diff --git a/Makefile b/Makefile index b12b5202e..64fae8f44 100644 --- a/Makefile +++ b/Makefile @@ -51,7 +51,7 @@ integration-test: test valid-purl-report.txt # Remove and/or revert all targets to their repository versions: clean: - rm -Rf registry/ontologies.nt registry/ontologies.ttl registry/ontologies.yml sparql-consistency-report.txt jenkins-output.txt valid-purl-report.txt valid-purl-report.txt.tmp _site/ tmp/ reports/ + rm -Rf registry/ontologies.nt registry/ontologies.ttl registry/ontologies.yml sparql-consistency-report.txt valid-purl-report.txt valid-purl-report.txt.tmp _site/ tmp/ reports/ git checkout _config.yml registry/ontologies.jsonld registry/ontologies.ttl registry/ontologies.yml @@ -236,10 +236,5 @@ valid-purl-report.txt: registry/ontologies.yml sparql-consistency-report.txt: registry/ontologies.yml ./util/processor.py -i $< sparql-compare > $@.tmp && mv $@.tmp $@ -# output of central OBO build -# See FAQ for more details, and also README.md -jenkins-output.txt: - wget http://build.berkeleybop.org/job/simple-build-obo-all/lastBuild/consoleFull -O $@ - reports/%.csv: registry/ontologies.ttl sparql/%.sparql arq --data $< --query sparql/$*.sparql --results csv > $@.tmp && mv $@.tmp $@ diff --git a/README.md b/README.md index 1dd1537d3..d68cc02b7 100644 --- a/README.md +++ b/README.md @@ -116,36 +116,6 @@ do is make further edits to fix the syntax error. TODO: add a quick guide to yaml, and the tags we use. -## Central OBO library build - -(see also the FAQ entry on this) - -The central OBO build runs here: - - * http://build.berkeleybop.org/job/simple-build-obo-all/ - -It takes as metadata input the yml file from this repository. It makes -use of the `build` object. - -The output of this job is a set of obo and owl files deposited in - - * http://berkeleybop.org/ontologies/ - -Depending on the build configuration, this may also make additional files. See for example: - - * http://berkeleybop.org/ontologies/uberon/ - -A http://berkeleybop.org/ontologies/ URL should never be handed out directly. This service exists so that: - - * Un PURL-registered ontologies will have a fall-through - * Registered PURL ontologies that do not want to take charge of either OBO or OWL generation will have a place to 302-redirect to - -This job will fail if ontologies marked as `infallible` fail. To debug, the full log of the last build can be examined: - - * https://build.berkeleybop.org/job/simple-build-obo-all/lastBuild/consoleFull - -(Look for the text "should not fail") - ## Instructions for Website Development See [README-sitedev.md](README-sitedev.md) diff --git a/_config.yml b/_config.yml index 3cf6bb110..56177e835 100644 --- a/_config.yml +++ b/_config.yml @@ -144,10 +144,6 @@ ontologies: and datasets for use in quantitative analyses. user: https://gardian.bigdata.cgiar.org/ - activity_status: active - build: - checkout: git clone https://github.com/insect-morphology/aism - path: . - system: git contact: email: entiminae@gmail.com github: JCGiron @@ -185,10 +181,6 @@ ontologies: title: Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) tracker: https://github.com/insect-morphology/aism/issues - activity_status: active - build: - checkout: git clone https://github.com/EBISPOT/amphx_ontology.git - path: . - system: git contact: email: hescriva@obs-banyuls.fr github: hescriva @@ -217,9 +209,6 @@ ontologies: title: The Amphioxus Development and Anatomy Ontology tracker: https://github.com/EBISPOT/amphx_ontology/issues - activity_status: active - build: - method: obo2owl - source_url: https://raw.githubusercontent.com/obophenotype/ascomycete-phenotype-ontology/master/apo.obo contact: email: stacia@stanford.edu github: srengel @@ -416,12 +405,6 @@ ontologies: title: Biomarker Ontology tracker: https://github.com/SCAI-BIO/BiomarkerOntology/issues - activity_status: active - build: - checkout: git clone https://github.com/obophenotype/biological-spatial-ontology.git - infallible: 1 - method: vcs - path: src/ontology - system: git contact: email: cjmungall@lbl.gov github: cmungall @@ -452,10 +435,6 @@ ontologies: title: Biological Spatial Ontology tracker: https://github.com/obophenotype/biological-spatial-ontology/issues - activity_status: active - build: - checkout: git clone https://github.com/BRENDA-Enzymes/BTO.git - path: . - system: git contact: email: c.dudek@tu-braunschweig.de github: chdudek @@ -489,9 +468,6 @@ ontologies: title: BRENDA tissue / enzyme source tracker: https://github.com/BRENDA-Enzymes/BTO/issues - activity_status: active - build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/cdao.owl contact: email: balhoff@renci.org github: balhoff @@ -519,10 +495,6 @@ ontologies: title: Comparative Data Analysis Ontology tracker: https://github.com/evoinfo/cdao/issues - activity_status: active - build: - checkout: git clone https://github.com/CompositionalDietaryNutritionOntology/cdno.git - path: . - system: git contact: email: landreshdz@gmail.com github: LilyAndres @@ -565,10 +537,6 @@ ontologies: - label: CHEBI title: EBI CHEBI Browser url: http://www.ebi.ac.uk/chebi/chebiOntology.do?treeView=true&chebiId=CHEBI:24431#graphView - build: - infallible: 1 - method: obo2owl - source_url: ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo contact: email: amalik@ebi.ac.uk github: amalik01 @@ -627,9 +595,6 @@ ontologies: url: http://zfin.org/action/expression/experiment?id=ZDB-EXP-190627-10 user: http://zfin.org - activity_status: active - build: - method: owl2obo - source_url: https://raw.githubusercontent.com/semanticchemistry/semanticchemistry/master/ontology/cheminf.owl contact: email: egon.willighagen@gmail.com github: egonw @@ -987,10 +952,6 @@ ontologies: type: annotation user: http://fantom5-collaboration.gsc.riken.jp/ - activity_status: active - build: - checkout: git clone https://github.com/luis-gonzalez-m/Collembola.git - path: . - system: git contact: email: lagonzalezmo@unal.edu.co github: luis-gonzalez-m @@ -1052,10 +1013,6 @@ ontologies: title: Cell Line Ontology tracker: https://github.com/CLO-Ontology/CLO/issues - activity_status: active - build: - checkout: git clone https://github.com/EBISPOT/clyh_ontology.git - path: . - system: git contact: email: lucas.leclere@obs-banyuls.fr github: Leclere-L @@ -1091,9 +1048,6 @@ ontologies: - label: RGD title: RGD Ontology Browser url: http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=CMO:0000000 - build: - method: obo2owl - source_url: https://download.rgd.mcw.edu/ontology/clinical_measurement/clinical_measurement.obo contact: email: jrsmith@mcw.edu github: jrsjrs @@ -1222,10 +1176,6 @@ ontologies: title: Coleoptera Anatomy Ontology (COLAO) tracker: https://github.com/insect-morphology/colao/issues - activity_status: active - build: - checkout: git clone https://github.com/data2health/contributor-role-ontology.git - path: src/ontology - system: git contact: email: whimar@ohsu.edu github: marijane @@ -1311,12 +1261,6 @@ ontologies: title: 'CTO: Core Ontology of Clinical Trials' tracker: https://github.com/ClinicalTrialOntology/CTO/issues - activity_status: active - build: - method: owl2obo - publications: - - id: http://dx.doi.org/10.3233/978-1-61499-438-1-409 - title: The Cardiovascular Disease Ontology - source_url: http://purl.obolibrary.org/obo/cvdo.owl contact: email: paul.fabry@usherbrooke.ca github: pfabry @@ -1340,10 +1284,6 @@ ontologies: title: Cardiovascular Disease Ontology tracker: https://github.com/OpenLHS/CVDO/issues - activity_status: active - build: - insert_ontology_id: true - method: obo2owl - source_url: https://raw.githubusercontent.com/dictyBase/migration-data/master/ontologies/dicty_anatomy.obo contact: email: pfey@northwestern.edu github: pfey03 @@ -1378,10 +1318,6 @@ ontologies: tracker: https://github.com/dictyBase/migration-data/issues twitter: dictybase - activity_status: active - build: - checkout: git clone https://github.com/obophenotype/dicty-phenotype-ontology.git - path: . - system: git contact: email: pfey@northwestern.edu github: pfey03 @@ -1443,8 +1379,6 @@ ontologies: - label: DO title: DO Browser url: https://disease-ontology.org/ - build: - source_url: https://raw.githubusercontent.com/DiseaseOntology/DiseaseDriversOntology/refs/heads/main/src/ontology/disdriv.owl contact: email: lynn.schriml@gmail.com github: lschriml @@ -1486,10 +1420,6 @@ ontologies: - label: DO title: DO Browser url: https://disease-ontology.org/do - build: - infallible: 1 - method: obo2owl - source_url: https://raw.githubusercontent.com/DiseaseOntology/HumanDiseaseOntology/master/src/ontology/doid.obo contact: email: lynn.schriml@gmail.com github: lschriml @@ -1557,10 +1487,6 @@ ontologies: - label: FB title: FlyBase Browser url: http://flybase.org/.bin/cvreport.html?cvterm=FBcv:0000347 - build: - checkout: git clone https://github.com/FlyBase/drosophila-phenotype-ontolog.git - path: . - system: git contact: email: cp390@cam.ac.uk github: Clare72 @@ -1600,9 +1526,6 @@ ontologies: url: http://flybase.org/cgi-bin/cvreport.html?rel=is_a&id=FBcv:0002030 user: http://flybase.org - activity_status: active - build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/dron.owl contact: email: hoganwr@gmail.com github: hoganwr @@ -1670,10 +1593,6 @@ ontologies: title: Data Use Ontology tracker: https://github.com/EBISPOT/DUO/issues - activity_status: active - build: - checkout: git clone https://github.com/echinoderm-ontology/ecao_ontology.git - path: . - system: git contact: email: ettensohn@cmu.edu github: ettensohn @@ -1876,10 +1795,6 @@ ontologies: title: Environmental conditions, treatments and exposures ontology tracker: https://github.com/EnvironmentOntology/environmental-exposure-ontology/issues - activity_status: active - build: - method: obo2owl - notes: new url soon - source_url: ftp://ftp.hgu.mrc.ac.uk/pub/MouseAtlas/Anatomy/EMAPA.obo contact: email: Terry.Hayamizu@jax.org github: tfhayamizu @@ -2103,11 +2018,6 @@ ontologies: title: Exposure ontology tracker: https://github.com/CTDbase/exposure-ontology/issues - activity_status: active - build: - checkout: git clone https://github.com/obophenotype/fungal-anatomy-ontology.git - infallible: 1 - method: vcs - system: git contact: email: vw253@cam.ac.uk github: ValWood @@ -2136,10 +2046,6 @@ ontologies: title: Fungal gross anatomy tracker: https://github.com/obophenotype/fungal-anatomy-ontology/issues - activity_status: active - build: - checkout: git clone https://github.com/foundingGIDE/fbbi.git - path: . - system: git contact: email: damien@gerbi-gmb.de github: gouttegd @@ -2199,10 +2105,6 @@ ontologies: - label: BioPortal title: BioPortal Browser url: http://bioportal.bioontology.org/ontologies/FB-BT?p=classes - build: - checkout: git clone https://github.com/FlyBase/drosophila-anatomy-developmental-ontology.git - path: . - system: git contact: email: cp390@cam.ac.uk github: Clare72 @@ -2267,10 +2169,6 @@ ontologies: - label: FB title: FlyBase Browser url: http://flybase.org/.bin/cvreport.html?cvterm=FBcv:0000013 - build: - checkout: git clone https://github.com/FlyBase/flybase-controlled-vocabulary.git - path: . - system: git contact: email: cp390@cam.ac.uk github: Clare72 @@ -2310,10 +2208,6 @@ ontologies: - label: FB title: FlyBase Browser url: http://flybase.org/.bin/cvreport.html?cvterm=FBdv:00007008 - build: - checkout: git clone https://github.com/FlyBase/drosophila-developmental-ontology.git - path: . - system: git contact: email: cp390@cam.ac.uk github: Clare72 @@ -2381,9 +2275,6 @@ ontologies: title: Food Interactions with Drugs Evidence Ontology tracker: https://gitub.u-bordeaux.fr/erias/fideo/issues - activity_status: active - build: - method: owl2obo - source_url: https://github.com/flora-phenotype-ontology/flopoontology/raw/master/ontology/flopo.owl contact: email: robert.hoehndorf@kaust.edu.sa github: leechuck @@ -2569,10 +2460,6 @@ ontologies: title: FuTRES Ontology of Vertebrate Traits tracker: https://github.com/futres/fovt/issues - activity_status: active - build: - infallible: 1 - method: obo2owl - source_url: https://raw.githubusercontent.com/pombase/fypo/master/release/fypo.owl contact: email: vw253@cam.ac.uk github: ValWood @@ -2745,10 +2632,6 @@ ontologies: title: Genomic Epidemiology Ontology tracker: https://github.com/GenEpiO/genepio/issues/ - activity_status: active - build: - checkout: git clone https://github.com/monarch-initiative/GENO-ontology.git - path: src/ontology - system: git contact: email: mhb120@gmail.com github: mbrush @@ -2806,10 +2689,6 @@ ontologies: - label: Composition Browser title: GNOme Glycan Composition Browser url: https://gnome.glyomics.org/CompositionBrowser.html?HexNAc=4&Hex=5&dHex=1&NeuAc=2 - build: - checkout: git clone https://github.com/glygen-glycan-data/GNOme.git - path: . - system: git contact: email: nje5@georgetown.edu github: edwardsnj @@ -3092,9 +2971,6 @@ ontologies: url: https://www.ebi.ac.uk/ols/ontologies/foodon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHANCESTRO_0004&viewMode=All&siblings=false user: http://foodon.org - activity_status: active - build: - checkout: git clone https://github.com/hymao/hao.git - system: git contact: email: diapriid@gmail.com github: mjy @@ -3129,11 +3005,6 @@ ontologies: title: Hymenoptera Anatomy Ontology tracker: https://github.com/hymao/hao/issues - activity_status: active - build: - checkout: git clone https://github.com/BgeeDB/homology-ontology.git - method: vcs - path: src/ontology - system: git contact: email: bgee@sib.swiss github: fbastian @@ -3246,9 +3117,6 @@ ontologies: title: Hypertension Ontology tracker: https://github.com/aellenhicks/htn_owl/issues - activity_status: active - build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/iao.owl contact: email: zhengj2007@gmail.com github: zhengj2007 @@ -3349,9 +3217,6 @@ ontologies: that has over 20 institutes involved. user: http://kpmp.org - activity_status: active - build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/ido.owl contact: email: Lindsay.Cowell@utsouthwestern.edu github: lgcowell @@ -3528,10 +3393,6 @@ ontologies: seeAlso: https://doi.org/10.25504/FAIRsharing.q9neh8 user: http://www.informatics.jax.org/expression.shtml - activity_status: active - build: - checkout: git clone https://github.com/monarch-initiative/MAxO.git - path: . - system: git contact: email: Leigh.Carmody@jax.org github: LCCarmody @@ -3679,9 +3540,6 @@ ontologies: for linking machine learning information from biomedical research user: https://github.com/UTHealth-Ontology/MCRO-Software - activity_status: active - build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/mf.owl contact: email: janna.hastings@gmail.com github: jannahastings @@ -3706,9 +3564,6 @@ ontologies: title: Mental Functioning Ontology tracker: https://github.com/jannahastings/mental-functioning-ontology/issues - activity_status: active - build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/mfoem.owl contact: email: janna.hastings@gmail.com github: jannahastings @@ -3757,10 +3612,6 @@ ontologies: title: Mental Disease Ontology tracker: https://github.com/jannahastings/mental-functioning-ontology/issues - activity_status: active - build: - insert_ontology_id: true - method: obo2owl - source_url: https://raw.githubusercontent.com/HUPO-PSI/psi-mi-CV/master/psi-mi.obo contact: email: luana.licata@gmail.com github: luanalicata @@ -3821,9 +3672,6 @@ ontologies: - label: RGD title: RGD Ontology Browser url: http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000 - build: - method: obo2owl - source_url: https://download.rgd.mcw.edu/ontology/measurement_method/measurement_method.obo contact: email: jrsmith@mcw.edu github: jrsjrs @@ -3859,9 +3707,6 @@ ontologies: title: Measurement method ontology tracker: https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology/issues - activity_status: active - build: - method: obo2owl - source_url: https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/mmusdv/mmusdv.obo contact: email: frederic.bastian@unil.ch github: fbastian @@ -3888,10 +3733,6 @@ ontologies: title: Mouse Developmental Stages tracker: https://github.com/obophenotype/developmental-stage-ontologies/issues - activity_status: active - build: - insert_ontology_id: true - method: obo2owl - source_url: https://raw.githubusercontent.com/HUPO-PSI/psi-mod-CV/master/PSI-MOD.obo contact: email: pierre-alain.binz@chuv.ch github: pabinz @@ -4036,9 +3877,6 @@ ontologies: type: annotation user: https://www.humancellatlas.org/ - activity_status: active - build: - method: owl2obo - source_url: https://raw.githubusercontent.com/rsc-ontologies/rxno/master/mop.owl contact: email: batchelorc@rsc.org github: batchelorc @@ -4157,10 +3995,6 @@ ontologies: url: https://www.mousephenotype.org/data/phenotypes/MP:0013522 user: https://www.mousephenotype.org/ - activity_status: active - build: - insert_ontology_id: true - method: obo2owl - source_url: https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo contact: email: pns12@hermes.cam.ac.uk github: PaulNSchofield @@ -4248,9 +4082,6 @@ ontologies: type: annotation user: https://www.iedb.org/ - activity_status: active - build: - method: obo2owl - source_url: https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo contact: email: joshua.adam.klein@gmail.com github: mobiusklein @@ -4294,9 +4125,6 @@ ontologies: - label: BioPortal title: BioPortal Ontology Browser url: https://bioportal.bioontology.org/ontologies/NBO - build: - method: owl2obo - source_url: https://raw.githubusercontent.com/obo-behavior/behavior-ontology/master/nbo.owl contact: email: g.gkoutos@bham.ac.uk github: gkoutos @@ -4413,9 +4241,6 @@ ontologies: title: NCI Thesaurus OBO Edition tracker: https://github.com/ncit-obo-org/ncit-obo-edition/issues - activity_status: active - build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/ncro/prebuild/ncro.owl contact: email: huang@southalabama.edu github: Huang-OMIT @@ -4470,9 +4295,6 @@ ontologies: title: Next Generation Biobanking Ontology tracker: https://github.com/Dalalghamdi/NGBO/issues - activity_status: active - build: - checkout: git clone https://github.com/SpeciesFileGroup/nomen.git - system: git canonical: nomen.owl contact: email: diapriid@gmail.com @@ -4515,9 +4337,6 @@ ontologies: type: application user: https://taxonworks.org - activity_status: active - build: - method: owl2obo - source_url: https://raw.githubusercontent.com/OAE-ontology/OAE/master/src/oae_merged.owl contact: email: yongqunh@med.umich.edu github: yongqunh @@ -4680,8 +4499,6 @@ ontologies: - label: BioPortal title: BioPortal Browser url: http://bioportal.bioontology.org/ontologies/OBI?p=classes - build: - source_url: http://purl.obofoundry.org/obo/obi/repository/trunk/src/ontology/branches/ contact: email: bpeters@lji.org github: bpeters42 @@ -4903,9 +4720,6 @@ ontologies: title: Ontology for General Medical Science tracker: https://github.com/OGMS/ogms/issues - activity_status: active - build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/ohd.owl contact: email: wdduncan@gmail.com github: wdduncan @@ -5052,9 +4866,6 @@ ontologies: type: owl_import user: http://obofoundry.org - activity_status: active - build: - method: obo2owl - source_url: https://raw.githubusercontent.com/microbialphenotypes/OMP-ontology-files/master/omp.obo contact: email: jimhu@tamu.edu github: jimhu-tamu @@ -5083,9 +4894,6 @@ ontologies: title: Ontology