diff --git a/_config.yml b/_config.yml index 3f9121eba..be4c17b15 100644 --- a/_config.yml +++ b/_config.yml @@ -123,9 +123,7 @@ ontologies: title: Ontology for Biomedical Investigations tracker: http://purl.obofoundry.org/obo/obi/tracker - browsers: - - {label: Aber-OWL, title: Aber-OWL Ontology Browser, url: 'http://aber-owl.net/ontology/PATO'} - {label: BioPortal, title: BioPortal Ontology Browser, url: 'https://bioportal.bioontology.org/ontologies/PATO'} - - {label: OntoBee, title: OntoBee Browser, url: 'http://www.ontobee.org/browser/index.php?o=PATO'} build: {infallible: 1, method: obo2owl, source_url: 'https://raw.githubusercontent.com/pato-ontology/pato/master/pato.obo'} contact: {email: g.gkoutos@gmail.com, label: George Gkoutos} description: An ontology of phenotypic qualities (properties, attributes or characteristics) @@ -256,7 +254,7 @@ ontologies: products: - {id: aero.owl, ontology_purl: 'http://purl.obolibrary.org/obo/aero.owl'} title: Adverse Event Reporting Ontology -- build: {method: obo2owl, source_url: 'http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/ascomycete_phenotype.obo'} +- build: {method: obo2owl, source_url: 'https://raw.githubusercontent.com/obophenotype/ascomycete-phenotype-ontology/master/apo.obo'} contact: {email: maria@genome.stanford.edu, label: Maria Costanza} description: A structured controlled vocabulary for the phenotypes of Ascomycete fungi @@ -267,6 +265,7 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/apo.owl products: - {id: apo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/apo.owl'} + - {id: apo.obo, ontology_purl: 'http://purl.obolibrary.org/obo/apo.obo'} taxon: {id: 'NCBITaxon:4890', label: Ascomycota} title: Ascomycete phenotype ontology - contact: {email: jiezheng@upenn.edu, label: Jie Zheng} @@ -1305,9 +1304,7 @@ ontologies: termgenie: http://mp.termgenie.org title: Mammalian phenotype tracker: https://github.com/obophenotype/mammalian-phenotype-ontology/issues -- browsers: - - {label: Aber-OWL, title: Aber-OWL Ontology Repository, url: 'http://aber-owl.net/ontology/MPATH'} - build: {method: obo2owl, source_url: 'https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo'} +- build: {method: obo2owl, source_url: 'https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo'} contact: {email: pns12@cam.ac.uk, label: Paul Schofield} description: A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes @@ -1356,9 +1353,7 @@ ontologies: - {id: ms.owl, ontology_purl: 'http://purl.obolibrary.org/obo/ms.owl'} title: Mass spectrometry ontology - browsers: - - {label: Aber-OWL, title: Aber-OWL Ontology Browser, url: 'http://aber-owl.net/ontology/NBO'} - {label: BioPortal, title: BioPortal Ontology Browser, url: 'https://bioportal.bioontology.org/ontologies/NBO'} - - {label: OntoBee, title: OntoBee Ontology Browser, url: 'http://www.ontobee.org/browser/index.php?o=NBO'} build: {checkout: 'git clone https://github.com/bio-ontology-research-group/behavior-ontology.git', method: vcs, path: ., system: git} contact: {email: g.gkoutos@gmail.com, label: George Gkoutos} @@ -1408,6 +1403,22 @@ ontologies: layout: ontology_detail title: NCI Thesaurus uri_prefix: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl# +- browsers: null + contact: {email: huang@southalabama.edu, label: Jingshan Huang} + description: An ontology for non-coding RNA, both of biological origin, and engineered. + domain: experiments + homepage: http://omnisearch.soc.southalabama.edu/OntologyFile.aspx + id: ncro + layout: ontology_detail + license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png', + url: 'http://creativecommons.org/licenses/by/4.0/'} + mailing_list: ncro-devel@googlegroups.com + ontology_purl: http://purl.obolibrary.org/obo/ncro.owl + products: + - {id: ncro/dev/ncro.owl, ontology_purl: 