type: obo-basic-ontology} - - connects: - - {id: uberon} - - {id: zfa} - description: Taxonomic equivalence axioms connecting zebrafish-specific classes - to generic uberon counterparts - id: uberon/bridge/uberon-bridge-to-zfa.owl - ontology_purl: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-zfa.owl - page: https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies - title: Uberon bridge to ZFA - type: BridgeOntology - - connects: - - {id: uberon} - - {id: ma} - description: Taxonomic equivalence axioms connecting adult mouse specific classes - to generic uberon counterparts - id: uberon/bridge/uberon-bridge-to-ma.owl - ontology_purl: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-ma.owl - page: https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies - title: Uberon bridge to MA - type: BridgeOntology - - {description: Extended uberon plus all metazoan ontologies, id: uberon/composite-metazoan.owl, - mireots_from: ehdaa2, ontology_purl: 'http://purl.obolibrary.org/obo/uberon/composite-metazoan.owl', - page: 'https://github.com/obophenotype/uberon/wiki/Multi-species-composite-ontologies', - taxon: Metazoa, title: Uberon composite metazoan ontology, type: MergedOntology} - - {id: uberon/composite-vertebrate.owl, mireots_from: ehdaa2, ontology_purl: 'http://purl.obolibrary.org/obo/uberon/composite-vertebrate.owl', - page: 'https://github.com/obophenotype/uberon/wiki/Multi-species-composite-ontologies', - taxon: Metazoa, title: Uberon composite vertebrate ontology, type: MergedOntology} - publications: - - {id: 'http://www.ncbi.nlm.nih.gov/pubmed/22293552', title: 'Uberon, an integrative - multi-species anatomy ontology'} - - {id: 'http://www.ncbi.nlm.nih.gov/pubmed/25009735', title: Unification of multi-species - vertebrate anatomy ontologies for comparative biology in Uberon} - redirects: - - {match: releases/, url: 'http://svn.code.sf.net/p/obo/svn/uberon/releases/'} - - {match: '', url: 'http://berkeleybop.org/ontologies/uberon/'} - releases: http://purl.obolibrary.org/obo/uberon/releases/ - repository: https://github.com/obophenotype/uberon - taxon: {id: 'NCBITaxon:33208', label: Metazoa} - title: Uberon multi-species anatomy ontology - tracker: https://github.com/obophenotype/uberon/issues - twitter: uberanat - type: owl:Ontology - usages: - - description: Bgee is a database to retrieve and compare gene expression patterns - between animal species. Bgee in using Uberon to annotate the site of expression, - and Bgee curators one the major contributors to the ontology. - examples: - - {description: Uberon terms used to annotate expression of human hemoglobin subunit - beta, url: 'http://bgee.org/?page=gene&gene_id=ENSG00000244734'} - seeAlso: https://www.biosharing.org/biodbcore-000228 - type: annotation - user: http://bgee.org/ - - {description: 'The National Human Genome Research Institute (NHGRI) launched a - public research consortium named ENCODE, the Encyclopedia Of DNA Elements, in - September 2003, to carry out a project to identify all functional elements in - the human genome sequence. The ENCODE DCC users Uberon to annotate samples', - reference: 'https://doi.org/10.1093/database/bav010', seeAlso: 'https://www.biosharing.org/biodbcore-000034', - type: annotation, user: 'https://www.encodeproject.org/'} - - description: FANTOM5 is using Uberon and CL to annotate samples allowing for transcriptome - analyses with cell-type and tissue-level specificity. - examples: - - {description: FANTOM5 samples annotated to telencephalon or its parts, url: 'http://fantom.gsc.riken.jp/5/sstar/UBERON:0001893'} - type: annotation - user: http://fantom5-collaboration.gsc.riken.jp/ - - {description: Querying expression and phenotype data, type: query, user: 'https://monarchinitiative.org/'} - - description: Querying for functional annotations relevant to a tissue - examples: - - {description: GO annotations relevant to the uberon class for brain, url: 'http://amigo.geneontology.org/amigo/term/UBERON:0000955'} - label: GO Database - type: query - user: https://geneontology.org/ - - {description: 'The Phenoscape project is both a major driver of and contributor - to Uberon, contibuting thousands of terms. The teleost (bony fishes) component - of Uberon was derived from the Teleost Anatomy Ontology, developed by the Phenoscape - group. Most of the high level design of the skeletal system comes from the Vertebrate - Skeletal Anatomy Ontology (VSAO), also created by the Phenoscape group. Phenoscape - curators continue to extend the ontology, covering a wide variety of tetrapod - structures, with an emphasis on the appendicular system.', label: Phenoscape, - user: 'http://phenoscape.org'} - - {label: Neuroscience Information Framework, type: Database, url: 'https://neuinfo.org/'} - - {label: SciCrunch, type: Database, url: 'https://scicrunch.org/'} - - {label: SCPortalen, reference: 'https://doi.org/10.1093/nar/gkx949', type: Database, - url: 'http://single-cell.clst.riken.jp/'} - - {description: ChEMBL uses Uberon to describe organ/tissue information in assays, - label: ChEMBL, reference: 'https://doi.org/10.1093/nar/gky1075', type: Database, - url: 'https://www.ebi.ac.uk/chembl/'} - wikidata_template: https://en.wikipedia.org/wiki/Template:Uberon - - -- activity_status: active - build: {checkout: 'git clone https://github.com/EBISPOT/duo.git', path: ., system: git} - contact: {email: mcourtot@gmail.com, github: mcourtot, label: Melanie Courtot} - dependencies: - - {id: iao} - - {id: bfo} - description: DUO is an ontology which represent data use conditions. - homepage: https://github.com/EBISPOT/DUO - id: duo - jobs: - - {id: 'https://travis-ci.org/EBISPOT/DUO', type: travis-ci} - layout: ontology_detail - license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png', - url: 'http://creativecommons.org/licenses/by/3.0/'} - ontology_purl: http://purl.obolibrary.org/obo/duo.owl - products: - - {id: duo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/duo.owl'} - title: The Data Use Ontology - tracker: https://github.com/EBISPOT/DUO/issues - preferred_root_term: - - http://purl.obolibrary.org/obo/DUO_0000001 - - http://purl.obolibrary.org/obo/DUO_0000017 - - http://purl.obolibrary.org/obo/OBI_0000066 -- activity_status: active - build: {method: owl2obo, source_url: 'https://raw.githubusercontent.com/allysonlister/swo/master/release/swo_inferred.owl'} - contact: {email: allyson.lister@oerc.ox.ac.uk, label: Allyson Lister} - description: The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community. - homepage: https://github.com/allysonlister/swo - id: swo - layout: ontology_detail - license: {label: CC BY 4.0, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png', - url: 'https://creativecommons.org/licenses/by/4.0/'} - ontology_purl: http://purl.obolibrary.org/obo/swo.owl - products: - - {id: swo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/swo.owl'} - title: Software ontology