of Microbial Phenotypes tracker: https://github.com/microbialphenotypes/OMP-ontology/issues - activity_status: active - build: - method: owl2obo - source_url: https://github.com/mcwdsi/OMRSE contact: email: hoganwr@gmail.com github: hoganwr @@ -5283,8 +5091,6 @@ ontologies: - label: OntoBee title: OntoBee Browser url: https://ontobee.org/ontology/ONTONEO - build: - source_url: https://raw.githubusercontent.com/ontoneo-project/Ontoneo/master/ontoneo.owl contact: email: fernanda.farinelli@gmail.com github: FernandaFarinelli @@ -5671,9 +5477,6 @@ ontologies: title: Population and Community Ontology tracker: https://github.com/PopulationAndCommunityOntology/pco/issues - activity_status: active - build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/pdro.owl contact: email: paul.fabry@usherbrooke.ca github: pfabry @@ -5980,11 +5783,6 @@ ontologies: - label: PRO title: PRO Home url: http://proconsortium.org - build: - infallible: 0 - method: obo2owl - oort_args: --no-reasoner - source_url: https://proconsortium.org/download/current/pro_nonreasoned.obo contact: email: dan5@georgetown.edu github: nataled @@ -6076,10 +5874,6 @@ ontologies: title: Process Chemistry Ontology tracker: https://github.com/proco-ontology/PROCO/issues - activity_status: active - build: - checkout: https://github.com/Display-Lab/psdo.git - path: . - system: git contact: email: zachll@umich.edu github: zachll @@ -6150,9 +5944,6 @@ ontologies: - label: RGD title: RGD Ontology Browser url: http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=PW:0000001 - build: - method: obo2owl - source_url: https://download.rgd.mcw.edu/ontology/pathway/pathway.obo contact: email: gthayman@mcw.edu github: gthayman @@ -6313,9 +6104,6 @@ ontologies: - label: RGD title: RGD Ontology Browser url: http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=RS:0000457 - build: - method: obo2owl - source_url: https://download.rgd.mcw.edu/ontology/rat_strain/rat_strain.obo contact: email: sjwang@mcw.edu github: shurjenw @@ -6350,9 +6138,6 @@ ontologies: title: Rat Strain Ontology tracker: https://github.com/rat-genome-database/RS-Rat-Strain-Ontology/issues - activity_status: active - build: - method: owl2obo - source_url: https://raw.githubusercontent.com/rsc-ontologies/rxno/master/rxno.owl contact: email: batchelorc@rsc.org github: batchelorc @@ -6379,10 +6164,6 @@ ontologies: title: Name Reaction Ontology tracker: https://github.com/rsc-ontologies/rxno/issues - activity_status: active - build: - checkout: git clone https://github.com/monarch-initiative/SEPIO-ontology.git - path: src/ontology - system: git contact: email: mhb120@gmail.com github: mbrush @@ -6449,10 +6230,6 @@ ontologies: title: Space Life Sciences Ontology tracker: https://github.com/nasa/LSDAO/issues - activity_status: active - build: - method: obo2owl - notes: SWITCH - source_url: https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/so.obo contact: email: keilbeck@genetics.utah.edu github: keilbeck @@ -6501,10 +6278,6 @@ ontologies: title: Sequence types and features ontology tracker: https://github.com/The-Sequence-Ontology/SO-Ontologies/issues - activity_status: active - build: - insert_ontology_id: true - method: obo2owl - source_url: https://raw.githubusercontent.com/obophenotype/spider-ontology/master/spider_comparative_biology.obo contact: email: ramirez@macn.gov.ar github: martinjramirez @@ -6636,10 +6409,6 @@ ontologies: title: Software ontology tracker: https://github.com/allysonlister/swo/issues - activity_status: active - build: - infallible: 1 - method: obo2owl - source_url: https://raw.githubusercontent.com/DiseaseOntology/SymptomOntology/master/src/ontology/symp.obo contact: email: lynn.schriml@gmail.com github: lschriml @@ -6825,10 +6594,6 @@ ontologies: url: http://archive.gramene.org/db/ontology/search?id=TO:0000286 user: http://gramene.org/ - activity_status: active - build: - infallible: 1 - method: obo2owl - source_url: https://raw.githubusercontent.com/DiseaseOntology/PathogenTransmissionOntology/master/src/ontology/trans.obo contact: email: lynn.schriml@gmail.com github: lschriml @@ -6957,11 +6722,6 @@ ontologies: - label: KnowledgeSpace title: INCF KnowledgeSpace Portal url: https://knowledge-space.org/index.php/pages/view/UBERON:0000061 - build: - checkout: git clone https://github.com/obophenotype/uberon.git - email_cc: cjmungall@lbl.gov - infallible: 1 - system: git canonical: uberon.owl contact: email: cjmungall@lbl.gov @@ -7137,9 +6897,6 @@ ontologies: user: https://www.ebi.ac.uk/chembl/ wikidata_template: https://en.wikipedia.org/wiki/Template:Uberon - activity_status: active - build: - method: obo2owl - source_url: https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo contact: email: g.gkoutos@gmail.com github: gkoutos @@ -7171,10 +6928,6 @@ ontologies: title: Units of measurement ontology tracker: https://github.com/bio-ontology-research-group/unit-ontology/issues - activity_status: active - build: - method: archive - path: archive/ontology - source_url: http://build.berkeleybop.org/job/build-pheno-ontologies/lastSuccessfulBuild/artifact/*zip*/archive.zip contact: email: jmcl@ebi.ac.uk github: jamesamcl @@ -7304,8 +7057,6 @@ ontologies: type: annotation user: https://www.cellosaurus.org/index.html - activity_status: active - build: - source_url: https://raw.githubusercontent.com/vaccineontology/VO/master/src/VO_merged.owl contact: email: yongqunh@med.umich.edu github: yongqunh @@ -7365,10 +7116,6 @@ ontologies: url: http://www.hipc-dashboard.org/#vaccine/vo-0000044 user: https://immunespace.org/ - activity_status: active - build: - checkout: svn co http://phenotype-ontologies.googlecode.com/svn/trunk/src/ontology/vt - method: vcs - system: svn contact: email: caripark@iastate.edu github: caripark @@ -7445,10 +7192,6 @@ ontologies: - description: Phenoscape uses VTO to annotate systematics data user: http://phenoscape.org - activity_status: active - build: - checkout: git clone https://github.com/obophenotype/c-elegans-gross-anatomy-ontology.git - path: . - system: git contact: email: raymond@caltech.edu github: raymond91125 @@ -7492,10 +7235,6 @@ ontologies: type: annotation user: https://www.wormbase.org/ - activity_status: active - build: - checkout: git clone https://github.com/obophenotype/c-elegans-development-ontology.git - path: . - system: git contact: email: cgrove@caltech.edu github: chris-grove @@ -7541,10 +7280,6 @@ ontologies: type: annotation user: https://www.wormbase.org/ - activity_status: active - build: - checkout: git clone https://github.com/obophenotype/c-elegans-phenotype-ontology.git - path: . - system: git contact: email: cgrove@caltech.edu github: chris-grove @@ -7603,10 +7338,6 @@ ontologies: type: annotation user: https://monarchinitiative.org/ - activity_status: active - build: - infallible: 0 - method: obo2owl - source_url: https://raw.githubusercontent.com/xenopus-anatomy/xao/master/xenopus_anatomy.obo contact: email: Erik.Segerdell@cchmc.org github: seger @@ -7653,9 +7384,6 @@ ontologies: - label: RGD title: RGD Ontology Browser url: http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000 - build: - method: obo2owl - source_url: https://download.rgd.mcw.edu/ontology/experimental_condition/experimental_condition.obo contact: email: jrsmith@mcw.edu github: jrsjrs @@ -7765,9 +7493,6 @@ ontologies: title: Xenopus Phenotype Ontology tracker: https://github.com/obophenotype/xenopus-phenotype-ontology/issues - activity_status: active - build: - method: obo2owl - source_url: https://raw.githubusercontent.com/ybradford/zebrafish-experimental-conditions-ontology/master/zeco.obo contact: email: ybradford@zfin.org github: ybradford @@ -7799,11 +7524,6 @@ ontologies: title: Zebrafish Experimental Conditions Ontology tracker: https://github.com/ybradford/zebrafish-experimental-conditions-ontology/issues - activity_status: active - build: - infallible: 1 - method: obo2owl - notes: may be ready to switch to vcs soon - source_url: https://raw.githubusercontent.com/cerivs/zebrafish-anatomical-ontology/master/src/zebrafish_anatomy.obo contact: email: van_slyke@zfin.org github: cerivs @@ -7845,10 +7565,6 @@ ontologies: url: http://zfin.org/ZFA:0000029 user: http://zfin.org - activity_status: active - build: - infallible: 1 - method: obo2owl - source_url: https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/zfs/zfs.obo contact: email: van_slyke@zfin.org github: cerivs @@ -7926,10 +7642,6 @@ ontologies: type: annotation user: https://monarchinitiative.org/ - activity_status: active - build: - checkout: git clone https://github.com/Superraptor/GSSO.git - path: . - system: git contact: email: kronkcj@mail.uc.edu github: Superraptor @@ -8136,9 +7848,6 @@ ontologies: - label: OntoBee title: OntoBee url: https://www.ontobee.org/ontology/KISAO - build: - method: owl2obo - source_url: https://raw.githubusercontent.com/SED-ML/KiSAO/deploy/kisao.owl contact: email: jonrkarr@gmail.com github: jonrkarr @@ -8205,10 +7914,6 @@ ontologies: type: annotation user: https://biosimulators.org/ - activity_status: active - build: - insert_ontology_id: true - method: obo2owl - source_url: http://www.ebi.ac.uk/sbo/exports/Main/SBO_OBO.obo contact: email: sheriff@ebi.ac.uk github: rsmsheriff @@ -8232,10 +7937,6 @@ ontologies: title: Systems Biology Ontology tracker: https://github.com/EBI-BioModels/SBO/issues - activity_status: active - build: - checkout: git clone https://github.com/scdodev/scdo-ontology.git - path: . - system: git contact: email: giant.plankton@gmail.com github: JadeHotchkiss @@ -8305,11 +8006,6 @@ ontologies: title: Sickle Cell Disease Ontology tracker: https://github.com/scdodev/scdo-ontology/issues - activity_status: orphaned - build: - infallible: 1 - insert_ontology_id: true - method: obo2owl - source_url: ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/fix.obo contact: email: null label: chEBI @@ -8327,9 +8023,6 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/fix.obo title: Physico-chemical methods and properties - activity_status: orphaned - build: - method: owl2obo - source_url: https://svn.code.sf.net/p/mamo-ontology/code/tags/latest/mamo-xml.owl description: The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. @@ -8349,10 +8042,6 @@ ontologies: title: Mathematical modeling ontology tracker: http://sourceforge.net/p/mamo-ontology/tickets/ - activity_status: orphaned - build: - insert_ontology_id: true - method: obo2owl - source_url: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/physicochemical/rex.obo description: An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. domain: chemistry and biochemistry @@ -8364,10 +8053,6 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/rex.owl title: Physico-chemical process - activity_status: orphaned - build: - checkout: git clone https://github.com/obophenotype/sibo.git - method: vcs - system: git contact: email: cjmungall@lbl.gov label: Chris Mungall @@ -8394,9 +8079,6 @@ ontologies: title: Social Insect Behavior Ontology tracker: https://github.com/obophenotype/sibo/issues - activity_status: orphaned - build: - method: obo2owl - source_url: http://variationontology.org/vario_download/vario.obo contact: email: mauno.vihinen@med.lu.se github: maunov @@ -8555,9 +8237,6 @@ ontologies: title: Ontology of Genetic Susceptibility Factor tracker: https://github.com/linikujp/OGSF/issues - activity_status: inactive - build: - method: obo2owl - source_url: https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/olatdv/olatdv.obo contact: email: frederic.bastian@unil.ch github: fbastian @@ -8584,9 +8263,6 @@ ontologies: title: Medaka Developmental Stages tracker: https://github.com/obophenotype/developmental-stage-ontologies/issues - activity_status: inactive - build: - method: obo2owl - source_url: https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/pdumdv/pdumdv.obo contact: email: frederic.bastian@unil.ch github: fbastian @@ -8613,11 +8289,6 @@ ontologies: title: Platynereis Developmental Stages tracker: https://github.com/obophenotype/developmental-stage-ontologies/issues - activity_status: inactive - build: - checkout: git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git - method: vcs - path: src/ontology - system: git contact: email: J.Bard@ed.ac.uk label: Jonathan Bard @@ -8669,11 +8340,6 @@ ontologies: title: Cephalopod Ontology tracker: https://github.com/obophenotype/cephalopod-ontology/issues - activity_status: inactive - build: - checkout: git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git - method: vcs - path: src/ontology - system: git contact: email: J.Bard@ed.ac.uk label: Jonathan Bard @@ -8708,10 +8374,6 @@ ontologies: title: Human developmental anatomy, abstract tracker: https://github.com/obophenotype/human-developmental-anatomy-ontology/issues - activity_status: inactive - build: - insert_ontology_id: true - method: obo2owl - source_url: http://svn.code.sf.net/p/obo/svn/fma-conversion/trunk/fma2_obo.obo contact: email: mejino@u.washington.edu label: Onard Mejino @@ -8791,10 +8453,6 @@ ontologies: - label: RNAO title: RNA Ontology jOWL Browser url: http://bgsu-rna.github.io/rnao/ - build: - checkout: git clone https://github.com/BGSU-RNA/rnao.git - method: vcs - system: git contact: email: BatchelorC@rsc.org label: Colin Batchelor @@ -8927,9 +8585,6 @@ ontologies: layout: ontology_detail title: Animal natural history and life history - activity_status: inactive - build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/aero.owl contact: email: mcourtot@gmail.com label: Melanie Courtot @@ -8988,10 +8643,6 @@ ontologies: title: Beta Cell Genomics Ontology tracker: https://github.com/obi-bcgo/bcgo/issues - activity_status: inactive - build: - insert_ontology_id: true - method: obo2owl - source_url: http://4dx.embl.de/4DXpress_4d/edocs/bilateria_mrca.obo contact: email: henrich@embl.de github: ThorstenHen @@ -9022,10 +8673,6 @@ ontologies: replaced_by: molecular_function title: Gene Regulation Ontology - activity_status: inactive - build: - method: obo2owl - notes: moving to owl soon - source_url: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/caro.obo contact: email: haendel@ohsu.edu github: mellybelly @@ -9128,11 +8775,6 @@ ontologies: label: Homo sapiens title: Human developmental anatomy, abstract version - activity_status: inactive - build: - insert_ontology_id: true - method: obo2owl - notes: new url soon - source_url: ftp://ftp.hgu.mrc.ac.uk/pub/MouseAtlas/Anatomy/EMAP_combined.obo contact: email: Terry.Hayamizu@jax.org github: tfhayamizu @@ -9155,9 +8797,6 @@ ontologies: label: Mus title: Mouse gross anatomy and development, timed - activity_status: inactive - build: - method: obo2owl - source_url: https://github.com/Planteome/plant-environment-ontology/blob/master/plant-environment-ontology.obo.owl contact: email: jaiswalp@science.oregonstate.edu github: jaiswalp @@ -9200,9 +8839,6 @@ ontologies: url: http://archive.gramene.org/db/ontology/search?id=EO:0007174 user: http://gramene.org/ - activity_status: inactive - build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/epo.owl description: An ontology designed to support the semantic annotation of epidemiology resources domain: health @@ -9216,9 +8852,6 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/epo.owl title: Epidemiology Ontology - activity_status: inactive - build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/ero.owl contact: email: Marc_Ciriello@hms.harvard.edu label: Marc Ciriello @@ -9250,10 +8883,6 @@ ontologies: layout: ontology_detail title: eVOC (Expressed Sequence Annotation for Humans) - activity_status: inactive - build: - insert_ontology_id: true - method: obo2owl - source_url: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/taxonomy/fly_taxonomy.obo contact: email: cp390@cam.ac.uk github: Clare72 @@ -9276,9 +8905,6 @@ ontologies: label: Drosophila title: Fly taxonomy - activity_status: inactive - build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/flu.owl contact: email: burkesquires@gmail.com label: Burke Squires @@ -9315,10 +8941,6 @@ ontologies: layout: ontology_detail title: Habronattus courtship - activity_status: inactive - build: - insert_ontology_id: true - method: obo2owl - source_url: http://download.baderlab.org/INOH/ontologies/EventOntology_172.obo domain: chemistry and biochemistry homepage: http://www.inoh.org id: iev @@ -9326,10 +8948,6 @@ ontologies: layout: ontology_detail title: Event (INOH pathway ontology) - activity_status: inactive - build: - insert_ontology_id: true - method: obo2owl - source_url: https://web.archive.org/web/20131127090937/http://www.inoh.org/ontologies/MoleculeRoleOntology.obo contact: email: curator@inoh.org label: INOH curators @@ -9350,9 +8968,6 @@ ontologies: layout: ontology_detail title: Protein Domains - activity_status: inactive - build: - method: owl2obo - source_url: http://www.lipidprofiles.com/LipidOntology contact: email: bakerc@unb.ca label: Christopher Baker @@ -9491,9 +9106,6 @@ ontologies: replaced_by: uberon title: NIF Gross Anatomy - activity_status: inactive - build: - method: owl2obo - source_url: https://msi-workgroups.svn.sourceforge.net/svnroot/msi-workgroups/ontology/NMR.owl contact: email: schober@imbi.uni-freiburg.de label: Schober Daniel @@ -9655,10 +9267,6 @@ ontologies: label: Homo sapiens title: Subcellular anatomy ontology - activity_status: inactive - build: - insert_ontology_id: true - method: obo2owl - source_url: https://raw.githubusercontent.com/HUPO-PSI/gelml/master/CV/sep.obo contact: email: psidev-gps-dev@lists.sourceforge.net label: SEP developers via the PSI and MSI mailing lists @@ -9716,9 +9324,6 @@ ontologies: label: Homo sapiens title: Terminology of Anatomy of Human Histology - activity_status: inactive - build: - method: obo2owl - source_url: http://purl.obolibrary.org/obo/tao.obo contact: email: wasila.dahdul@usd.edu label: Wasila Dahdul @@ -9758,9 +9363,6 @@ ontologies: replaced_by: uberon title: Vertebrate Homologous Ontology Group Ontology - activity_status: inactive - build: - method: obo2owl - source_url: http://phenoscape.svn.sourceforge.net/svnroot/phenoscape/tags/vocab-releases/VSAO/vsao.obo contact: email: wasila.dahdul@usd.edu label: Wasila Dahdul diff --git a/_posts/2016-11-26-S3-switch.md b/_posts/2016-11-26-S3-switch.md index df23b7487..862102ec2 100644 --- a/_posts/2016-11-26-S3-switch.md +++ b/_posts/2016-11-26-S3-switch.md @@ -20,7 +20,7 @@ These purls should always be used to reference the ontology. Maintainers of ontologies have the option of deciding what their PURL resolves to. Many choose to resolve to the [central OBO build -URLs](http://obofoundry.org/faq/what-is-the-build-field). +URLs](https://web.archive.org/web/20230326002924/http://obofoundry.org/faq/what-is-the-build-field). Historically these have always resolved to http://berkeleybop.org/ontologies/ -- we have recently changed this to diff --git a/faq/index.md b/faq/index.md index 49f7ba8e6..93ce805ce 100644 --- a/faq/index.md +++ b/faq/index.md @@ -28,7 +28,6 @@ title: OBO Foundry Frequently Asked Questions - [How do I edit the metadata for my ontology?](/faq/how-do-i-edit-metadata.html) - [What are permissible values in the metadata file, e.g. for 'publications'?](/faq/permissible-metadata-content.html) -- [What is the `build` object in the ontology metadata?](/faq/what-is-the-build-field.html) - [What