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Dev OLS config
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henrietteharmse committed Jan 3, 2020
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20 changes: 18 additions & 2 deletions ols-config-importer/application.properties
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Expand Up @@ -2,5 +2,21 @@ logging.level.org.springframework=ERROR
logging.level.ch.qos.logback.*=ERROR
spring.main.show_banner=false

spring.data.mongodb.database ols
ols.obofoundry.ontology.config obo-config.yaml
logging.file /nfs/spot/tomcats/OLS.DEV.SNARF.8880/logs/ols.log
logging.config /nfs/spot/sw/dev/ols/interfaces/logback-spring.xml

spring.data.solr.host http://snarf.ebi.ac.uk:8993/solr
ols.solr.search.core ontology
ols.solr.suggest.core autosuggest

spring.data.mongodb.host snarf.ebi.ac.uk
spring.data.mongodb.database ols-dev

obo.db.xrefs file:/nfs/spot/sw/dev/ols/config/db-xrefs.yaml

ols.obofoundry.ontology.config file:/nfs/spot/sw/dev/ols/config/foundry-ontologies.yaml
ols.ontology.config file:/nfs/spot/sw/dev/ols/config/ols-ontologies.yaml

ols.downloads.folder /nfs/spot/data/dev/ols/downloads

annotationproperty.preferredroot.term=http://www.ebi.ac.uk/ols/vocabulary/hasPreferredRootTerm
206 changes: 206 additions & 0 deletions ols-config-importer/foundry-ontologies.yaml
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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: [email protected], 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: [email protected], infallible: 1, method: vcs, system: svn}
canonical: uberon.owl
contact: {email: [email protected], 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: [email protected], 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: [email protected], 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
34 changes: 0 additions & 34 deletions ols-config-importer/obo-config.yaml
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29 changes: 0 additions & 29 deletions ols-config-importer/ols-config.yaml
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