does it mean for an ontology to be flagged as 'inactive', 'unresponsive', 'orphaned' or 'obsolete'?](/docs/OntologyStatus.html) ### OBO Foundry Dashboard diff --git a/faq/what-is-the-build-field.md b/faq/what-is-the-build-field.md deleted file mode 100644 index eefebba04..000000000 --- a/faq/what-is-the-build-field.md +++ /dev/null @@ -1,134 +0,0 @@ ---- -layout: faq -title: OBO central builds ---- - -## What does the build object do in my YAML configuration? - -Most ontology metadata files contain a `build` field (see other FAQ -entries for how to view and edit metadata files). - -For example, the [mouse anatomy](/ontology/ma.html) yaml file `ma.md` has the following: - -``` -... -build: - source_url: ftp://ftp.informatics.jax.org/pub/reports/adult_mouse_anatomy.obo - method: obo2owl -... -``` - -These are the instructions for the central OBO Foundry build pipeline that -runs nightly, which ensures creation of correct obo and owl files for -each ontology. - -The output goes here: - -- http://ontologies.berkeleybop.org/ - -You can choose to entirely ignore the output of this pipeline for your -ontology. However, it provides a convenient fall-through for groups -who are not running their own release pipelines. Historically many -groups in OBO have just produced a single obo file, e.g. on their ftp -site, and the central build has ensured owl and roundtripped obo (as -well as additional services such as validation). - -## Where does the job run? - -The continuous integration job runs here: - -- http://build.berkeleybop.org/job/simple-build-obo-all/ - -It takes as metadata input the yml file from this repository. It makes -use of the `build` object. - -This job will fail if ontologies marked as `infallible` fail. To debug, the full log of the last build can be examined: - -- https://build.berkeleybop.org/job/simple-build-obo-all/lastBuild/consoleFull - -(Look for the text "should not fail") - -## Warning - -A http://ontologies.berkeleybop.org/ URL should never be handed out directly. This service exists so that: - -- Un PURL-registered ontologies will have a fall-through -- Registered PURL ontologies that do not want to take charge of either OBO or OWL generation will have a place to 302-redirect to - -## What are some of the methods? - -The build object takes a number of different methods: - -- obo2owl: creates a release folder using an obo file as source -- owl2obo: creates a release folder using an owl file as source -- archive: copies a release folder (e.g. from an existing CI job) to the bbop ontology repository -- vcs: does a git or svn checkout and copies the resulting folder - -For more details, ask a question on the tracker or see the script: - -- https://github.com/owlcollab/owltools/blob/master/OWLTools-Oort/bin/build-obo-ontologies.pl - -## Assumptions - -### Ontology URI - -If you are using the obo2owl or owl2obo method, you should make sure -that the ontology URI is set correctly. This should be set to whatever -is intended as the final URI for the ontology. - -Assume we have an ontology with ID space `FOO`. For the owl2obo method, the file will contain: - -``` - -``` - -For obo2owl, the file should contain: - -``` -ontology: foo -``` - -(the obo2owl method builds in assumptions about the ID policy for ontology URIs). - -Note that some legacy `.obo` files do not include an ontology -header. For those, we add an extra line in the `build` object in the -metadata file: - -``` -build: - source_url: http://some.old.url.org/my/foo.obo - method: obo2owl - insert_ontology_id: true -``` - -This will use the `id` field to set the ontology ID/URI correctly. - -This currently only works for owl2obo. If you are going from OWL, you -should use the final URI for your ontology - this assumption is built in. - -Note that if the id/uri is not set correctly and you don't auto-insert -the id using the directive above, then the build for your ontology will fail! - -## How do I tell if the build for my ontology failed? - -Note that the jenkins job will still succeed even if your ontology -build fails (unless the `is_infallible` field is set). Currently the -only way around this is to download the jenkins report and examine it. - -If that does not sound ideal, remember the central build is a fallback -system, and includes many legacy/grandfathered ontologies. - -## How do I take control of my own builds - -You do not need to rely on the OBO central builds! - -You can use an existing tool like -[robot](https://github.com/ontodev/robot/) and a Makefile. See some -existing github repositories for examples. - -You would make your own releases (I recommend using the github release mechanism) - -You can then configure your ontology entries in OCLC to point to the -location in your repository (or to where you choose to release them, e.g. S3) - -Another option is to use a CI system to build your ontology. diff --git a/faq/where-is-the-obo-file.md b/faq/where-is-the-obo-file.md index 686f3f69f..c3d837dce 100644 --- a/faq/where-is-the-obo-file.md +++ b/faq/where-is-the-obo-file.md @@ -46,6 +46,4 @@ Developers can OPTIONALLY produce ontologies in other formats. These are convent It does not matter to us if you maintain the source for your ontology in obo or owl or some hybrid. You have the option of either publishing -the alternate format yourself (using a tool like ROBOT) _or_ you can -have the OBO central build pipeline do this for you. For more -information, see the FAQ entry [What is the Build field?](what-is-the-build-field.md). +the alternate format yourself (using a tool like ROBOT). diff --git a/ontology/aeo.md b/ontology/aeo.md index a32becad9..0d3417ecc 100644 --- a/ontology/aeo.md +++ b/ontology/aeo.md @@ -2,11 +2,6 @@ layout: ontology_detail id: aeo title: Anatomical Entity Ontology -build: - checkout: git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git - method: vcs - path: src/ontology - system: git contact: email: J.Bard@ed.ac.uk label: Jonathan Bard diff --git a/ontology/aero.md b/ontology/aero.md index 6e0068968..4b047ee57 100644 --- a/ontology/aero.md +++ b/ontology/aero.md @@ -2,9 +2,6 @@ layout: ontology_detail id: aero title: Adverse Event Reporting Ontology -build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/aero.owl contact: email: mcourtot@gmail.com label: Melanie Courtot diff --git a/ontology/aism.md b/ontology/aism.md index b6f4a4ea7..c8310b8f8 100644 --- a/ontology/aism.md +++ b/ontology/aism.md @@ -2,10 +2,6 @@ layout: ontology_detail id: aism title: Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) -build: - checkout: git clone https://github.com/insect-morphology/aism - path: . - system: git contact: email: entiminae@gmail.com github: JCGiron diff --git a/ontology/amphx.md b/ontology/amphx.md index ecd61c5a1..4c933a9ca 100644 --- a/ontology/amphx.md +++ b/ontology/amphx.md @@ -2,10 +2,6 @@ layout: ontology_detail id: amphx title: The Amphioxus Development and Anatomy Ontology -build: - checkout: git clone https://github.com/EBISPOT/amphx_ontology.git - path: . - system: git contact: email: hescriva@obs-banyuls.fr github: hescriva diff --git a/ontology/apo.md b/ontology/apo.md index 247127b48..156ff8e9e 100644 --- a/ontology/apo.md +++ b/ontology/apo.md @@ -2,9 +2,6 @@ layout: ontology_detail id: apo title: Ascomycete phenotype ontology -build: - method: obo2owl - source_url: https://raw.githubusercontent.com/obophenotype/ascomycete-phenotype-ontology/master/apo.obo contact: email: stacia@stanford.edu github: srengel diff --git a/ontology/bila.md b/ontology/bila.md index baa8ce8ad..6695fb73a 100644 --- a/ontology/bila.md +++ b/ontology/bila.md @@ -2,10 +2,6 @@ layout: ontology_detail id: bila title: Bilateria anatomy -build: - insert_ontology_id: true - method: obo2owl - source_url: http://4dx.embl.de/4DXpress_4d/edocs/bilateria_mrca.obo contact: email: henrich@embl.de github: ThorstenHen diff --git a/ontology/bspo.md b/ontology/bspo.md index 24b88c4fa..cbe25497b 100644 --- a/ontology/bspo.md +++ b/ontology/bspo.md @@ -2,12 +2,6 @@ layout: ontology_detail id: bspo title: Biological Spatial Ontology -build: - checkout: git clone https://github.com/obophenotype/biological-spatial-ontology.git - infallible: 1 - method: vcs - path: src/ontology - system: git contact: email: cjmungall@lbl.gov github: cmungall diff --git a/ontology/bto.md b/ontology/bto.md index 7acb4f83c..86caf1296 100644 --- a/ontology/bto.md +++ b/ontology/bto.md @@ -2,10 +2,6 @@ layout: ontology_detail id: bto title: BRENDA tissue / enzyme source -build: - checkout: git clone https://github.com/BRENDA-Enzymes/BTO.git - path: . - system: git contact: email: c.dudek@tu-braunschweig.de github: chdudek diff --git a/ontology/caro.md b/ontology/caro.md index 07c7d6cc8..6ed970d38 100644 --- a/ontology/caro.md +++ b/ontology/caro.md @@ -2,10 +2,6 @@ layout: ontology_detail id: caro title: Common Anatomy Reference Ontology -build: - method: obo2owl - notes: moving to owl soon - source_url: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/caro.obo contact: email: haendel@ohsu.edu github: mellybelly diff --git a/ontology/cdao.md b/ontology/cdao.md index eacacfe7e..d406e3e7b 100644 --- a/ontology/cdao.md +++ b/ontology/cdao.md @@ -2,9 +2,6 @@ layout: ontology_detail id: cdao title: Comparative Data Analysis Ontology -build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/cdao.owl contact: email: balhoff@renci.org github: balhoff diff --git a/ontology/cdno.md b/ontology/cdno.md index 91ae41cb8..5d58f78e7 100644 --- a/ontology/cdno.md +++ b/ontology/cdno.md @@ -2,10 +2,6 @@ layout: ontology_detail id: cdno title: Compositional Dietary Nutrition Ontology -build: - checkout: git clone https://github.com/CompositionalDietaryNutritionOntology/cdno.git - path: . - system: git contact: email: landreshdz@gmail.com github: LilyAndres diff --git a/ontology/chebi.md b/ontology/chebi.md index 07193e9ed..7c1e601d1 100644 --- a/ontology/chebi.md +++ b/ontology/chebi.md @@ -6,10 +6,6 @@ browsers: - title: EBI CHEBI Browser label: CHEBI url: http://www.ebi.ac.uk/chebi/chebiOntology.do?treeView=true&chebiId=CHEBI:24431#graphView -build: - infallible: 1 - method: obo2owl - source_url: ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo contact: email: amalik@ebi.ac.uk github: amalik01 diff --git a/ontology/cheminf.md b/ontology/cheminf.md index 2fdee7cec..313e54090 100644 --- a/ontology/cheminf.md +++ b/ontology/cheminf.md @@ -2,9 +2,6 @@ layout: ontology_detail id: cheminf title: Chemical Information Ontology -build: - method: owl2obo - source_url: https://raw.githubusercontent.com/semanticchemistry/semanticchemistry/master/ontology/cheminf.owl contact: email: egon.willighagen@gmail.com github: egonw diff --git a/ontology/clao.md b/ontology/clao.md index c096ef9c1..0a34eed66 100644 --- a/ontology/clao.md +++ b/ontology/clao.md @@ -2,10 +2,6 @@ layout: ontology_detail id: clao title: Collembola Anatomy Ontology -build: - checkout: git clone https://github.com/luis-gonzalez-m/Collembola.git - path: . - system: git contact: email: lagonzalezmo@unal.edu.co github: luis-gonzalez-m diff --git a/ontology/clyh.md b/ontology/clyh.md index 4d092ccdc..14cfde873 100644 --- a/ontology/clyh.md +++ b/ontology/clyh.md @@ -2,10 +2,6 @@ layout: ontology_detail id: clyh title: Clytia hemisphaerica Development and Anatomy Ontology -build: - checkout: git clone https://github.com/EBISPOT/clyh_ontology.git - path: . - system: git contact: email: lucas.leclere@obs-banyuls.fr github: Leclere-L diff --git a/ontology/cmo.md b/ontology/cmo.md index e4a006e41..1a52da917 100644 --- a/ontology/cmo.md +++ b/ontology/cmo.md @@ -6,9 +6,6 @@ browsers: - title: RGD Ontology Browser label: RGD url: http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=CMO:0000000 -build: - method: obo2owl - source_url: https://download.rgd.mcw.edu/ontology/clinical_measurement/clinical_measurement.obo contact: email: jrsmith@mcw.edu github: jrsjrs diff --git a/ontology/cro.md b/ontology/cro.md index c991c4a73..230d7582a 100644 --- a/ontology/cro.md +++ b/ontology/cro.md @@ -2,10 +2,6 @@ layout: ontology_detail id: cro title: Contributor Role Ontology -build: - checkout: git clone https://github.com/data2health/contributor-role-ontology.git - path: src/ontology - system: git contact: email: whimar@ohsu.edu github: marijane diff --git a/ontology/cvdo.md b/ontology/cvdo.md index 29f5d1db6..9c559af37 100644 --- a/ontology/cvdo.md +++ b/ontology/cvdo.md @@ -2,12 +2,6 @@ layout: ontology_detail id: cvdo title: Cardiovascular Disease Ontology -build: - method: owl2obo - publications: - - id: http://dx.doi.org/10.3233/978-1-61499-438-1-409 - title: The Cardiovascular Disease Ontology - source_url: http://purl.obolibrary.org/obo/cvdo.owl contact: email: paul.fabry@usherbrooke.ca github: pfabry diff --git a/ontology/ddanat.md b/ontology/ddanat.md index 4096810f2..47d89457e 100644 --- a/ontology/ddanat.md +++ b/ontology/ddanat.md @@ -2,10 +2,6 @@ layout: ontology_detail id: ddanat title: Dictyostelium discoideum anatomy -build: - insert_ontology_id: true - method: obo2owl - source_url: https://raw.githubusercontent.com/dictyBase/migration-data/master/ontologies/dicty_anatomy.obo contact: email: pfey@northwestern.edu github: pfey03 diff --git a/ontology/ddpheno.md b/ontology/ddpheno.md index 439d705f9..bb74d2c1a 100644 --- a/ontology/ddpheno.md +++ b/ontology/ddpheno.md @@ -2,10 +2,6 @@ layout: ontology_detail id: ddpheno title: Dictyostelium discoideum phenotype ontology -build: - checkout: git clone https://github.com/obophenotype/dicty-phenotype-ontology.git - path: . - system: git contact: email: pfey@northwestern.edu github: pfey03 diff --git a/ontology/disdriv.md b/ontology/disdriv.md index 91a27ef32..4c4b82cc7 100644 --- a/ontology/disdriv.md +++ b/ontology/disdriv.md @@ -6,8 +6,6 @@ browsers: - title: DO Browser label: DO url: https://disease-ontology.org/ -build: - source_url: https://raw.githubusercontent.com/DiseaseOntology/DiseaseDriversOntology/refs/heads/main/src/ontology/disdriv.owl contact: email: lynn.schriml@gmail.com github: lschriml diff --git a/ontology/doid.md b/ontology/doid.md index fab3fee14..97a51031f 100644 --- a/ontology/doid.md +++ b/ontology/doid.md @@ -6,10 +6,6 @@ browsers: - title: DO Browser label: DO url: https://disease-ontology.org/do -build: - infallible: 1 - method: obo2owl - source_url: https://raw.githubusercontent.com/DiseaseOntology/HumanDiseaseOntology/master/src/ontology/doid.obo contact: email: lynn.schriml@gmail.com github: lschriml diff --git a/ontology/dpo.md b/ontology/dpo.md index 58b431300..637a5ec02 100644 --- a/ontology/dpo.md +++ b/ontology/dpo.md @@ -6,10 +6,6 @@ browsers: - title: FlyBase Browser label: FB url: http://flybase.org/.bin/cvreport.html?cvterm=FBcv:0000347 -build: - checkout: git clone https://github.com/FlyBase/drosophila-phenotype-ontolog.git - path: . - system: git contact: email: cp390@cam.ac.uk github: Clare72 diff --git a/ontology/dron.md b/ontology/dron.md index d9d8ce91c..0d64eb3f3 100644 --- a/ontology/dron.md +++ b/ontology/dron.md @@ -2,9 +2,6 @@ layout: ontology_detail id: dron title: The Drug Ontology -build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/dron.owl contact: email: hoganwr@gmail.com github: hoganwr diff --git a/ontology/ecao.md b/ontology/ecao.md index ff2d6536b..42babbead 100644 --- a/ontology/ecao.md +++ b/ontology/ecao.md @@ -2,10 +2,6 @@ layout: ontology_detail id: ecao title: The Echinoderm Anatomy and Development Ontology -build: - checkout: git clone https://github.com/echinoderm-ontology/ecao_ontology.git - path: . - system: git contact: email: ettensohn@cmu.edu github: ettensohn diff --git a/ontology/ehdaa2.md b/ontology/ehdaa2.md index 77113fed0..753831ad1 100644 --- a/ontology/ehdaa2.md +++ b/ontology/ehdaa2.md @@ -2,11 +2,6 @@ layout: ontology_detail id: ehdaa2 title: Human developmental anatomy, abstract -build: - checkout: git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git - method: vcs - path: src/ontology - system: git contact: email: J.Bard@ed.ac.uk label: Jonathan Bard diff --git a/ontology/emap.md b/ontology/emap.md index 72152a1cc..92c4db323 100644 --- a/ontology/emap.md +++ b/ontology/emap.md @@ -2,11 +2,6 @@ layout: ontology_detail id: emap title: Mouse gross anatomy and development, timed -build: - insert_ontology_id: true - method: obo2owl - notes: new url soon - source_url: ftp://ftp.hgu.mrc.ac.uk/pub/MouseAtlas/Anatomy/EMAP_combined.obo contact: email: Terry.Hayamizu@jax.org github: tfhayamizu diff --git a/ontology/emapa.md b/ontology/emapa.md index 53a50b375..0115dee2a 100644 --- a/ontology/emapa.md +++ b/ontology/emapa.md @@ -2,10 +2,6 @@ layout: ontology_detail id: emapa title: Mouse Developmental Anatomy Ontology -build: - method: obo2owl - notes: new url soon - source_url: ftp://ftp.hgu.mrc.ac.uk/pub/MouseAtlas/Anatomy/EMAPA.obo contact: email: Terry.Hayamizu@jax.org github: tfhayamizu diff --git a/ontology/eo.md b/ontology/eo.md index bd5ceb55d..89642fdca 100644 --- a/ontology/eo.md +++ b/ontology/eo.md @@ -2,9 +2,6 @@ layout: ontology_detail id: eo title: Plant Environment Ontology -build: - method: obo2owl - source_url: https://github.com/Planteome/plant-environment-ontology/blob/master/plant-environment-ontology.obo.owl contact: email: jaiswalp@science.oregonstate.edu github: jaiswalp diff --git a/ontology/epo.md b/ontology/epo.md index a3bc83599..2eae81c4d 100644 --- a/ontology/epo.md +++ b/ontology/epo.md @@ -2,9 +2,6 @@ layout: ontology_detail id: epo title: Epidemiology Ontology -build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/epo.owl description: An ontology designed to support the semantic annotation of epidemiology resources domain: health homepage: https://code.google.com/p/epidemiology-ontology/ diff --git a/ontology/ero.md b/ontology/ero.md index 05a992ec5..bfecf9632 100644 --- a/ontology/ero.md +++ b/ontology/ero.md @@ -2,9 +2,6 @@ layout: ontology_detail id: ero title: eagle-i resource ontology -build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/ero.owl contact: email: Marc_Ciriello@hms.harvard.edu label: Marc Ciriello diff --git a/ontology/fao.md b/ontology/fao.md index fd4892033..128727ee3 100644 --- a/ontology/fao.md +++ b/ontology/fao.md @@ -2,11 +2,6 @@ layout: ontology_detail id: fao title: Fungal gross anatomy -build: - checkout: git clone https://github.com/obophenotype/fungal-anatomy-ontology.git - infallible: 1 - method: vcs - system: git contact: email: vw253@cam.ac.uk github: ValWood diff --git a/ontology/fbbi.md b/ontology/fbbi.md index f596cb8f7..d88dee064 100644 --- a/ontology/fbbi.md +++ b/ontology/fbbi.md @@ -2,10 +2,6 @@ layout: ontology_detail id: fbbi title: Biological Imaging Methods Ontology -build: - checkout: git clone https://github.com/foundingGIDE/fbbi.git - path: . - system: git contact: email: damien@gerbi-gmb.de github: gouttegd diff --git a/ontology/fbbt.md b/ontology/fbbt.md index edca1dd0d..cb31a491d 100644 --- a/ontology/fbbt.md +++ b/ontology/fbbt.md @@ -12,10 +12,6 @@ browsers: - title: BioPortal Browser label: BioPortal url: http://bioportal.bioontology.org/ontologies/FB-BT?p=classes -build: - checkout: git clone https://github.com/FlyBase/drosophila-anatomy-developmental-ontology.git - path: . - system: git contact: email: cp390@cam.ac.uk github: Clare72 diff --git a/ontology/fbcv.md b/ontology/fbcv.md index f3c73b63c..327000994 100644 --- a/ontology/fbcv.md +++ b/ontology/fbcv.md @@ -6,10 +6,6 @@ browsers: - title: FlyBase Browser label: FB url: http://flybase.org/.bin/cvreport.html?cvterm=FBcv:0000013 -build: - checkout: git clone https://github.com/FlyBase/flybase-controlled-vocabulary.git - path: . - system: git contact: email: cp390@cam.ac.uk github: Clare72 diff --git a/ontology/fbdv.md b/ontology/fbdv.md index 4db903f10..65fc00f28 100644 --- a/ontology/fbdv.md +++ b/ontology/fbdv.md @@ -6,10 +6,6 @@ browsers: - title: FlyBase Browser label: FB url: http://flybase.org/.bin/cvreport.html?cvterm=FBdv:00007008 -build: - checkout: git clone https://github.com/FlyBase/drosophila-developmental-ontology.git - path: . - system: git contact: email: cp390@cam.ac.uk github: Clare72 diff --git a/ontology/fbsp.md b/ontology/fbsp.md index 09cb89800..b77a99d7e 100644 --- a/ontology/fbsp.md +++ b/ontology/fbsp.md @@ -2,10 +2,6 @@ layout: ontology_detail id: fbsp title: Fly taxonomy -build: - insert_ontology_id: true - method: obo2owl - source_url: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/taxonomy/fly_taxonomy.obo contact: email: cp390@cam.ac.uk github: Clare72 diff --git a/ontology/fix.md b/ontology/fix.md index d72030ffe..a646fc6cb 100644 --- a/ontology/fix.md +++ b/ontology/fix.md @@ -2,11 +2,6 @@ layout: ontology_detail id: fix title: Physico-chemical methods and properties -build: - infallible: 1 - insert_ontology_id: true - method: obo2owl - source_url: ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/fix.obo contact: email: null label: chEBI diff --git a/ontology/flopo.md b/ontology/flopo.md index 9d8c798e6..ba8166ad6 100644 --- a/ontology/flopo.md +++ b/ontology/flopo.md @@ -2,9 +2,6 @@ layout: ontology_detail id: flopo title: Flora Phenotype Ontology -build: - method: owl2obo - source_url: https://github.com/flora-phenotype-ontology/flopoontology/raw/master/ontology/flopo.owl contact: email: robert.hoehndorf@kaust.edu.sa github: leechuck diff --git a/ontology/flu.md b/ontology/flu.md index 2ba808650..8137948a9 100644 --- a/ontology/flu.md +++ b/ontology/flu.md @@ -2,9 +2,6 @@ layout: ontology_detail id: flu title: Influenza Ontology -build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/flu.owl contact: email: burkesquires@gmail.com label: Burke Squires diff --git a/ontology/fma.md b/ontology/fma.md index 20e9fae09..619f980ab 100644 --- a/ontology/fma.md +++ b/ontology/fma.md @@ -2,10 +2,6 @@ layout: ontology_detail id: fma title: Foundational Model of Anatomy Ontology (subset) -build: - insert_ontology_id: true - method: obo2owl - source_url: http://svn.code.sf.net/p/obo/svn/fma-conversion/trunk/fma2_obo.obo contact: email: mejino@u.washington.edu label: Onard Mejino diff --git a/ontology/fypo.md b/ontology/fypo.md index b0f5aa559..a2c26c22b 100644 --- a/ontology/fypo.md +++ b/ontology/fypo.md @@ -2,10 +2,6 @@ layout: ontology_detail id: fypo title: Fission Yeast Phenotype Ontology -build: - infallible: 1 - method: obo2owl - source_url: https://raw.githubusercontent.com/pombase/fypo/master/release/fypo.owl contact: email: vw253@cam.ac.uk github: ValWood diff --git a/ontology/geno.md b/ontology/geno.md index 7f2eb123c..fcb884cf8 100644 --- a/ontology/geno.md +++ b/ontology/geno.md @@ -2,10 +2,6 @@ layout: ontology_detail id: geno title: Genotype Ontology -build: - checkout: git clone https://github.com/monarch-initiative/GENO-ontology.git - path: src/ontology - system: git contact: email: mhb120@gmail.com github: mbrush diff --git a/ontology/gno.md b/ontology/gno.md index e1c791d47..5edf95ef0 100644 --- a/ontology/gno.md +++ b/ontology/gno.md @@ -9,10 +9,6 @@ browsers: - title: GNOme Glycan Composition Browser label: Composition Browser url: https://gnome.glyomics.org/CompositionBrowser.html?HexNAc=4&Hex=5&dHex=1&NeuAc=2 -build: - checkout: git clone https://github.com/glygen-glycan-data/GNOme.git - path: . - system: git contact: email: nje5@georgetown.edu github: edwardsnj diff --git a/ontology/gsso.md b/ontology/gsso.md index 2a21785e7..7dadc8248 100644 --- a/ontology/gsso.md +++ b/ontology/gsso.md @@ -2,10 +2,6 @@ layout: ontology_detail id: gsso title: Gender, Sex, and Sexual Orientation (GSSO) ontology -build: - checkout: git clone https://github.com/Superraptor/GSSO.git - path: . - system: git contact: email: kronkcj@mail.uc.edu github: Superraptor diff --git a/ontology/hao.md b/ontology/hao.md index da572e470..a85828c8e 100644 --- a/ontology/hao.md +++ b/ontology/hao.md @@ -2,9 +2,6 @@ layout: ontology_detail id: hao title: Hymenoptera Anatomy Ontology -build: - checkout: git clone https://github.com/hymao/hao.git - system: git contact: email: diapriid@gmail.com github: mjy diff --git a/ontology/hom.md b/ontology/hom.md index 11c2409ea..6507c3ad9 100644 --- a/ontology/hom.md +++ b/ontology/hom.md @@ -2,11 +2,6 @@ layout: ontology_detail id: hom title: Homology Ontology -build: - checkout: git clone https://github.com/BgeeDB/homology-ontology.git - method: vcs - path: src/ontology - system: git contact: email: bgee@sib.swiss github: fbastian diff --git a/ontology/iao.md b/ontology/iao.md index 5b94f29fc..7381ae99a 100644 --- a/ontology/iao.md +++ b/ontology/iao.md @@ -2,9 +2,6 @@ layout: ontology_detail id: iao title: Information Artifact Ontology -build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/iao.owl contact: email: zhengj2007@gmail.com github: zhengj2007 diff --git a/ontology/ido.md b/ontology/ido.md index 4de0cf254..0bac3b622 100644 --- a/ontology/ido.md +++ b/ontology/ido.md @@ -2,9 +2,6 @@ layout: ontology_detail id: ido title: Infectious Disease Ontology -build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/ido.owl contact: email: Lindsay.Cowell@utsouthwestern.edu github: lgcowell diff --git a/ontology/iev.md b/ontology/iev.md index 5765e9ab2..127730d36 100644 --- a/ontology/iev.md +++ b/ontology/iev.md @@ -2,10 +2,6 @@ layout: ontology_detail id: iev title: Event (INOH pathway ontology) -build: - insert_ontology_id: true - method: obo2owl - source_url: http://download.baderlab.org/INOH/ontologies/EventOntology_172.obo domain: chemistry and biochemistry homepage: http://www.inoh.org is_obsolete: true diff --git a/ontology/imr.md b/ontology/imr.md index 5baf84a74..8211ac22e 100644 --- a/ontology/imr.md +++ b/ontology/imr.md @@ -2,10 +2,6 @@ layout: ontology_detail id: imr title: Molecule role (INOH Protein name/family name ontology) -build: - insert_ontology_id: true - method: obo2owl - source_url: https://web.archive.org/web/20131127090937/http://www.inoh.org/ontologies/MoleculeRoleOntology.obo contact: email: curator@inoh.org label: INOH curators diff --git a/ontology/kisao.md b/ontology/kisao.md index ada4f660f..6350e25df 100644 --- a/ontology/kisao.md +++ b/ontology/kisao.md @@ -12,9 +12,6 @@ browsers: - title: OntoBee label: OntoBee url: https://www.ontobee.org/ontology/KISAO -build: - method: owl2obo - source_url: https://raw.githubusercontent.com/SED-ML/KiSAO/deploy/kisao.owl contact: email: jonrkarr@gmail.com github: jonrkarr diff --git a/ontology/lipro.md b/ontology/lipro.md index ad2da4abe..ec827858e 100644 --- a/ontology/lipro.md +++ b/ontology/lipro.md @@ -2,9 +2,6 @@ layout: ontology_detail id: lipro title: Lipid Ontology -build: - method: owl2obo - source_url: http://www.lipidprofiles.com/LipidOntology contact: email: bakerc@unb.ca label: Christopher Baker diff --git a/ontology/mamo.md b/ontology/mamo.md index 85c1fc7f0..11306eec2 100644 --- a/ontology/mamo.md +++ b/ontology/mamo.md @@ -2,9 +2,6 @@ layout: ontology_detail id: mamo title: Mathematical modeling ontology -build: - method: owl2obo - source_url: https://svn.code.sf.net/p/mamo-ontology/code/tags/latest/mamo-xml.owl description: The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. domain: simulation homepage: http://sourceforge.net/p/mamo-ontology/wiki/Home/ diff --git a/ontology/maxo.md b/ontology/maxo.md index ecc449d7c..ce735781e 100644 --- a/ontology/maxo.md +++ b/ontology/maxo.md @@ -2,10 +2,6 @@ layout: ontology_detail id: maxo title: Medical Action Ontology -build: - checkout: git clone https://github.com/monarch-initiative/MAxO.git - path: . - system: git contact: email: Leigh.Carmody@jax.org github: LCCarmody diff --git a/ontology/mf.md b/ontology/mf.md index 03e33fd1e..af2a9d078 100644 --- a/ontology/mf.md +++ b/ontology/mf.md @@ -2,9 +2,6 @@ layout: ontology_detail id: mf title: Mental Functioning Ontology -build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/mf.owl contact: email: janna.hastings@gmail.com github: jannahastings diff --git a/ontology/mfoem.md b/ontology/mfoem.md index 265342cc9..e5ab0266f 100644 --- a/ontology/mfoem.md +++ b/ontology/mfoem.md @@ -2,9 +2,6 @@ layout: ontology_detail id: mfoem title: Emotion Ontology -build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/mfoem.owl contact: email: janna.hastings@gmail.com github: jannahastings diff --git a/ontology/mi.md b/ontology/mi.md index 73429076a..a7ecf4542 100644 --- a/ontology/mi.md +++ b/ontology/mi.md @@ -2,10 +2,6 @@ layout: ontology_detail id: mi title: Molecular Interactions Controlled Vocabulary -build: - insert_ontology_id: true - method: obo2owl - source_url: https://raw.githubusercontent.com/HUPO-PSI/psi-mi-CV/master/psi-mi.obo contact: email: luana.licata@gmail.com github: luanalicata diff --git a/ontology/mmo.md b/ontology/mmo.md index ca33a5959..118d544de 100644 --- a/ontology/mmo.md +++ b/ontology/mmo.md @@ -6,9 +6,6 @@ browsers: - title: RGD Ontology Browser label: RGD url: http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000 -build: - method: obo2owl - source_url: https://download.rgd.mcw.edu/ontology/measurement_method/measurement_method.obo contact: email: jrsmith@mcw.edu github: jrsjrs diff --git a/ontology/mmusdv.md b/ontology/mmusdv.md index 8ea598d35..521d4e72c 100644 --- a/ontology/mmusdv.md +++ b/ontology/mmusdv.md @@ -2,9 +2,6 @@ layout: ontology_detail id: mmusdv title: Mouse Developmental Stages -build: - method: obo2owl - source_url: https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/mmusdv/mmusdv.obo contact: email: frederic.bastian@unil.ch github: fbastian diff --git a/ontology/mod.md b/ontology/mod.md index 1b7366950..54a9e5ee0 100644 --- a/ontology/mod.md +++ b/ontology/mod.md @@ -2,10 +2,6 @@ layout: ontology_detail id: mod title: Protein modification -build: - insert_ontology_id: true - method: obo2owl - source_url: https://raw.githubusercontent.com/HUPO-PSI/psi-mod-CV/master/PSI-MOD.obo contact: email: pierre-alain.binz@chuv.ch github: pabinz diff --git a/ontology/mop.md b/ontology/mop.md index f23895aad..1bdc1af0e 100644 --- a/ontology/mop.md +++ b/ontology/mop.md @@ -2,9 +2,6 @@ layout: ontology_detail id: mop title: Molecular Process Ontology -build: - method: owl2obo - source_url: https://raw.githubusercontent.com/rsc-ontologies/rxno/master/mop.owl contact: email: batchelorc@rsc.org github: batchelorc diff --git a/ontology/mpath.md b/ontology/mpath.md index 6f6621686..b90bd561b 100644 --- a/ontology/mpath.md +++ b/ontology/mpath.md @@ -2,10 +2,6 @@ layout: ontology_detail id: mpath title: Mouse pathology ontology -build: - insert_ontology_id: true - method: obo2owl - source_url: https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo contact: email: pns12@hermes.cam.ac.uk github: PaulNSchofield diff --git a/ontology/ms.md b/ontology/ms.md index e30672d7c..3f9acdb34 100644 --- a/ontology/ms.md +++ b/ontology/ms.md @@ -2,9 +2,6 @@ layout: ontology_detail id: ms title: Mass spectrometry ontology -build: - method: obo2owl - source_url: https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo contact: email: joshua.adam.klein@gmail.com github: mobiusklein diff --git a/ontology/nbo.md b/ontology/nbo.md index e1b5b337b..0d4fe0842 100644 --- a/ontology/nbo.md +++ b/ontology/nbo.md @@ -6,9 +6,6 @@ browsers: - title: BioPortal Ontology Browser label: BioPortal url: https://bioportal.bioontology.org/ontologies/NBO -build: - method: owl2obo - source_url: https://raw.githubusercontent.com/obo-behavior/behavior-ontology/master/nbo.owl contact: email: g.gkoutos@bham.ac.uk github: gkoutos diff --git a/ontology/ncro.md b/ontology/ncro.md index a7622af42..1735b5104 100644 --- a/ontology/ncro.md +++ b/ontology/ncro.md @@ -2,9 +2,6 @@ layout: ontology_detail id: ncro title: Non-Coding RNA Ontology -build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/ncro/prebuild/ncro.owl contact: email: huang@southalabama.edu github: Huang-OMIT diff --git a/ontology/nmr.md b/ontology/nmr.md index 49338144f..addd0c6f2 100644 --- a/ontology/nmr.md +++ b/ontology/nmr.md @@ -2,9 +2,6 @@ layout: ontology_detail id: nmr title: NMR-instrument specific component of metabolomics investigations -build: - method: owl2obo - source_url: https://msi-workgroups.svn.sourceforge.net/svnroot/msi-workgroups/ontology/NMR.owl contact: email: schober@imbi.uni-freiburg.de label: Schober Daniel diff --git a/ontology/nomen.md b/ontology/nomen.md index 04ca43a2a..05184dad0 100644 --- a/ontology/nomen.md +++ b/ontology/nomen.md @@ -2,9 +2,6 @@ layout: ontology_detail id: nomen title: NOMEN - A nomenclatural ontology for biological names -build: - checkout: git clone https://github.com/SpeciesFileGroup/nomen.git - system: git canonical: nomen.owl contact: email: diapriid@gmail.com diff --git a/ontology/oae.md b/ontology/oae.md index 99a6ab8a0..d8b479993 100644 --- a/ontology/oae.md +++ b/ontology/oae.md @@ -2,9 +2,6 @@ layout: ontology_detail id: oae title: Ontology of Adverse Events -build: - method: owl2obo - source_url: https://raw.githubusercontent.com/OAE-ontology/OAE/master/src/oae_merged.owl contact: email: yongqunh@med.umich.edu github: yongqunh diff --git a/ontology/obi.md b/ontology/obi.md index 9fb6670e0..0c4ad9aec 100644 --- a/ontology/obi.md +++ b/ontology/obi.md @@ -6,8 +6,6 @@ browsers: - title: BioPortal Browser label: BioPortal url: http://bioportal.bioontology.org/ontologies/OBI?p=classes -build: - source_url: http://purl.obofoundry.org/obo/obi/repository/trunk/src/ontology/branches/ contact: email: bpeters@lji.org github: bpeters42 diff --git a/ontology/ohd.md b/ontology/ohd.md index dc66e0e94..8d32b2378 100644 --- a/ontology/ohd.md +++ b/ontology/ohd.md @@ -2,9 +2,6 @@ layout: ontology_detail id: ohd title: Oral Health and Disease Ontology -build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/ohd.owl contact: email: wdduncan@gmail.com github: wdduncan diff --git a/ontology/olatdv.md b/ontology/olatdv.md index 4449c76e5..a8553851b 100644 --- a/ontology/olatdv.md +++ b/ontology/olatdv.md @@ -2,9 +2,6 @@ layout: ontology_detail id: olatdv title: Medaka Developmental Stages -build: - method: obo2owl - source_url: https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/olatdv/olatdv.obo contact: email: frederic.bastian@unil.ch github: fbastian diff --git a/ontology/omp.md b/ontology/omp.md index caee6d0c5..2c3930db5 100644 --- a/ontology/omp.md +++ b/ontology/omp.md @@ -2,9 +2,6 @@ layout: ontology_detail id: omp title: Ontology of Microbial Phenotypes -build: - method: obo2owl - source_url: https://raw.githubusercontent.com/microbialphenotypes/OMP-ontology-files/master/omp.obo contact: email: jimhu@tamu.edu github: jimhu-tamu diff --git a/ontology/omrse.md b/ontology/omrse.md index 3d1b7b4c7..a24f86bc3 100644 --- a/ontology/omrse.md +++ b/ontology/omrse.md @@ -2,9 +2,6 @@ layout: ontology_detail id: omrse title: Ontology for Modeling and Representation of Social Entities -build: - method: owl2obo - source_url: https://github.com/mcwdsi/OMRSE contact: email: hoganwr@gmail.com github: hoganwr diff --git a/ontology/ontoneo.md b/ontology/ontoneo.md index dbe152d48..ca3c78da4 100644 --- a/ontology/ontoneo.md +++ b/ontology/ontoneo.md @@ -9,8 +9,6 @@ browsers: - title: OntoBee Browser label: OntoBee url: https://ontobee.org/ontology/ONTONEO -build: - source_url: https://raw.githubusercontent.com/ontoneo-project/Ontoneo/master/ontoneo.owl contact: email: fernanda.farinelli@gmail.com github: FernandaFarinelli diff --git a/ontology/pdro.md b/ontology/pdro.md index bf5fd067b..7d587b7f0 100644 --- a/ontology/pdro.md +++ b/ontology/pdro.md @@ -2,9 +2,6 @@ layout: ontology_detail id: pdro title: The Prescription of Drugs Ontology -build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/pdro.owl contact: email: paul.fabry@usherbrooke.ca github: pfabry diff --git a/ontology/pdumdv.md b/ontology/pdumdv.md index d29601e77..496098999 100644 --- a/ontology/pdumdv.md +++ b/ontology/pdumdv.md @@ -2,9 +2,6 @@ layout: ontology_detail id: pdumdv title: Platynereis Developmental Stages -build: - method: obo2owl - source_url: https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/pdumdv/pdumdv.obo contact: email: frederic.bastian@unil.ch github: fbastian diff --git a/ontology/pr.md b/ontology/pr.md index 43f139898..ecd082ccf 100644 --- a/ontology/pr.md +++ b/ontology/pr.md @@ -9,11 +9,6 @@ browsers: - title: PRO Home label: PRO url: http://proconsortium.org -build: - infallible: 0 - method: obo2owl - oort_args: --no-reasoner - source_url: https://proconsortium.org/download/current/pro_nonreasoned.obo contact: email: dan5@georgetown.edu github: nataled diff --git a/ontology/psdo.md b/ontology/psdo.md index a393e1444..0e59de81d 100644 --- a/ontology/psdo.md +++ b/ontology/psdo.md @@ -2,10 +2,6 @@ layout: ontology_detail id: psdo title: Performance Summary Display Ontology -build: - checkout: https://github.com/Display-Lab/psdo.git - path: . - system: git contact: email: zachll@umich.edu github: zachll diff --git a/ontology/pw.md b/ontology/pw.md index 9a082ceb5..7bd1a8d49 100644 --- a/ontology/pw.md +++ b/ontology/pw.md @@ -6,9 +6,6 @@ browsers: - title: RGD Ontology Browser label: RGD url: http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=PW:0000001 -build: - method: obo2owl - source_url: https://download.rgd.mcw.edu/ontology/pathway/pathway.obo contact: email: gthayman@mcw.edu github: gthayman diff --git a/ontology/rex.md b/ontology/rex.md index 4c66e3d59..0c775b440 100644 --- a/ontology/rex.md +++ b/ontology/rex.md @@ -2,10 +2,6 @@ layout: ontology_detail id: rex title: Physico-chemical process -build: - insert_ontology_id: true - method: obo2owl - source_url: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/physicochemical/rex.obo description: An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. domain: chemistry and biochemistry products: diff --git a/ontology/rnao.md b/ontology/rnao.md index 6c3ec266f..f36c0e491 100644 --- a/ontology/rnao.md +++ b/ontology/rnao.md @@ -6,10 +6,6 @@ browsers: - title: RNA Ontology jOWL Browser label: RNAO url: http://bgsu-rna.github.io/rnao/ -build: - checkout: git clone https://github.com/BGSU-RNA/rnao.git - method: vcs - system: git contact: email: BatchelorC@rsc.org label: Colin Batchelor diff --git a/ontology/rs.md b/ontology/rs.md index cb5f8006c..0c68be155 100644 --- a/ontology/rs.md +++ b/ontology/rs.md @@ -6,9 +6,6 @@ browsers: - title: RGD Ontology Browser label: RGD url: http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=RS:0000457 -build: - method: obo2owl - source_url: https://download.rgd.mcw.edu/ontology/rat_strain/rat_strain.obo contact: email: sjwang@mcw.edu github: shurjenw diff --git a/ontology/rxno.md b/ontology/rxno.md index c3e14f3c8..84af1ed79 100644 --- a/ontology/rxno.md +++ b/ontology/rxno.md @@ -2,9 +2,6 @@ layout: ontology_detail id: rxno title: Name Reaction Ontology -build: - method: owl2obo - source_url: https://raw.githubusercontent.com/rsc-ontologies/rxno/master/rxno.owl contact: email: batchelorc@rsc.org github: batchelorc diff --git a/ontology/sbo.md b/ontology/sbo.md index f746dcaa2..3b8ca3577 100644 --- a/ontology/sbo.md +++ b/ontology/sbo.md @@ -2,10 +2,6 @@ layout: ontology_detail id: sbo title: Systems Biology Ontology -build: - insert_ontology_id: true - method: obo2owl - source_url: http://www.ebi.ac.uk/sbo/exports/Main/SBO_OBO.obo contact: email: sheriff@ebi.ac.uk github: rsmsheriff diff --git a/ontology/scdo.md b/ontology/scdo.md index 6b8fa3573..dff3d60e9 100644 --- a/ontology/scdo.md +++ b/ontology/scdo.md @@ -2,10 +2,6 @@ layout: ontology_detail id: scdo title: Sickle Cell Disease Ontology -build: - checkout: git clone https://github.com/scdodev/scdo-ontology.git - path: . - system: git contact: email: giant.plankton@gmail.com github: JadeHotchkiss diff --git a/ontology/sep.md b/ontology/sep.md index ef56ce7f9..675b9d107 100644 --- a/ontology/sep.md +++ b/ontology/sep.md @@ -2,10 +2,6 @@ layout: ontology_detail id: sep title: Sample processing and separation techniques -build: - insert_ontology_id: true - method: obo2owl - source_url: https://raw.githubusercontent.com/HUPO-PSI/gelml/master/CV/sep.obo contact: email: psidev-gps-dev@lists.sourceforge.net label: SEP developers via the PSI and MSI mailing lists diff --git a/ontology/sepio.md b/ontology/sepio.md index 334277340..b6136d8fe 100644 --- a/ontology/sepio.md +++ b/ontology/sepio.md @@ -2,10 +2,6 @@ layout: ontology_detail id: sepio title: Scientific Evidence and Provenance Information Ontology -build: - checkout: git clone https://github.com/monarch-initiative/SEPIO-ontology.git - path: src/ontology - system: git contact: email: mhb120@gmail.com github: mbrush diff --git a/ontology/sibo.md b/ontology/sibo.md index 67ea02bd6..b4c6da68c 100644 --- a/ontology/sibo.md +++ b/ontology/sibo.md @@ -2,10 +2,6 @@ layout: ontology_detail id: sibo title: Social Insect Behavior Ontology -build: - checkout: git clone https://github.com/obophenotype/sibo.git - method: vcs - system: git contact: email: cjmungall@lbl.gov label: Chris Mungall diff --git a/ontology/so.md b/ontology/so.md index 2364f4aaa..57246cfdd 100644 --- a/ontology/so.md +++ b/ontology/so.md @@ -2,10 +2,6 @@ layout: ontology_detail id: so title: Sequence types and features ontology -build: - method: obo2owl - notes: SWITCH - source_url: https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/so.obo contact: email: keilbeck@genetics.utah.edu github: keilbeck diff --git a/ontology/spd.md b/ontology/spd.md index f0fa194de..b8c3a8fa8 100644 --- a/ontology/spd.md +++ b/ontology/spd.md @@ -2,10 +2,6 @@ layout: ontology_detail id: spd title: Spider Ontology -build: - insert_ontology_id: true - method: obo2owl - source_url: https://raw.githubusercontent.com/obophenotype/spider-ontology/master/spider_comparative_biology.obo contact: email: ramirez@macn.gov.ar github: martinjramirez diff --git a/ontology/symp.md b/ontology/symp.md index 0f05998c7..b1546f529 100644 --- a/ontology/symp.md +++ b/ontology/symp.md @@ -2,10 +2,6 @@ layout: ontology_detail id: symp title: Symptom Ontology -build: - infallible: 1 - method: obo2owl - source_url: https://raw.githubusercontent.com/DiseaseOntology/SymptomOntology/master/src/ontology/symp.obo contact: email: lynn.schriml@gmail.com github: lschriml diff --git a/ontology/tao.md b/ontology/tao.md index 2da55c53d..5fc83bb81 100644 --- a/ontology/tao.md +++ b/ontology/tao.md @@ -2,9 +2,6 @@ layout: ontology_detail id: tao title: Teleost Anatomy Ontology -build: - method: obo2owl - source_url: http://purl.obolibrary.org/obo/tao.obo contact: email: wasila.dahdul@usd.edu label: Wasila Dahdul diff --git a/ontology/trans.md b/ontology/trans.md index 7432e6e38..dda8b7b2d 100644 --- a/ontology/trans.md +++ b/ontology/trans.md @@ -2,10 +2,6 @@ layout: ontology_detail id: trans title: Pathogen Transmission Ontology -build: - infallible: 1 - method: obo2owl - source_url: https://raw.githubusercontent.com/DiseaseOntology/PathogenTransmissionOntology/master/src/ontology/trans.obo contact: email: lynn.schriml@gmail.com github: lschriml diff --git a/ontology/uberon.md b/ontology/uberon.md index 1cd435226..51d7c1f51 100644 --- a/ontology/uberon.md +++ b/ontology/uberon.md @@ -18,11 +18,6 @@ browsers: - title: INCF KnowledgeSpace Portal label: KnowledgeSpace url: https://knowledge-space.org/index.php/pages/view/UBERON:0000061 -build: - checkout: git clone https://github.com/obophenotype/uberon.git - email_cc: cjmungall@lbl.gov - infallible: 1 - system: git canonical: uberon.owl contact: email: cjmungall@lbl.gov diff --git a/ontology/uo.md b/ontology/uo.md index c3af9a1e6..66dfbc1fd 100644 --- a/ontology/uo.md +++ b/ontology/uo.md @@ -2,9 +2,6 @@ layout: ontology_detail id: uo title: Units of measurement ontology -build: - method: obo2owl - source_url: https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo contact: email: g.gkoutos@gmail.com github: gkoutos diff --git a/ontology/upheno.md b/ontology/upheno.md index 3ae3a456f..a6ba6f4b5 100644 --- a/ontology/upheno.md +++ b/ontology/upheno.md @@ -2,10 +2,6 @@ layout: ontology_detail id: upheno title: Unified Phenotype Ontology (uPheno) -build: - method: archive - path: archive/ontology - source_url: http://build.berkeleybop.org/job/build-pheno-ontologies/lastSuccessfulBuild/artifact/*zip*/archive.zip contact: email: jmcl@ebi.ac.uk github: jamesamcl diff --git a/ontology/vario.md b/ontology/vario.md index 3f3e4ec39..523881964 100644 --- a/ontology/vario.md +++ b/ontology/vario.md @@ -2,9 +2,6 @@ layout: ontology_detail id: vario title: Variation Ontology -build: - method: obo2owl - source_url: http://variationontology.org/vario_download/vario.obo contact: email: mauno.vihinen@med.lu.se github: maunov diff --git a/ontology/vo.md b/ontology/vo.md index 4bf4a337d..e6aeb5adb 100644 --- a/ontology/vo.md +++ b/ontology/vo.md @@ -2,8 +2,6 @@ layout: ontology_detail id: vo title: Vaccine Ontology -build: - source_url: https://raw.githubusercontent.com/vaccineontology/VO/master/src/VO_merged.owl contact: email: yongqunh@med.umich.edu github: yongqunh diff --git a/ontology/vsao.md b/ontology/vsao.md index ced5307a0..1780bd393 100644 --- a/ontology/vsao.md +++ b/ontology/vsao.md @@ -2,9 +2,6 @@ layout: ontology_detail id: vsao title: Vertebrate Skeletal Anatomy Ontology- -build: - method: obo2owl - source_url: http://phenoscape.svn.sourceforge.net/svnroot/phenoscape/tags/vocab-releases/VSAO/vsao.obo contact: email: wasila.dahdul@usd.edu label: Wasila Dahdul diff --git a/ontology/vt.md b/ontology/vt.md index d6967b3c8..37ef5e0d8 100644 --- a/ontology/vt.md +++ b/ontology/vt.md @@ -2,10 +2,6 @@ layout: ontology_detail id: vt title: Vertebrate trait ontology -build: - checkout: svn co http://phenotype-ontologies.googlecode.com/svn/trunk/src/ontology/vt - method: vcs - system: svn contact: email: caripark@iastate.edu github: caripark diff --git a/ontology/wbbt.md b/ontology/wbbt.md index df8c1940b..140c703e4 100644 --- a/ontology/wbbt.md +++ b/ontology/wbbt.md @@ -2,10 +2,6 @@ layout: ontology_detail id: wbbt title: C. elegans Gross Anatomy Ontology -build: - checkout: git clone https://github.com/obophenotype/c-elegans-gross-anatomy-ontology.git - path: . - system: git contact: email: raymond@caltech.edu github: raymond91125 diff --git a/ontology/wbls.md b/ontology/wbls.md index a96e64697..a00616352 100644 --- a/ontology/wbls.md +++ b/ontology/wbls.md @@ -2,10 +2,6 @@ layout: ontology_detail id: wbls title: C. elegans development ontology -build: - checkout: git clone https://github.com/obophenotype/c-elegans-development-ontology.git - path: . - system: git contact: email: cgrove@caltech.edu github: chris-grove diff --git a/ontology/wbphenotype.md b/ontology/wbphenotype.md index 80ffd9163..82ed037a2 100644 --- a/ontology/wbphenotype.md +++ b/ontology/wbphenotype.md @@ -2,10 +2,6 @@ layout: ontology_detail id: wbphenotype title: C. elegans phenotype -build: - checkout: git clone https://github.com/obophenotype/c-elegans-phenotype-ontology.git - path: . - system: git contact: email: cgrove@caltech.edu github: chris-grove diff --git a/ontology/xao.md b/ontology/xao.md index 3a1391ac0..3abf67bde 100644 --- a/ontology/xao.md +++ b/ontology/xao.md @@ -2,10 +2,6 @@ layout: ontology_detail id: xao title: Xenopus Anatomy Ontology -build: - infallible: 0 - method: obo2owl - source_url: https://raw.githubusercontent.com/xenopus-anatomy/xao/master/xenopus_anatomy.obo contact: email: Erik.Segerdell@cchmc.org github: seger diff --git a/ontology/xco.md b/ontology/xco.md index 4ed14055f..d2c9f0f62 100644 --- a/ontology/xco.md +++ b/ontology/xco.md @@ -6,9 +6,6 @@ browsers: - title: RGD Ontology Browser label: RGD url: http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000 -build: - method: obo2owl - source_url: https://download.rgd.mcw.edu/ontology/experimental_condition/experimental_condition.obo contact: email: jrsmith@mcw.edu github: jrsjrs diff --git a/ontology/zeco.md b/ontology/zeco.md index 6e4a4c1cb..c71691c7e 100644 --- a/ontology/zeco.md +++ b/ontology/zeco.md @@ -2,9 +2,6 @@ layout: ontology_detail id: zeco title: Zebrafish Experimental Conditions Ontology -build: - method: obo2owl - source_url: https://raw.githubusercontent.com/ybradford/zebrafish-experimental-conditions-ontology/master/zeco.obo contact: email: ybradford@zfin.org github: ybradford diff --git a/ontology/zfa.md b/ontology/zfa.md index b8b447ddc..088843b56 100644 --- a/ontology/zfa.md +++ b/ontology/zfa.md @@ -2,11 +2,6 @@ layout: ontology_detail id: zfa title: Zebrafish anatomy and development ontology -build: - infallible: 1 - method: obo2owl - notes: may be ready to switch to vcs soon - source_url: https://raw.githubusercontent.com/cerivs/zebrafish-anatomical-ontology/master/src/zebrafish_anatomy.obo contact: email: van_slyke@zfin.org github: cerivs diff --git a/ontology/zfs.md b/ontology/zfs.md index b254fa381..def13ff81 100644 --- a/ontology/zfs.md +++ b/ontology/zfs.md @@ -2,10 +2,6 @@ layout: ontology_detail id: zfs title: Zebrafish developmental stages ontology -build: - infallible: 1 - method: obo2owl - source_url: https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/zfs/zfs.obo contact: email: van_slyke@zfin.org github: cerivs diff --git a/registry/ontologies.jsonld b/registry/ontologies.jsonld index 141351520..78151f729 100644 --- a/registry/ontologies.jsonld +++ b/registry/ontologies.jsonld @@ -182,11 +182,6 @@ }, { "activity_status": "active", - "build": { - "checkout": "git clone https://github.com/insect-morphology/aism", - "path": ".", - "system": "git" - }, "contact": { "email": "entiminae@gmail.com", "github": "JCGiron", @@ -245,11 +240,6 @@ }, { "activity_status": "active", - "build": { - "checkout": "git clone https://github.com/EBISPOT/amphx_ontology.git", - "path": ".", - "system": "git" - }, "contact": { "email": "hescriva@obs-banyuls.fr", "github": "hescriva", @@ -289,10 +279,6 @@ }, { "activity_status": "active", - "build": { - "method": "obo2owl", - "source_url": "https://raw.githubusercontent.com/obophenotype/ascomycete-phenotype-ontology/master/apo.obo" - }, "contact": { "email": "stacia@stanford.edu", "github": "srengel", @@ -553,13 +539,6 @@ }, { "activity_status": "active", - "build": { - "checkout": "git clone https://github.com/obophenotype/biological-spatial-ontology.git", - "infallible": 1, - "method": "vcs", - "path": "src/ontology", - "system": "git" - }, "contact": { "email": "cjmungall@lbl.gov", "github": "cmungall", @@ -600,11 +579,6 @@ }, { "activity_status": "active", - "build": { - "checkout": "git clone https://github.com/BRENDA-Enzymes/BTO.git", - "path": ".", - "system": "git" - }, "contact": { "email": "c.dudek@tu-braunschweig.de", "github": "chdudek", @@ -650,10 +624,6 @@ }, { "activity_status": "active", - "build": { - "method": "owl2obo", - "source_url": "http://purl.obolibrary.org/obo/cdao.owl" - }, "contact": { "email": "balhoff@renci.org", "github": "balhoff", @@ -690,11 +660,6 @@ }, { "activity_status": "active", - "build": { - "checkout": "git clone https://github.com/CompositionalDietaryNutritionOntology/cdno.git", - "path": ".", - "system": "git" - }, "contact": { "email": "landreshdz@gmail.com", "github": "LilyAndres", @@ -761,11 +726,6 @@ "url": "http://www.ebi.ac.uk/chebi/chebiOntology.do?treeView=true&chebiId=CHEBI:24431#graphView" } ], - "build": { - "infallible": 1, - "method": "obo2owl", - "source_url": "ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo" - }, "contact": { "email": "amalik@ebi.ac.uk", "github": "amalik01", @@ -855,10 +815,6 @@ }, { "activity_status": "active", - "build": { - "method": "owl2obo", - "source_url": "https://raw.githubusercontent.com/semanticchemistry/semanticchemistry/master/ontology/cheminf.owl" - }, "contact": { "email": "egon.willighagen@gmail.com", "github": "egonw", @@ -1347,11 +1303,6 @@ }, { "activity_status": "active", - "build": { - "checkout": "git clone https://github.com/luis-gonzalez-m/Collembola.git", - "path": ".", - "system": "git" - }, "contact": { "email": "lagonzalezmo@unal.edu.co", "github": "luis-gonzalez-m", @@ -1442,11 +1393,6 @@ }, { "activity_status": "active", - "build": { - "checkout": "git clone https://github.com/EBISPOT/clyh_ontology.git", - "path": ".", - "system": "git" - }, "contact": { "email": "lucas.leclere@obs-banyuls.fr", "github": "Leclere-L", @@ -1500,10 +1446,6 @@ "url": "http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=CMO:0000000" } ], - "build": { - "method": "obo2owl", - "source_url": "https://download.rgd.mcw.edu/ontology/clinical_measurement/clinical_measurement.obo" - }, "contact": { "email": "jrsmith@mcw.edu", "github": "jrsjrs", @@ -1686,11 +1628,6 @@ }, { "activity_status": "active", - "build": { - "checkout": "git clone https://github.com/data2health/contributor-role-ontology.git", - "path": "src/ontology", - "system": "git" - }, "contact": { "email": "whimar@ohsu.edu", "github": "marijane", @@ -1797,16 +1734,6 @@ }, { "activity_status": "active", - "build": { - "method": "owl2obo", - "publications": [ - { - "id": "http://dx.doi.org/10.3233/978-1-61499-438-1-409", - "title": "The Cardiovascular Disease Ontology" - } - ], - "source_url": "http://purl.obolibrary.org/obo/cvdo.owl" - }, "contact": { "email": "paul.fabry@usherbrooke.ca", "github": "pfabry", @@ -1837,11 +1764,6 @@ }, { "activity_status": "active", - "build": { - "insert_ontology_id": true, - "method": "obo2owl", - "source_url": "https://raw.githubusercontent.com/dictyBase/migration-data/master/ontologies/dicty_anatomy.obo" - }, "contact": { "email": "pfey@northwestern.edu", "github": "pfey03", @@ -1887,11 +1809,6 @@ }, { "activity_status": "active", - "build": { - "checkout": "git clone https://github.com/obophenotype/dicty-phenotype-ontology.git", - "path": ".", - "system": "git" - }, "contact": { "email": "pfey@northwestern.edu", "github": "pfey03", @@ -1974,9 +1891,6 @@ "url": "https://disease-ontology.org/" } ], - "build": { - "source_url": "https://raw.githubusercontent.com/DiseaseOntology/DiseaseDriversOntology/refs/heads/main/src/ontology/disdriv.owl" - }, "contact": { "email": "lynn.schriml@gmail.com", "github": "lschriml", @@ -2034,11 +1948,6 @@ "url": "https://disease-ontology.org/do" } ], - "build": { - "infallible": 1, - "method": "obo2owl", - "source_url": "https://raw.githubusercontent.com/DiseaseOntology/HumanDiseaseOntology/master/src/ontology/doid.obo" - }, "contact": { "email": "lynn.schriml@gmail.com", "github": "lschriml", @@ -2138,11 +2047,6 @@ "url": "http://flybase.org/.bin/cvreport.html?cvterm=FBcv:0000347" } ], - "build": { - "checkout": "git clone https://github.com/FlyBase/drosophila-phenotype-ontolog.git", - "path": ".", - "system": "git" - }, "contact": { "email": "cp390@cam.ac.uk", "github": "Clare72", @@ -2203,10 +2107,6 @@ }, { "activity_status": "active", - "build": { - "method": "owl2obo", - "source_url": "http://purl.obolibrary.org/obo/dron.owl" - }, "contact": { "email": "hoganwr@gmail.com", "github": "hoganwr", @@ -2294,11 +2194,6 @@ }, { "activity_status": "active", - "build": { - "checkout": "git clone https://github.com/echinoderm-ontology/ecao_ontology.git", - "path": ".", - "system": "git" - }, "contact": { "email": "ettensohn@cmu.edu", "github": "ettensohn", @@ -2605,11 +2500,6 @@ }, { "activity_status": "active", - "build": { - "method": "obo2owl", - "notes": "new url soon", - "source_url": "ftp://ftp.hgu.mrc.ac.uk/pub/MouseAtlas/Anatomy/EMAPA.obo" - }, "contact": { "email": "Terry.Hayamizu@jax.org", "github": "tfhayamizu", @@ -2936,12 +2826,6 @@ }, { "activity_status": "active", - "build": { - "checkout": "git clone https://github.com/obophenotype/fungal-anatomy-ontology.git", - "infallible": 1, - "method": "vcs", - "system": "git" - }, "contact": { "email": "vw253@cam.ac.uk", "github": "ValWood", @@ -2980,11 +2864,6 @@ }, { "activity_status": "active", - "build": { - "checkout": "git clone https://github.com/foundingGIDE/fbbi.git", - "path": ".", - "system": "git" - }, "contact": { "email": "damien@gerbi-gmb.de", "github": "gouttegd", @@ -3084,11 +2963,6 @@ "url": "http://bioportal.bioontology.org/ontologies/FB-BT?p=classes" } ], - "build": { - "checkout": "git clone https://github.com/FlyBase/drosophila-anatomy-developmental-ontology.git", - "path": ".", - "system": "git" - }, "contact": { "email": "cp390@cam.ac.uk", "github": "Clare72", @@ -3194,11 +3068,6 @@ "url": "http://flybase.org/.bin/cvreport.html?cvterm=FBcv:0000013" } ], - "build": { - "checkout": "git clone https://github.com/FlyBase/flybase-controlled-vocabulary.git", - "path": ".", - "system": "git" - }, "contact": { "email": "cp390@cam.ac.uk", "github": "Clare72", @@ -3257,11 +3126,6 @@ "url": "http://flybase.org/.bin/cvreport.html?cvterm=FBdv:00007008" } ], - "build": { - "checkout": "git clone https://github.com/FlyBase/drosophila-developmental-ontology.git", - "path": ".", - "system": "git" - }, "contact": { "email": "cp390@cam.ac.uk", "github": "Clare72", @@ -3355,10 +3219,6 @@ }, { "activity_status": "active", - "build": { - "method": "owl2obo", - "source_url": "https://github.com/flora-phenotype-ontology/flopoontology/raw/master/ontology/flopo.owl" - }, "contact": { "email": "robert.hoehndorf@kaust.edu.sa", "github": "leechuck", @@ -3629,11 +3489,6 @@ }, { "activity_status": "active", - "build": { - "infallible": 1, - "method": "obo2owl", - "source_url": "https://raw.githubusercontent.com/pombase/fypo/master/release/fypo.owl" - }, "contact": { "email": "vw253@cam.ac.uk", "github": "ValWood", @@ -3884,11 +3739,6 @@ }, { "activity_status": "active", - "build": { - "checkout": "git clone https://github.com/monarch-initiative/GENO-ontology.git", - "path": "src/ontology", - "system": "git" - }, "contact": { "email": "mhb120@gmail.com", "github": "mbrush", @@ -3965,11 +3815,6 @@ "url": "https://gnome.glyomics.org/CompositionBrowser.html?HexNAc=4&Hex=5&dHex=1&NeuAc=2" } ], - "build": { - "checkout": "git clone https://github.com/glygen-glycan-data/GNOme.git", - "path": ".", - "system": "git" - }, "contact": { "email": "nje5@georgetown.edu", "github": "edwardsnj", @@ -4362,10 +4207,6 @@ }, { "activity_status": "active", - "build": { - "checkout": "git clone https://github.com/hymao/hao.git", - "system": "git" - }, "contact": { "email": "diapriid@gmail.com", "github": "mjy", @@ -4414,12 +4255,6 @@ }, { "activity_status": "active", - "build": { - "checkout": "git clone https://github.com/BgeeDB/homology-ontology.git", - "method": "vcs", - "path": "src/ontology", - "system": "git" - }, "contact": { "email": "bgee@sib.swiss", "github": "fbastian", @@ -4571,10 +4406,6 @@ }, { "activity_status": "active", - "build": { - "method": "owl2obo", - "source_url": "http://purl.obolibrary.org/obo/iao.owl" - }, "contact": { "email": "zhengj2007@gmail.com", "github": "zhengj2007", @@ -4709,10 +4540,6 @@ }, { "activity_status": "active", - "build": { - "method": "owl2obo", - "source_url": "http://purl.obolibrary.org/obo/ido.owl" - }, "contact": { "email": "Lindsay.Cowell@utsouthwestern.edu", "github": "lgcowell", @@ -4966,11 +4793,6 @@ }, { "activity_status": "active", - "build": { - "checkout": "git clone https://github.com/monarch-initiative/MAxO.git", - "path": ".", - "system": "git" - }, "contact": { "email": "Leigh.Carmody@jax.org", "github": "LCCarmody", @@ -5216,10 +5038,6 @@ }, { "activity_status": "active", - "build": { - "method": "owl2obo", - "source_url": "http://purl.obolibrary.org/obo/mf.owl" - }, "contact": { "email": "janna.hastings@gmail.com", "github": "jannahastings", @@ -5250,10 +5068,6 @@ }, { "activity_status": "active", - "build": { - "method": "owl2obo", - "source_url": "http://purl.obolibrary.org/obo/mfoem.owl" - }, "contact": { "email": "janna.hastings@gmail.com", "github": "jannahastings", @@ -5314,11 +5128,6 @@ }, { "activity_status": "active", - "build": { - "insert_ontology_id": true, - "method": "obo2owl", - "source_url": "https://raw.githubusercontent.com/HUPO-PSI/psi-mi-CV/master/psi-mi.obo" - }, "contact": { "email": "luana.licata@gmail.com", "github": "luanalicata", @@ -5399,10 +5208,6 @@ "url": "http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000" } ], - "build": { - "method": "obo2owl", - "source_url": "https://download.rgd.mcw.edu/ontology/measurement_method/measurement_method.obo" - }, "contact": { "email": "jrsmith@mcw.edu", "github": "jrsjrs", @@ -5451,10 +5256,6 @@ }, { "activity_status": "active", - "build": { - "method": "obo2owl", - "source_url": "https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/mmusdv/mmusdv.obo" - }, "contact": { "email": "frederic.bastian@unil.ch", "github": "fbastian", @@ -5490,11 +5291,6 @@ }, { "activity_status": "active", - "build": { - "insert_ontology_id": true, - "method": "obo2owl", - "source_url": "https://raw.githubusercontent.com/HUPO-PSI/psi-mod-CV/master/PSI-MOD.obo" - }, "contact": { "email": "pierre-alain.binz@chuv.ch", "github": "pabinz", @@ -5691,10 +5487,6 @@ }, { "activity_status": "active", - "build": { - "method": "owl2obo", - "source_url": "https://raw.githubusercontent.com/rsc-ontologies/rxno/master/mop.owl" - }, "contact": { "email": "batchelorc@rsc.org", "github": "batchelorc", @@ -5851,11 +5643,6 @@ }, { "activity_status": "active", - "build": { - "insert_ontology_id": true, - "method": "obo2owl", - "source_url": "https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo" - }, "contact": { "email": "pns12@hermes.cam.ac.uk", "github": "PaulNSchofield", @@ -5972,10 +5759,6 @@ }, { "activity_status": "active", - "build": { - "method": "obo2owl", - "source_url": "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo" - }, "contact": { "email": "joshua.adam.klein@gmail.com", "github": "mobiusklein", @@ -6038,10 +5821,6 @@ "url": "https://bioportal.bioontology.org/ontologies/NBO" } ], - "build": { - "method": "owl2obo", - "source_url": "https://raw.githubusercontent.com/obo-behavior/behavior-ontology/master/nbo.owl" - }, "contact": { "email": "g.gkoutos@bham.ac.uk", "github": "gkoutos", @@ -6195,10 +5974,6 @@ }, { "activity_status": "active", - "build": { - "method": "owl2obo", - "source_url": "http://purl.obolibrary.org/obo/ncro/prebuild/ncro.owl" - }, "contact": { "email": "huang@southalabama.edu", "github": "Huang-OMIT", @@ -6263,10 +6038,6 @@ }, { "activity_status": "active", - "build": { - "checkout": "git clone https://github.com/SpeciesFileGroup/nomen.git", - "system": "git" - }, "canonical": "nomen.owl", "contact": { "email": "diapriid@gmail.com", @@ -6321,10 +6092,6 @@ }, { "activity_status": "active", - "build": { - "method": "owl2obo", - "source_url": "https://raw.githubusercontent.com/OAE-ontology/OAE/master/src/oae_merged.owl" - }, "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", @@ -6556,9 +6323,6 @@ "url": "http://bioportal.bioontology.org/ontologies/OBI?p=classes" } ], - "build": { - "source_url": "http://purl.obofoundry.org/obo/obi/repository/trunk/src/ontology/branches/" - }, "contact": { "email": "bpeters@lji.org", "github": "bpeters42", @@ -6843,10 +6607,6 @@ }, { "activity_status": "active", - "build": { - "method": "owl2obo", - "source_url": "http://purl.obolibrary.org/obo/ohd.owl" - }, "contact": { "email": "wdduncan@gmail.com", "github": "wdduncan", @@ -7028,10 +6788,6 @@ }, { "activity_status": "active", - "build": { - "method": "obo2owl", - "source_url": "https://raw.githubusercontent.com/microbialphenotypes/OMP-ontology-files/master/omp.obo" - }, "contact": { "email": "jimhu@tamu.edu", "github": "jimhu-tamu", @@ -7072,10 +6828,6 @@ }, { "activity_status": "active", - "build": { - "method": "owl2obo", - "source_url": "https://github.com/mcwdsi/OMRSE" - }, "contact": { "email": "hoganwr@gmail.com", "github": "hoganwr", @@ -7364,9 +7116,6 @@ "url": "https://ontobee.org/ontology/ONTONEO" } ], - "build": { - "source_url": "https://raw.githubusercontent.com/ontoneo-project/Ontoneo/master/ontoneo.owl" - }, "contact": { "email": "fernanda.farinelli@gmail.com", "github": "FernandaFarinelli", @@ -7925,10 +7674,6 @@ }, { "activity_status": "active", - "build": { - "method": "owl2obo", - "source_url": "http://purl.obolibrary.org/obo/pdro.owl" - }, "contact": { "email": "paul.fabry@usherbrooke.ca", "github": "pfabry", @@ -8369,12 +8114,6 @@ "url": "http://proconsortium.org" } ], - "build": { - "infallible": 0, - "method": "obo2owl", - "oort_args": "--no-reasoner", - "source_url": "https://proconsortium.org/download/current/pro_nonreasoned.obo" - }, "contact": { "email": "dan5@georgetown.edu", "github": "nataled", @@ -8509,11 +8248,6 @@ }, { "activity_status": "active", - "build": { - "checkout": "https://github.com/Display-Lab/psdo.git", - "path": ".", - "system": "git" - }, "contact": { "email": "zachll@umich.edu", "github": "zachll", @@ -8618,10 +8352,6 @@ "url": "http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=PW:0000001" } ], - "build": { - "method": "obo2owl", - "source_url": "https://download.rgd.mcw.edu/ontology/pathway/pathway.obo" - }, "contact": { "email": "gthayman@mcw.edu", "github": "gthayman", @@ -8860,10 +8590,6 @@ "url": "http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=RS:0000457" } ], - "build": { - "method": "obo2owl", - "source_url": "https://download.rgd.mcw.edu/ontology/rat_strain/rat_strain.obo" - }, "contact": { "email": "sjwang@mcw.edu", "github": "shurjenw", @@ -8910,10 +8636,6 @@ }, { "activity_status": "active", - "build": { - "method": "owl2obo", - "source_url": "https://raw.githubusercontent.com/rsc-ontologies/rxno/master/rxno.owl" - }, "contact": { "email": "batchelorc@rsc.org", "github": "batchelorc", @@ -8946,11 +8668,6 @@ }, { "activity_status": "active", - "build": { - "checkout": "git clone https://github.com/monarch-initiative/SEPIO-ontology.git", - "path": "src/ontology", - "system": "git" - }, "contact": { "email": "mhb120@gmail.com", "github": "mbrush", @@ -9037,11 +8754,6 @@ }, { "activity_status": "active", - "build": { - "method": "obo2owl", - "notes": "SWITCH", - "source_url": "https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/so.obo" - }, "contact": { "email": "keilbeck@genetics.utah.edu", "github": "keilbeck", @@ -9106,11 +8818,6 @@ }, { "activity_status": "active", - "build": { - "insert_ontology_id": true, - "method": "obo2owl", - "source_url": "https://raw.githubusercontent.com/obophenotype/spider-ontology/master/spider_comparative_biology.obo" - }, "contact": { "email": "ramirez@macn.gov.ar", "github": "martinjramirez", @@ -9274,11 +8981,6 @@ }, { "activity_status": "active", - "build": { - "infallible": 1, - "method": "obo2owl", - "source_url": "https://raw.githubusercontent.com/DiseaseOntology/SymptomOntology/master/src/ontology/symp.obo" - }, "contact": { "email": "lynn.schriml@gmail.com", "github": "lschriml", @@ -9535,11 +9237,6 @@ }, { "activity_status": "active", - "build": { - "infallible": 1, - "method": "obo2owl", - "source_url": "https://raw.githubusercontent.com/DiseaseOntology/PathogenTransmissionOntology/master/src/ontology/trans.obo" - }, "contact": { "email": "lynn.schriml@gmail.com", "github": "lschriml", @@ -9724,12 +9421,6 @@ "url": "https://knowledge-space.org/index.php/pages/view/UBERON:0000061" } ], - "build": { - "checkout": "git clone https://github.com/obophenotype/uberon.git", - "email_cc": "cjmungall@lbl.gov", - "infallible": 1, - "system": "git" - }, "canonical": "uberon.owl", "contact": { "email": "cjmungall@lbl.gov", @@ -9983,10 +9674,6 @@ }, { "activity_status": "active", - "build": { - "method": "obo2owl", - "source_url": "https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo" - }, "contact": { "email": "g.gkoutos@gmail.com", "github": "gkoutos", @@ -10032,11 +9719,6 @@ }, { "activity_status": "active", - "build": { - "method": "archive", - "path": "archive/ontology", - "source_url": "http://build.berkeleybop.org/job/build-pheno-ontologies/lastSuccessfulBuild/artifact/*zip*/archive.zip" - }, "contact": { "email": "jmcl@ebi.ac.uk", "github": "jamesamcl", @@ -10211,9 +9893,6 @@ }, { "activity_status": "active", - "build": { - "source_url": "https://raw.githubusercontent.com/vaccineontology/VO/master/src/VO_merged.owl" - }, "contact": { "email": "yongqunh@med.umich.edu", "github": "yongqunh", @@ -10300,11 +9979,6 @@ }, { "activity_status": "active", - "build": { - "checkout": "svn co http://phenotype-ontologies.googlecode.com/svn/trunk/src/ontology/vt", - "method": "vcs", - "system": "svn" - }, "contact": { "email": "caripark@iastate.edu", "github": "caripark", @@ -10413,11 +10087,6 @@ }, { "activity_status": "active", - "build": { - "checkout": "git clone https://github.com/obophenotype/c-elegans-gross-anatomy-ontology.git", - "path": ".", - "system": "git" - }, "contact": { "email": "raymond@caltech.edu", "github": "raymond91125", @@ -10481,11 +10150,6 @@ }, { "activity_status": "active", - "build": { - "checkout": "git clone https://github.com/obophenotype/c-elegans-development-ontology.git", - "path": ".", - "system": "git" - }, "contact": { "email": "cgrove@caltech.edu", "github": "chris-grove", @@ -10552,11 +10216,6 @@ }, { "activity_status": "active", - "build": { - "checkout": "git clone https://github.com/obophenotype/c-elegans-phenotype-ontology.git", - "path": ".", - "system": "git" - }, "contact": { "email": "cgrove@caltech.edu", "github": "chris-grove", @@ -10641,11 +10300,6 @@ }, { "activity_status": "active", - "build": { - "infallible": 0, - "method": "obo2owl", - "source_url": "https://raw.githubusercontent.com/xenopus-anatomy/xao/master/xenopus_anatomy.obo" - }, "contact": { "email": "Erik.Segerdell@cchmc.org", "github": "seger", @@ -10714,10 +10368,6 @@ "url": "http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000" } ], - "build": { - "method": "obo2owl", - "source_url": "https://download.rgd.mcw.edu/ontology/experimental_condition/experimental_condition.obo" - }, "contact": { "email": "jrsmith@mcw.edu", "github": "jrsjrs", @@ -10877,10 +10527,6 @@ }, { "activity_status": "active", - "build": { - "method": "obo2owl", - "source_url": "https://raw.githubusercontent.com/ybradford/zebrafish-experimental-conditions-ontology/master/zeco.obo" - }, "contact": { "email": "ybradford@zfin.org", "github": "ybradford", @@ -10923,12 +10569,6 @@ }, { "activity_status": "active", - "build": { - "infallible": 1, - "method": "obo2owl", - "notes": "may be ready to switch to vcs soon", - "source_url": "https://raw.githubusercontent.com/cerivs/zebrafish-anatomical-ontology/master/src/zebrafish_anatomy.obo" - }, "contact": { "email": "van_slyke@zfin.org", "github": "cerivs", @@ -10986,11 +10626,6 @@ }, { "activity_status": "active", - "build": { - "infallible": 1, - "method": "obo2owl", - "source_url": "https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/zfs/zfs.obo" - }, "contact": { "email": "van_slyke@zfin.org", "github": "cerivs", @@ -11107,11 +10742,6 @@ }, { "activity_status": "active", - "build": { - "checkout": "git clone https://github.com/Superraptor/GSSO.git", - "path": ".", - "system": "git" - }, "contact": { "email": "kronkcj@mail.uc.edu", "github": "Superraptor", @@ -11377,10 +11007,6 @@ "url": "https://www.ontobee.org/ontology/KISAO" } ], - "build": { - "method": "owl2obo", - "source_url": "https://raw.githubusercontent.com/SED-ML/KiSAO/deploy/kisao.owl" - }, "contact": { "email": "jonrkarr@gmail.com", "github": "jonrkarr", @@ -11481,11 +11107,6 @@ }, { "activity_status": "active", - "build": { - "insert_ontology_id": true, - "method": "obo2owl", - "source_url": "http://www.ebi.ac.uk/sbo/exports/Main/SBO_OBO.obo" - }, "contact": { "email": "sheriff@ebi.ac.uk", "github": "rsmsheriff", @@ -11515,11 +11136,6 @@ }, { "activity_status": "active", - "build": { - "checkout": "git clone https://github.com/scdodev/scdo-ontology.git", - "path": ".", - "system": "git" - }, "contact": { "email": "giant.plankton@gmail.com", "github": "JadeHotchkiss", @@ -11665,12 +11281,6 @@ }, { "activity_status": "orphaned", - "build": { - "infallible": 1, - "insert_ontology_id": true, - "method": "obo2owl", - "source_url": "ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/fix.obo" - }, "contact": { "email": null, "label": "chEBI" @@ -11696,10 +11306,6 @@ }, { "activity_status": "orphaned", - "build": { - "method": "owl2obo", - "source_url": "https://svn.code.sf.net/p/mamo-ontology/code/tags/latest/mamo-xml.owl" - }, "description": "The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features.", "domain": "simulation", "homepage": "http://sourceforge.net/p/mamo-ontology/wiki/Home/", @@ -11723,11 +11329,6 @@ }, { "activity_status": "orphaned", - "build": { - "insert_ontology_id": true, - "method": "obo2owl", - "source_url": "http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/physicochemical/rex.obo" - }, "description": "An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time.", "domain": "chemistry and biochemistry", "id": "rex", @@ -11743,11 +11344,6 @@ }, { "activity_status": "orphaned", - "build": { - "checkout": "git clone https://github.com/obophenotype/sibo.git", - "method": "vcs", - "system": "git" - }, "contact": { "email": "cjmungall@lbl.gov", "label": "Chris Mungall", @@ -11784,10 +11380,6 @@ }, { "activity_status": "orphaned", - "build": { - "method": "obo2owl", - "source_url": "http://variationontology.org/vario_download/vario.obo" - }, "contact": { "email": "mauno.vihinen@med.lu.se", "github": "maunov", @@ -11996,10 +11588,6 @@ }, { "activity_status": "inactive", - "build": { - "method": "obo2owl", - "source_url": "https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/olatdv/olatdv.obo" - }, "contact": { "email": "frederic.bastian@unil.ch", "github": "fbastian", @@ -12035,10 +11623,6 @@ }, { "activity_status": "inactive", - "build": { - "method": "obo2owl", - "source_url": "https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/pdumdv/pdumdv.obo" - }, "contact": { "email": "frederic.bastian@unil.ch", "github": "fbastian", @@ -12074,12 +11658,6 @@ }, { "activity_status": "inactive", - "build": { - "checkout": "git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git", - "method": "vcs", - "path": "src/ontology", - "system": "git" - }, "contact": { "email": "J.Bard@ed.ac.uk", "label": "Jonathan Bard" @@ -12147,12 +11725,6 @@ }, { "activity_status": "inactive", - "build": { - "checkout": "git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git", - "method": "vcs", - "path": "src/ontology", - "system": "git" - }, "contact": { "email": "J.Bard@ed.ac.uk", "label": "Jonathan Bard" @@ -12205,11 +11777,6 @@ }, { "activity_status": "inactive", - "build": { - "insert_ontology_id": true, - "method": "obo2owl", - "source_url": "http://svn.code.sf.net/p/obo/svn/fma-conversion/trunk/fma2_obo.obo" - }, "contact": { "email": "mejino@u.washington.edu", "label": "Onard Mejino" @@ -12322,11 +11889,6 @@ "url": "http://bgsu-rna.github.io/rnao/" } ], - "build": { - "checkout": "git clone https://github.com/BGSU-RNA/rnao.git", - "method": "vcs", - "system": "git" - }, "contact": { "email": "BatchelorC@rsc.org", "label": "Colin Batchelor", @@ -12509,10 +12071,6 @@ }, { "activity_status": "inactive", - "build": { - "method": "owl2obo", - "source_url": "http://purl.obolibrary.org/obo/aero.owl" - }, "contact": { "email": "mcourtot@gmail.com", "label": "Melanie Courtot", @@ -12587,11 +12145,6 @@ }, { "activity_status": "inactive", - "build": { - "insert_ontology_id": true, - "method": "obo2owl", - "source_url": "http://4dx.embl.de/4DXpress_4d/edocs/bilateria_mrca.obo" - }, "contact": { "email": "henrich@embl.de", "github": "ThorstenHen", @@ -12632,11 +12185,6 @@ }, { "activity_status": "inactive", - "build": { - "method": "obo2owl", - "notes": "moving to owl soon", - "source_url": "http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/caro.obo" - }, "contact": { "email": "haendel@ohsu.edu", "github": "mellybelly", @@ -12769,12 +12317,6 @@ }, { "activity_status": "inactive", - "build": { - "insert_ontology_id": true, - "method": "obo2owl", - "notes": "new url soon", - "source_url": "ftp://ftp.hgu.mrc.ac.uk/pub/MouseAtlas/Anatomy/EMAP_combined.obo" - }, "contact": { "email": "Terry.Hayamizu@jax.org", "github": "tfhayamizu", @@ -12803,10 +12345,6 @@ }, { "activity_status": "inactive", - "build": { - "method": "obo2owl", - "source_url": "https://github.com/Planteome/plant-environment-ontology/blob/master/plant-environment-ontology.obo.owl" - }, "contact": { "email": "jaiswalp@science.oregonstate.edu", "github": "jaiswalp", @@ -12871,10 +12409,6 @@ }, { "activity_status": "inactive", - "build": { - "method": "owl2obo", - "source_url": "http://purl.obolibrary.org/obo/epo.owl" - }, "description": "An ontology designed to support the semantic annotation of epidemiology resources", "domain": "health", "homepage": "https://code.google.com/p/epidemiology-ontology/", @@ -12892,10 +12426,6 @@ }, { "activity_status": "inactive", - "build": { - "method": "owl2obo", - "source_url": "http://purl.obolibrary.org/obo/ero.owl" - }, "contact": { "email": "Marc_Ciriello@hms.harvard.edu", "label": "Marc Ciriello" @@ -12937,11 +12467,6 @@ }, { "activity_status": "inactive", - "build": { - "insert_ontology_id": true, - "method": "obo2owl", - "source_url": "http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/taxonomy/fly_taxonomy.obo" - }, "contact": { "email": "cp390@cam.ac.uk", "github": "Clare72", @@ -12971,10 +12496,6 @@ }, { "activity_status": "inactive", - "build": { - "method": "owl2obo", - "source_url": "http://purl.obolibrary.org/obo/flu.owl" - }, "contact": { "email": "burkesquires@gmail.com", "label": "Burke Squires" @@ -13023,11 +12544,6 @@ }, { "activity_status": "inactive", - "build": { - "insert_ontology_id": true, - "method": "obo2owl", - "source_url": "http://download.baderlab.org/INOH/ontologies/EventOntology_172.obo" - }, "domain": "chemistry and biochemistry", "homepage": "http://www.inoh.org", "id": "iev", @@ -13037,11 +12553,6 @@ }, { "activity_status": "inactive", - "build": { - "insert_ontology_id": true, - "method": "obo2owl", - "source_url": "https://web.archive.org/web/20131127090937/http://www.inoh.org/ontologies/MoleculeRoleOntology.obo" - }, "contact": { "email": "curator@inoh.org", "label": "INOH curators" @@ -13068,10 +12579,6 @@ }, { "activity_status": "inactive", - "build": { - "method": "owl2obo", - "source_url": "http://www.lipidprofiles.com/LipidOntology" - }, "contact": { "email": "bakerc@unb.ca", "label": "Christopher Baker", @@ -13250,10 +12757,6 @@ }, { "activity_status": "inactive", - "build": { - "method": "owl2obo", - "source_url": "https://msi-workgroups.svn.sourceforge.net/svnroot/msi-workgroups/ontology/NMR.owl" - }, "contact": { "email": "schober@imbi.uni-freiburg.de", "label": "Schober Daniel" @@ -13460,11 +12963,6 @@ }, { "activity_status": "inactive", - "build": { - "insert_ontology_id": true, - "method": "obo2owl", - "source_url": "https://raw.githubusercontent.com/HUPO-PSI/gelml/master/CV/sep.obo" - }, "contact": { "email": "psidev-gps-dev@lists.sourceforge.net", "label": "SEP developers via the PSI and MSI mailing lists" @@ -13540,10 +13038,6 @@ }, { "activity_status": "inactive", - "build": { - "method": "obo2owl", - "source_url": "http://purl.obolibrary.org/obo/tao.obo" - }, "contact": { "email": "wasila.dahdul@usd.edu", "label": "Wasila Dahdul", @@ -13597,10 +13091,6 @@ }, { "activity_status": "inactive", - "build": { - "method": "obo2owl", - "source_url": "http://phenoscape.svn.sourceforge.net/svnroot/phenoscape/tags/vocab-releases/VSAO/vsao.obo" - }, "contact": { "email": "wasila.dahdul@usd.edu", "label": "Wasila Dahdul", diff --git a/registry/ontologies.yml b/registry/ontologies.yml index 081f35d03..c4b85e5e2 100644 --- a/registry/ontologies.yml +++ b/registry/ontologies.yml @@ -127,10 +127,6 @@ ontologies: and datasets for use in quantitative analyses. user: https://gardian.bigdata.cgiar.org/ - activity_status: active - build: - checkout: git clone https://github.com/insect-morphology/aism - path: . - system: git contact: email: entiminae@gmail.com github: JCGiron @@ -168,10 +164,6 @@ ontologies: title: Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) tracker: https://github.com/insect-morphology/aism/issues - activity_status: active - build: - checkout: git clone https://github.com/EBISPOT/amphx_ontology.git - path: . - system: git contact: email: hescriva@obs-banyuls.fr github: hescriva @@ -200,9 +192,6 @@ ontologies: title: The Amphioxus Development and Anatomy Ontology tracker: https://github.com/EBISPOT/amphx_ontology/issues - activity_status: active - build: - method: obo2owl - source_url: https://raw.githubusercontent.com/obophenotype/ascomycete-phenotype-ontology/master/apo.obo contact: email: stacia@stanford.edu github: srengel @@ -399,12 +388,6 @@ ontologies: title: Biomarker Ontology tracker: https://github.com/SCAI-BIO/BiomarkerOntology/issues - activity_status: active - build: - checkout: git clone https://github.com/obophenotype/biological-spatial-ontology.git - infallible: 1 - method: vcs - path: src/ontology - system: git contact: email: cjmungall@lbl.gov github: cmungall @@ -435,10 +418,6 @@ ontologies: title: Biological Spatial Ontology tracker: https://github.com/obophenotype/biological-spatial-ontology/issues - activity_status: active - build: - checkout: git clone https://github.com/BRENDA-Enzymes/BTO.git - path: . - system: git contact: email: c.dudek@tu-braunschweig.de github: chdudek @@ -472,9 +451,6 @@ ontologies: title: BRENDA tissue / enzyme source tracker: https://github.com/BRENDA-Enzymes/BTO/issues - activity_status: active - build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/cdao.owl contact: email: balhoff@renci.org github: balhoff @@ -502,10 +478,6 @@ ontologies: title: Comparative Data Analysis Ontology tracker: https://github.com/evoinfo/cdao/issues - activity_status: active - build: - checkout: git clone https://github.com/CompositionalDietaryNutritionOntology/cdno.git - path: . - system: git contact: email: landreshdz@gmail.com github: LilyAndres @@ -548,10 +520,6 @@ ontologies: - label: CHEBI title: EBI CHEBI Browser url: http://www.ebi.ac.uk/chebi/chebiOntology.do?treeView=true&chebiId=CHEBI:24431#graphView - build: - infallible: 1 - method: obo2owl - source_url: ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo contact: email: amalik@ebi.ac.uk github: amalik01 @@ -610,9 +578,6 @@ ontologies: url: http://zfin.org/action/expression/experiment?id=ZDB-EXP-190627-10 user: http://zfin.org - activity_status: active - build: - method: owl2obo - source_url: https://raw.githubusercontent.com/semanticchemistry/semanticchemistry/master/ontology/cheminf.owl contact: email: egon.willighagen@gmail.com github: egonw @@ -970,10 +935,6 @@ ontologies: type: annotation user: http://fantom5-collaboration.gsc.riken.jp/ - activity_status: active - build: - checkout: git clone https://github.com/luis-gonzalez-m/Collembola.git - path: . - system: git contact: email: lagonzalezmo@unal.edu.co github: luis-gonzalez-m @@ -1035,10 +996,6 @@ ontologies: title: Cell Line Ontology tracker: https://github.com/CLO-Ontology/CLO/issues - activity_status: active - build: - checkout: git clone https://github.com/EBISPOT/clyh_ontology.git - path: . - system: git contact: email: lucas.leclere@obs-banyuls.fr github: Leclere-L @@ -1074,9 +1031,6 @@ ontologies: - label: RGD title: RGD Ontology Browser url: http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=CMO:0000000 - build: - method: obo2owl - source_url: https://download.rgd.mcw.edu/ontology/clinical_measurement/clinical_measurement.obo contact: email: jrsmith@mcw.edu github: jrsjrs @@ -1205,10 +1159,6 @@ ontologies: title: Coleoptera Anatomy Ontology (COLAO) tracker: https://github.com/insect-morphology/colao/issues - activity_status: active - build: - checkout: git clone https://github.com/data2health/contributor-role-ontology.git - path: src/ontology - system: git contact: email: whimar@ohsu.edu github: marijane @@ -1294,12 +1244,6 @@ ontologies: title: 'CTO: Core Ontology of Clinical Trials' tracker: https://github.com/ClinicalTrialOntology/CTO/issues - activity_status: active - build: - method: owl2obo - publications: - - id: http://dx.doi.org/10.3233/978-1-61499-438-1-409 - title: The Cardiovascular Disease Ontology - source_url: http://purl.obolibrary.org/obo/cvdo.owl contact: email: paul.fabry@usherbrooke.ca github: pfabry @@ -1323,10 +1267,6 @@ ontologies: title: Cardiovascular Disease Ontology tracker: https://github.com/OpenLHS/CVDO/issues - activity_status: active - build: - insert_ontology_id: true - method: obo2owl - source_url: https://raw.githubusercontent.com/dictyBase/migration-data/master/ontologies/dicty_anatomy.obo contact: email: pfey@northwestern.edu github: pfey03 @@ -1361,10 +1301,6 @@ ontologies: tracker: https://github.com/dictyBase/migration-data/issues twitter: dictybase - activity_status: active - build: - checkout: git clone https://github.com/obophenotype/dicty-phenotype-ontology.git - path: . - system: git contact: email: pfey@northwestern.edu github: pfey03 @@ -1426,8 +1362,6 @@ ontologies: - label: DO title: DO Browser url: https://disease-ontology.org/ - build: - source_url: https://raw.githubusercontent.com/DiseaseOntology/DiseaseDriversOntology/refs/heads/main/src/ontology/disdriv.owl contact: email: lynn.schriml@gmail.com github: lschriml @@ -1469,10 +1403,6 @@ ontologies: - label: DO title: DO Browser url: https://disease-ontology.org/do - build: - infallible: 1 - method: obo2owl - source_url: https://raw.githubusercontent.com/DiseaseOntology/HumanDiseaseOntology/master/src/ontology/doid.obo contact: email: lynn.schriml@gmail.com github: lschriml @@ -1540,10 +1470,6 @@ ontologies: - label: FB title: FlyBase Browser url: http://flybase.org/.bin/cvreport.html?cvterm=FBcv:0000347 - build: - checkout: git clone https://github.com/FlyBase/drosophila-phenotype-ontolog.git - path: . - system: git contact: email: cp390@cam.ac.uk github: Clare72 @@ -1583,9 +1509,6 @@ ontologies: url: http://flybase.org/cgi-bin/cvreport.html?rel=is_a&id=FBcv:0002030 user: http://flybase.org - activity_status: active - build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/dron.owl contact: email: hoganwr@gmail.com github: hoganwr @@ -1653,10 +1576,6 @@ ontologies: title: Data Use Ontology tracker: https://github.com/EBISPOT/DUO/issues - activity_status: active - build: - checkout: git clone https://github.com/echinoderm-ontology/ecao_ontology.git - path: . - system: git contact: email: ettensohn@cmu.edu github: ettensohn @@ -1859,10 +1778,6 @@ ontologies: title: Environmental conditions, treatments and exposures ontology tracker: https://github.com/EnvironmentOntology/environmental-exposure-ontology/issues - activity_status: active - build: - method: obo2owl - notes: new url soon - source_url: ftp://ftp.hgu.mrc.ac.uk/pub/MouseAtlas/Anatomy/EMAPA.obo contact: email: Terry.Hayamizu@jax.org github: tfhayamizu @@ -2086,11 +2001,6 @@ ontologies: title: Exposure ontology tracker: https://github.com/CTDbase/exposure-ontology/issues - activity_status: active - build: - checkout: git clone https://github.com/obophenotype/fungal-anatomy-ontology.git - infallible: 1 - method: vcs - system: git contact: email: vw253@cam.ac.uk github: ValWood @@ -2119,10 +2029,6 @@ ontologies: title: Fungal gross anatomy tracker: https://github.com/obophenotype/fungal-anatomy-ontology/issues - activity_status: active - build: - checkout: git clone https://github.com/foundingGIDE/fbbi.git - path: . - system: git contact: email: damien@gerbi-gmb.de github: gouttegd @@ -2182,10 +2088,6 @@ ontologies: - label: BioPortal title: BioPortal Browser url: http://bioportal.bioontology.org/ontologies/FB-BT?p=classes - build: - checkout: git clone https://github.com/FlyBase/drosophila-anatomy-developmental-ontology.git - path: . - system: git contact: email: cp390@cam.ac.uk github: Clare72 @@ -2250,10 +2152,6 @@ ontologies: - label: FB title: FlyBase Browser url: http://flybase.org/.bin/cvreport.html?cvterm=FBcv:0000013 - build: - checkout: git clone https://github.com/FlyBase/flybase-controlled-vocabulary.git - path: . - system: git contact: email: cp390@cam.ac.uk github: Clare72 @@ -2293,10 +2191,6 @@ ontologies: - label: FB title: FlyBase Browser url: http://flybase.org/.bin/cvreport.html?cvterm=FBdv:00007008 - build: - checkout: git clone https://github.com/FlyBase/drosophila-developmental-ontology.git - path: . - system: git contact: email: cp390@cam.ac.uk github: Clare72 @@ -2364,9 +2258,6 @@ ontologies: title: Food Interactions with Drugs Evidence Ontology tracker: https://gitub.u-bordeaux.fr/erias/fideo/issues - activity_status: active - build: - method: owl2obo - source_url: https://github.com/flora-phenotype-ontology/flopoontology/raw/master/ontology/flopo.owl contact: email: robert.hoehndorf@kaust.edu.sa github: leechuck @@ -2552,10 +2443,6 @@ ontologies: title: FuTRES Ontology of Vertebrate Traits tracker: https://github.com/futres/fovt/issues - activity_status: active - build: - infallible: 1 - method: obo2owl - source_url: https://raw.githubusercontent.com/pombase/fypo/master/release/fypo.owl contact: email: vw253@cam.ac.uk github: ValWood @@ -2728,10 +2615,6 @@ ontologies: title: Genomic Epidemiology Ontology tracker: https://github.com/GenEpiO/genepio/issues/ - activity_status: active - build: - checkout: git clone https://github.com/monarch-initiative/GENO-ontology.git - path: src/ontology - system: git contact: email: mhb120@gmail.com github: mbrush @@ -2789,10 +2672,6 @@ ontologies: - label: Composition Browser title: GNOme Glycan Composition Browser url: https://gnome.glyomics.org/CompositionBrowser.html?HexNAc=4&Hex=5&dHex=1&NeuAc=2 - build: - checkout: git clone https://github.com/glygen-glycan-data/GNOme.git - path: . - system: git contact: email: nje5@georgetown.edu github: edwardsnj @@ -3075,9 +2954,6 @@ ontologies: url: https://www.ebi.ac.uk/ols/ontologies/foodon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHANCESTRO_0004&viewMode=All&siblings=false user: http://foodon.org - activity_status: active - build: - checkout: git clone https://github.com/hymao/hao.git - system: git contact: email: diapriid@gmail.com github: mjy @@ -3112,11 +2988,6 @@ ontologies: title: Hymenoptera Anatomy Ontology tracker: https://github.com/hymao/hao/issues - activity_status: active - build: - checkout: git clone https://github.com/BgeeDB/homology-ontology.git - method: vcs - path: src/ontology - system: git contact: email: bgee@sib.swiss github: fbastian @@ -3229,9 +3100,6 @@ ontologies: title: Hypertension Ontology tracker: https://github.com/aellenhicks/htn_owl/issues - activity_status: active - build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/iao.owl contact: email: zhengj2007@gmail.com github: zhengj2007 @@ -3332,9 +3200,6 @@ ontologies: that has over 20 institutes involved. user: http://kpmp.org - activity_status: active - build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/ido.owl contact: email: Lindsay.Cowell@utsouthwestern.edu github: lgcowell @@ -3511,10 +3376,6 @@ ontologies: seeAlso: https://doi.org/10.25504/FAIRsharing.q9neh8 user: http://www.informatics.jax.org/expression.shtml - activity_status: active - build: - checkout: git clone https://github.com/monarch-initiative/MAxO.git - path: . - system: git contact: email: Leigh.Carmody@jax.org github: LCCarmody @@ -3662,9 +3523,6 @@ ontologies: for linking machine learning information from biomedical research user: https://github.com/UTHealth-Ontology/MCRO-Software - activity_status: active - build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/mf.owl contact: email: janna.hastings@gmail.com github: jannahastings @@ -3689,9 +3547,6 @@ ontologies: title: Mental Functioning Ontology tracker: https://github.com/jannahastings/mental-functioning-ontology/issues - activity_status: active - build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/mfoem.owl contact: email: janna.hastings@gmail.com github: jannahastings @@ -3740,10 +3595,6 @@ ontologies: title: Mental Disease Ontology tracker: https://github.com/jannahastings/mental-functioning-ontology/issues - activity_status: active - build: - insert_ontology_id: true - method: obo2owl - source_url: https://raw.githubusercontent.com/HUPO-PSI/psi-mi-CV/master/psi-mi.obo contact: email: luana.licata@gmail.com github: luanalicata @@ -3804,9 +3655,6 @@ ontologies: - label: RGD title: RGD Ontology Browser url: http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000 - build: - method: obo2owl - source_url: https://download.rgd.mcw.edu/ontology/measurement_method/measurement_method.obo contact: email: jrsmith@mcw.edu github: jrsjrs @@ -3842,9 +3690,6 @@ ontologies: title: Measurement method ontology tracker: https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology/issues - activity_status: active - build: - method: obo2owl - source_url: https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/mmusdv/mmusdv.obo contact: email: frederic.bastian@unil.ch github: fbastian @@ -3871,10 +3716,6 @@ ontologies: title: Mouse Developmental Stages tracker: https://github.com/obophenotype/developmental-stage-ontologies/issues - activity_status: active - build: - insert_ontology_id: true - method: obo2owl - source_url: https://raw.githubusercontent.com/HUPO-PSI/psi-mod-CV/master/PSI-MOD.obo contact: email: pierre-alain.binz@chuv.ch github: pabinz @@ -4019,9 +3860,6 @@ ontologies: type: annotation user: https://www.humancellatlas.org/ - activity_status: active - build: - method: owl2obo - source_url: https://raw.githubusercontent.com/rsc-ontologies/rxno/master/mop.owl contact: email: batchelorc@rsc.org github: batchelorc @@ -4140,10 +3978,6 @@ ontologies: url: https://www.mousephenotype.org/data/phenotypes/MP:0013522 user: https://www.mousephenotype.org/ - activity_status: active - build: - insert_ontology_id: true - method: obo2owl - source_url: https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo contact: email: pns12@hermes.cam.ac.uk github: PaulNSchofield @@ -4231,9 +4065,6 @@ ontologies: type: annotation user: https://www.iedb.org/ - activity_status: active - build: - method: obo2owl - source_url: https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo contact: email: joshua.adam.klein@gmail.com github: mobiusklein @@ -4277,9 +4108,6 @@ ontologies: - label: BioPortal title: BioPortal Ontology Browser url: https://bioportal.bioontology.org/ontologies/NBO - build: - method: owl2obo - source_url: https://raw.githubusercontent.com/obo-behavior/behavior-ontology/master/nbo.owl contact: email: g.gkoutos@bham.ac.uk github: gkoutos @@ -4396,9 +4224,6 @@ ontologies: title: NCI Thesaurus OBO Edition tracker: https://github.com/ncit-obo-org/ncit-obo-edition/issues - activity_status: active - build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/ncro/prebuild/ncro.owl contact: email: huang@southalabama.edu github: Huang-OMIT @@ -4453,9 +4278,6 @@ ontologies: title: Next Generation Biobanking Ontology tracker: https://github.com/Dalalghamdi/NGBO/issues - activity_status: active - build: - checkout: git clone https://github.com/SpeciesFileGroup/nomen.git - system: git canonical: nomen.owl contact: email: diapriid@gmail.com @@ -4498,9 +4320,6 @@ ontologies: type: application user: https://taxonworks.org - activity_status: active - build: - method: owl2obo - source_url: https://raw.githubusercontent.com/OAE-ontology/OAE/master/src/oae_merged.owl contact: email: yongqunh@med.umich.edu github: yongqunh @@ -4663,8 +4482,6 @@ ontologies: - label: BioPortal title: BioPortal Browser url: http://bioportal.bioontology.org/ontologies/OBI?p=classes - build: - source_url: http://purl.obofoundry.org/obo/obi/repository/trunk/src/ontology/branches/ contact: email: bpeters@lji.org github: bpeters42 @@ -4886,9 +4703,6 @@ ontologies: title: Ontology for General Medical Science tracker: https://github.com/OGMS/ogms/issues - activity_status: active - build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/ohd.owl contact: email: wdduncan@gmail.com github: wdduncan @@ -5035,9 +4849,6 @@ ontologies: type: owl_import user: http://obofoundry.org - activity_status: active - build: - method: obo2owl - source_url: https://raw.githubusercontent.com/microbialphenotypes/OMP-ontology-files/master/omp.obo contact: email: jimhu@tamu.edu github: jimhu-tamu @@ -5066,9 +4877,6 @@ ontologies: title: Ontology of Microbial Phenotypes tracker: https://github.com/microbialphenotypes/OMP-ontology/issues - activity_status: active - build: - method: owl2obo - source_url: https://github.com/mcwdsi/OMRSE contact: email: hoganwr@gmail.com github: hoganwr @@ -5266,8 +5074,6 @@ ontologies: - label: OntoBee title: OntoBee Browser url: https://ontobee.org/ontology/ONTONEO - build: - source_url: https://raw.githubusercontent.com/ontoneo-project/Ontoneo/master/ontoneo.owl contact: email: fernanda.farinelli@gmail.com github: FernandaFarinelli @@ -5654,9 +5460,6 @@ ontologies: title: Population and Community Ontology tracker: https://github.com/PopulationAndCommunityOntology/pco/issues - activity_status: active - build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/pdro.owl contact: email: paul.fabry@usherbrooke.ca github: pfabry @@ -5963,11 +5766,6 @@ ontologies: - label: PRO title: PRO Home url: http://proconsortium.org - build: - infallible: 0 - method: obo2owl - oort_args: --no-reasoner - source_url: https://proconsortium.org/download/current/pro_nonreasoned.obo contact: email: dan5@georgetown.edu github: nataled @@ -6059,10 +5857,6 @@ ontologies: title: Process Chemistry Ontology tracker: https://github.com/proco-ontology/PROCO/issues - activity_status: active - build: - checkout: https://github.com/Display-Lab/psdo.git - path: . - system: git contact: email: zachll@umich.edu github: zachll @@ -6133,9 +5927,6 @@ ontologies: - label: RGD title: RGD Ontology Browser url: http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=PW:0000001 - build: - method: obo2owl - source_url: https://download.rgd.mcw.edu/ontology/pathway/pathway.obo contact: email: gthayman@mcw.edu github: gthayman @@ -6296,9 +6087,6 @@ ontologies: - label: RGD title: RGD Ontology Browser url: http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=RS:0000457 - build: - method: obo2owl - source_url: https://download.rgd.mcw.edu/ontology/rat_strain/rat_strain.obo contact: email: sjwang@mcw.edu github: shurjenw @@ -6333,9 +6121,6 @@ ontologies: title: Rat Strain Ontology tracker: https://github.com/rat-genome-database/RS-Rat-Strain-Ontology/issues - activity_status: active - build: - method: owl2obo - source_url: https://raw.githubusercontent.com/rsc-ontologies/rxno/master/rxno.owl contact: email: batchelorc@rsc.org github: batchelorc @@ -6362,10 +6147,6 @@ ontologies: title: Name Reaction Ontology tracker: https://github.com/rsc-ontologies/rxno/issues - activity_status: active - build: - checkout: git clone https://github.com/monarch-initiative/SEPIO-ontology.git - path: src/ontology - system: git contact: email: mhb120@gmail.com github: mbrush @@ -6432,10 +6213,6 @@ ontologies: title: Space Life Sciences Ontology tracker: https://github.com/nasa/LSDAO/issues - activity_status: active - build: - method: obo2owl - notes: SWITCH - source_url: https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/so.obo contact: email: keilbeck@genetics.utah.edu github: keilbeck @@ -6484,10 +6261,6 @@ ontologies: title: Sequence types and features ontology tracker: https://github.com/The-Sequence-Ontology/SO-Ontologies/issues - activity_status: active - build: - insert_ontology_id: true - method: obo2owl - source_url: https://raw.githubusercontent.com/obophenotype/spider-ontology/master/spider_comparative_biology.obo contact: email: ramirez@macn.gov.ar github: martinjramirez @@ -6619,10 +6392,6 @@ ontologies: title: Software ontology tracker: https://github.com/allysonlister/swo/issues - activity_status: active - build: - infallible: 1 - method: obo2owl - source_url: https://raw.githubusercontent.com/DiseaseOntology/SymptomOntology/master/src/ontology/symp.obo contact: email: lynn.schriml@gmail.com github: lschriml @@ -6808,10 +6577,6 @@ ontologies: url: http://archive.gramene.org/db/ontology/search?id=TO:0000286 user: http://gramene.org/ - activity_status: active - build: - infallible: 1 - method: obo2owl - source_url: https://raw.githubusercontent.com/DiseaseOntology/PathogenTransmissionOntology/master/src/ontology/trans.obo contact: email: lynn.schriml@gmail.com github: lschriml @@ -6940,11 +6705,6 @@ ontologies: - label: KnowledgeSpace title: INCF KnowledgeSpace Portal url: https://knowledge-space.org/index.php/pages/view/UBERON:0000061 - build: - checkout: git clone https://github.com/obophenotype/uberon.git - email_cc: cjmungall@lbl.gov - infallible: 1 - system: git canonical: uberon.owl contact: email: cjmungall@lbl.gov @@ -7120,9 +6880,6 @@ ontologies: user: https://www.ebi.ac.uk/chembl/ wikidata_template: https://en.wikipedia.org/wiki/Template:Uberon - activity_status: active - build: - method: obo2owl - source_url: https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo contact: email: g.gkoutos@gmail.com github: gkoutos @@ -7154,10 +6911,6 @@ ontologies: title: Units of measurement ontology tracker: https://github.com/bio-ontology-research-group/unit-ontology/issues - activity_status: active - build: - method: archive - path: archive/ontology - source_url: http://build.berkeleybop.org/job/build-pheno-ontologies/lastSuccessfulBuild/artifact/*zip*/archive.zip contact: email: jmcl@ebi.ac.uk github: jamesamcl @@ -7287,8 +7040,6 @@ ontologies: type: annotation user: https://www.cellosaurus.org/index.html - activity_status: active - build: - source_url: https://raw.githubusercontent.com/vaccineontology/VO/master/src/VO_merged.owl contact: email: yongqunh@med.umich.edu github: yongqunh @@ -7348,10 +7099,6 @@ ontologies: url: http://www.hipc-dashboard.org/#vaccine/vo-0000044 user: https://immunespace.org/ - activity_status: active - build: - checkout: svn co http://phenotype-ontologies.googlecode.com/svn/trunk/src/ontology/vt - method: vcs - system: svn contact: email: caripark@iastate.edu github: caripark @@ -7428,10 +7175,6 @@ ontologies: - description: Phenoscape uses VTO to annotate systematics data user: http://phenoscape.org - activity_status: active - build: - checkout: git clone https://github.com/obophenotype/c-elegans-gross-anatomy-ontology.git - path: . - system: git contact: email: raymond@caltech.edu github: raymond91125 @@ -7475,10 +7218,6 @@ ontologies: type: annotation user: https://www.wormbase.org/ - activity_status: active - build: - checkout: git clone https://github.com/obophenotype/c-elegans-development-ontology.git - path: . - system: git contact: email: cgrove@caltech.edu github: chris-grove @@ -7524,10 +7263,6 @@ ontologies: type: annotation user: https://www.wormbase.org/ - activity_status: active - build: - checkout: git clone https://github.com/obophenotype/c-elegans-phenotype-ontology.git - path: . - system: git contact: email: cgrove@caltech.edu github: chris-grove @@ -7586,10 +7321,6 @@ ontologies: type: annotation user: https://monarchinitiative.org/ - activity_status: active - build: - infallible: 0 - method: obo2owl - source_url: https://raw.githubusercontent.com/xenopus-anatomy/xao/master/xenopus_anatomy.obo contact: email: Erik.Segerdell@cchmc.org github: seger @@ -7636,9 +7367,6 @@ ontologies: - label: RGD title: RGD Ontology Browser url: http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000 - build: - method: obo2owl - source_url: https://download.rgd.mcw.edu/ontology/experimental_condition/experimental_condition.obo contact: email: jrsmith@mcw.edu github: jrsjrs @@ -7748,9 +7476,6 @@ ontologies: title: Xenopus Phenotype Ontology tracker: https://github.com/obophenotype/xenopus-phenotype-ontology/issues - activity_status: active - build: - method: obo2owl - source_url: https://raw.githubusercontent.com/ybradford/zebrafish-experimental-conditions-ontology/master/zeco.obo contact: email: ybradford@zfin.org github: ybradford @@ -7782,11 +7507,6 @@ ontologies: title: Zebrafish Experimental Conditions Ontology tracker: https://github.com/ybradford/zebrafish-experimental-conditions-ontology/issues - activity_status: active - build: - infallible: 1 - method: obo2owl - notes: may be ready to switch to vcs soon - source_url: https://raw.githubusercontent.com/cerivs/zebrafish-anatomical-ontology/master/src/zebrafish_anatomy.obo contact: email: van_slyke@zfin.org github: cerivs @@ -7828,10 +7548,6 @@ ontologies: url: http://zfin.org/ZFA:0000029 user: http://zfin.org - activity_status: active - build: - infallible: 1 - method: obo2owl - source_url: https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/zfs/zfs.obo contact: email: van_slyke@zfin.org github: cerivs @@ -7909,10 +7625,6 @@ ontologies: type: annotation user: https://monarchinitiative.org/ - activity_status: active - build: - checkout: git clone https://github.com/Superraptor/GSSO.git - path: . - system: git contact: email: kronkcj@mail.uc.edu github: Superraptor @@ -8119,9 +7831,6 @@ ontologies: - label: OntoBee title: OntoBee url: https://www.ontobee.org/ontology/KISAO - build: - method: owl2obo - source_url: https://raw.githubusercontent.com/SED-ML/KiSAO/deploy/kisao.owl contact: email: jonrkarr@gmail.com github: jonrkarr @@ -8188,10 +7897,6 @@ ontologies: type: annotation user: https://biosimulators.org/ - activity_status: active - build: - insert_ontology_id: true - method: obo2owl - source_url: http://www.ebi.ac.uk/sbo/exports/Main/SBO_OBO.obo contact: email: sheriff@ebi.ac.uk github: rsmsheriff @@ -8215,10 +7920,6 @@ ontologies: title: Systems Biology Ontology tracker: https://github.com/EBI-BioModels/SBO/issues - activity_status: active - build: - checkout: git clone https://github.com/scdodev/scdo-ontology.git - path: . - system: git contact: email: giant.plankton@gmail.com github: JadeHotchkiss @@ -8288,11 +7989,6 @@ ontologies: title: Sickle Cell Disease Ontology tracker: https://github.com/scdodev/scdo-ontology/issues - activity_status: orphaned - build: - infallible: 1 - insert_ontology_id: true - method: obo2owl - source_url: ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/fix.obo contact: email: null label: chEBI @@ -8310,9 +8006,6 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/fix.obo title: Physico-chemical methods and properties - activity_status: orphaned - build: - method: owl2obo - source_url: https://svn.code.sf.net/p/mamo-ontology/code/tags/latest/mamo-xml.owl description: The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. @@ -8332,10 +8025,6 @@ ontologies: title: Mathematical modeling ontology tracker: http://sourceforge.net/p/mamo-ontology/tickets/ - activity_status: orphaned - build: - insert_ontology_id: true - method: obo2owl - source_url: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/physicochemical/rex.obo description: An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. domain: chemistry and biochemistry @@ -8347,10 +8036,6 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/rex.owl title: Physico-chemical process - activity_status: orphaned - build: - checkout: git clone https://github.com/obophenotype/sibo.git - method: vcs - system: git contact: email: cjmungall@lbl.gov label: Chris Mungall @@ -8377,9 +8062,6 @@ ontologies: title: Social Insect Behavior Ontology tracker: https://github.com/obophenotype/sibo/issues - activity_status: orphaned - build: - method: obo2owl - source_url: http://variationontology.org/vario_download/vario.obo contact: email: mauno.vihinen@med.lu.se github: maunov @@ -8538,9 +8220,6 @@ ontologies: title: Ontology of Genetic Susceptibility Factor tracker: https://github.com/linikujp/OGSF/issues - activity_status: inactive - build: - method: obo2owl - source_url: https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/olatdv/olatdv.obo contact: email: frederic.bastian@unil.ch github: fbastian @@ -8567,9 +8246,6 @@ ontologies: title: Medaka Developmental Stages tracker: https://github.com/obophenotype/developmental-stage-ontologies/issues - activity_status: inactive - build: - method: obo2owl - source_url: https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/pdumdv/pdumdv.obo contact: email: frederic.bastian@unil.ch github: fbastian @@ -8596,11 +8272,6 @@ ontologies: title: Platynereis Developmental Stages tracker: https://github.com/obophenotype/developmental-stage-ontologies/issues - activity_status: inactive - build: - checkout: git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git - method: vcs - path: src/ontology - system: git contact: email: J.Bard@ed.ac.uk label: Jonathan Bard @@ -8652,11 +8323,6 @@ ontologies: title: Cephalopod Ontology tracker: https://github.com/obophenotype/cephalopod-ontology/issues - activity_status: inactive - build: - checkout: git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git - method: vcs - path: src/ontology - system: git contact: email: J.Bard@ed.ac.uk label: Jonathan Bard @@ -8691,10 +8357,6 @@ ontologies: title: Human developmental anatomy, abstract tracker: https://github.com/obophenotype/human-developmental-anatomy-ontology/issues - activity_status: inactive - build: - insert_ontology_id: true - method: obo2owl - source_url: http://svn.code.sf.net/p/obo/svn/fma-conversion/trunk/fma2_obo.obo contact: email: mejino@u.washington.edu label: Onard Mejino @@ -8774,10 +8436,6 @@ ontologies: - label: RNAO title: RNA Ontology jOWL Browser url: http://bgsu-rna.github.io/rnao/ - build: - checkout: git clone https://github.com/BGSU-RNA/rnao.git - method: vcs - system: git contact: email: BatchelorC@rsc.org label: Colin Batchelor @@ -8910,9 +8568,6 @@ ontologies: layout: ontology_detail title: Animal natural history and life history - activity_status: inactive - build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/aero.owl contact: email: mcourtot@gmail.com label: Melanie Courtot @@ -8971,10 +8626,6 @@ ontologies: title: Beta Cell Genomics Ontology tracker: https://github.com/obi-bcgo/bcgo/issues - activity_status: inactive - build: - insert_ontology_id: true - method: obo2owl - source_url: http://4dx.embl.de/4DXpress_4d/edocs/bilateria_mrca.obo contact: email: henrich@embl.de github: ThorstenHen @@ -9005,10 +8656,6 @@ ontologies: replaced_by: molecular_function title: Gene Regulation Ontology - activity_status: inactive - build: - method: obo2owl - notes: moving to owl soon - source_url: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/caro.obo contact: email: haendel@ohsu.edu github: mellybelly @@ -9111,11 +8758,6 @@ ontologies: label: Homo sapiens title: Human developmental anatomy, abstract version - activity_status: inactive - build: - insert_ontology_id: true - method: obo2owl - notes: new url soon - source_url: ftp://ftp.hgu.mrc.ac.uk/pub/MouseAtlas/Anatomy/EMAP_combined.obo contact: email: Terry.Hayamizu@jax.org github: tfhayamizu @@ -9138,9 +8780,6 @@ ontologies: label: Mus title: Mouse gross anatomy and development, timed - activity_status: inactive - build: - method: obo2owl - source_url: https://github.com/Planteome/plant-environment-ontology/blob/master/plant-environment-ontology.obo.owl contact: email: jaiswalp@science.oregonstate.edu github: jaiswalp @@ -9183,9 +8822,6 @@ ontologies: url: http://archive.gramene.org/db/ontology/search?id=EO:0007174 user: http://gramene.org/ - activity_status: inactive - build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/epo.owl description: An ontology designed to support the semantic annotation of epidemiology resources domain: health @@ -9199,9 +8835,6 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/epo.owl title: Epidemiology Ontology - activity_status: inactive - build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/ero.owl contact: email: Marc_Ciriello@hms.harvard.edu label: Marc Ciriello @@ -9233,10 +8866,6 @@ ontologies: layout: ontology_detail title: eVOC (Expressed Sequence Annotation for Humans) - activity_status: inactive - build: - insert_ontology_id: true - method: obo2owl - source_url: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/taxonomy/fly_taxonomy.obo contact: email: cp390@cam.ac.uk github: Clare72 @@ -9259,9 +8888,6 @@ ontologies: label: Drosophila title: Fly taxonomy - activity_status: inactive - build: - method: owl2obo - source_url: http://purl.obolibrary.org/obo/flu.owl contact: email: burkesquires@gmail.com label: Burke Squires @@ -9298,10 +8924,6 @@ ontologies: layout: ontology_detail title: Habronattus courtship - activity_status: inactive - build: - insert_ontology_id: true - method: obo2owl - source_url: http://download.baderlab.org/INOH/ontologies/EventOntology_172.obo domain: chemistry and biochemistry homepage: http://www.inoh.org id: iev @@ -9309,10 +8931,6 @@ ontologies: layout: ontology_detail title: Event (INOH pathway ontology) - activity_status: inactive - build: - insert_ontology_id: true - method: obo2owl - source_url: https://web.archive.org/web/20131127090937/http://www.inoh.org/ontologies/MoleculeRoleOntology.obo contact: email: curator@inoh.org label: INOH curators @@ -9333,9 +8951,6 @@ ontologies: layout: ontology_detail title: Protein Domains - activity_status: inactive - build: - method: owl2obo - source_url: http://www.lipidprofiles.com/LipidOntology contact: email: bakerc@unb.ca label: Christopher Baker @@ -9474,9 +9089,6 @@ ontologies: replaced_by: uberon title: NIF Gross Anatomy - activity_status: inactive - build: - method: owl2obo - source_url: https://msi-workgroups.svn.sourceforge.net/svnroot/msi-workgroups/ontology/NMR.owl contact: email: schober@imbi.uni-freiburg.de label: Schober Daniel @@ -9638,10 +9250,6 @@ ontologies: label: Homo sapiens title: Subcellular anatomy ontology - activity_status: inactive - build: - insert_ontology_id: true - method: obo2owl - source_url: https://raw.githubusercontent.com/HUPO-PSI/gelml/master/CV/sep.obo contact: email: psidev-gps-dev@lists.sourceforge.net label: SEP developers via the PSI and MSI mailing lists @@ -9699,9 +9307,6 @@ ontologies: label: Homo sapiens title: Terminology of Anatomy of Human Histology - activity_status: inactive - build: - method: obo2owl - source_url: http://purl.obolibrary.org/obo/tao.obo contact: email: wasila.dahdul@usd.edu label: Wasila Dahdul @@ -9741,9 +9346,6 @@ ontologies: replaced_by: uberon title: Vertebrate Homologous Ontology Group Ontology - activity_status: inactive - build: - method: obo2owl - source_url: http://phenoscape.svn.sourceforge.net/svnroot/phenoscape/tags/vocab-releases/VSAO/vsao.obo contact: email: wasila.dahdul@usd.edu label: Wasila Dahdul diff --git a/src/obofoundry/remove_field.py b/src/obofoundry/remove_field.py new file mode 100644 index 000000000..333d46ca0 --- /dev/null +++ b/src/obofoundry/remove_field.py @@ -0,0 +1,51 @@ +"""A workflow for removing a field from all ontology markdown files' metadata.""" + +from io import StringIO +from pathlib import Path + +import click +import yaml + +from obofoundry.constants import ONTOLOGY_DIRECTORY +from obofoundry.standardize_metadata import ModifiedDumper + + +def remove_field(name: str) -> None: + """Remove the metadata key from all ontologies' metadata.""" + for path in ONTOLOGY_DIRECTORY.glob("*.md"): + remove_field_from_file(path, name) + + +def remove_field_from_file(path: Path, name: str) -> None: + """Update the given markdown file.""" + with open(path) as file: + lines = [line.rstrip("\n") for line in file] + + assert lines[0] == "---" + idx = min(i for i, line in enumerate(lines[1:], start=1) if line == "---") + + # Load the data like it is YAML + data = yaml.safe_load(StringIO("\n".join(lines[1:idx]))) + + if name in data: + del data[name] + + dumped = ModifiedDumper.dump(data) + + with open(path, "w") as file: + print("---", file=file) + print(dumped, file=file) + print("---", file=file) + for line in lines[idx + 1 :]: + print(line, file=file) + + +@click.command() +@click.argument("name") +def main(name: str) -> None: + """Remove the metadata key from all ontologies' metadata.""" + remove_field(name) + + +if __name__ == "__main__": + main() diff --git a/util/schema/registry_schema.json b/util/schema/registry_schema.json index c0b66cd6c..8a24ff039 100644 --- a/util/schema/registry_schema.json +++ b/util/schema/registry_schema.json @@ -46,9 +46,6 @@ ] } }, - "build": { - "suggest": false - }, "canonical": { "suggest": false },