'http://purl.obolibrary.org/obo/ncro/dev/ncro.owl', + title: NCRO development version} + title: non-coding RNA Ontology + tracker: https://github.com/OmniSearch/NCRO-Ontology-Files/issues - build: {method: owl2obo, source_url: 'http://svn.code.sf.net/p/oae/code/trunk/src/ontology/oae.owl'} contact: {email: yongqunh@med.umich.edu, label: Yongqunh He} description: A biomedical ontology in the domain of adverse events @@ -1667,8 +1678,8 @@ ontologies: - {id: rnao.owl, ontology_purl: 'http://purl.obolibrary.org/obo/rnao.owl'} - {id: rnao.obo, ontology_purl: 'http://purl.obolibrary.org/obo/rnao.obo'} title: RNA ontology -- build: {checkout: 'svn co http://obo-relations.googlecode.com/svn/trunk/src/ontology', - infallible: 1, method: vcs, system: svn} +- build: {checkout: 'git clone https://github.com/oborel/obo-relations.git', infallible: 1, + method: vcs, system: git} canonical: ro.owl contact: {email: cjmungall@lbl.gov, label: Chris Mungall} description: Relationship types shared across multiple ontologies @@ -1677,6 +1688,7 @@ ontologies: id: ro jobs: - {id: 'http://build.berkeleybop.org/job/build-ro', type: DryRunBuild} + - {id: 'https://travis-ci.org/oborel/obo-relations', type: travis-ci} layout: ontology_detail license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png', url: 'http://creativecommons.org/licenses/by/3.0/'} @@ -1890,7 +1902,10 @@ ontologies: - {id: tgma.owl, ontology_purl: 'http://purl.obolibrary.org/obo/tgma.owl'} taxon: {id: 'NCBITaxon:44484', label: Anopheles} title: Mosquito gross anatomy -- build: {infallible: 1, method: obo2owl, source_url: 'https://raw.githubusercontent.com/Planteome/plant-trait-ontology/master/to-release-files/plant-trait-ontology.obo'} +- browsers: + - {label: Planteome, title: Planteome browser, url: 'http://dev.planteome.org/amigo/term/TO:0000387'} + build: {checkout: 'git clone https://github.com/Planteome/plant-trait-ontology.git', + infallible: 1, method: vcs, path: ., system: git} contact: {email: jaiswalp@science.oregonstate.edu, label: Pankaj Jaiswal} description: A controlled vocabulary of describe phenotypic traits in plants. domain: phenotype @@ -1903,6 +1918,7 @@ ontologies: page: http://planteome.org/amigo/cgi-bin/crop_amigo/term_details?term=TO:0000387&session_id=815amigo1442021959 products: - {id: to.owl, ontology_purl: 'http://purl.obolibrary.org/obo/to.owl'} + - {id: to.obo, ontology_purl: 'http://purl.obolibrary.org/obo/to.obo'} publications: - {id: 'http://www.ncbi.nlm.nih.gov/pubmed/22847540', title: Ontologies as integrative tools for plant science.} diff --git a/ontology/ro.md b/ontology/ro.md index 33bcdff76..29cfc1703 100644 --- a/ontology/ro.md +++ b/ontology/ro.md @@ -3,8 +3,8 @@ layout: ontology_detail id: ro title: Relations Ontology build: - checkout: svn co http://obo-relations.googlecode.com/svn/trunk/src/ontology - system: svn + checkout: git clone https://github.com/oborel/obo-relations.git + system: git method: vcs infallible: 1 canonical: ro.owl diff --git a/registry/ontologies.jsonld b/registry/ontologies.jsonld index 96a6fddd5..4fa9c21b4 100644 --- a/registry/ontologies.jsonld +++ b/registry/ontologies.jsonld @@ -238,20 +238,10 @@ }, { "browsers": [ - { - "label": "Aber-OWL", - "title": "Aber-OWL Ontology Browser", - "url": "http://aber-owl.net/ontology/PATO" - }, { "label": "BioPortal", "title": "BioPortal Ontology Browser", "url": "https://bioportal.bioontology.org/ontologies/PATO" - }, - { - "label": "OntoBee", - "title": "OntoBee Browser", - "url": "http://www.ontobee.org/browser/index.php?o=PATO" } ], "build": { @@ -517,7 +507,7 @@ { "build": { "method": "obo2owl", - "source_url": "http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/ascomycete_phenotype.obo" + "source_url": "https://raw.githubusercontent.com/obophenotype/ascomycete-phenotype-ontology/master/apo.obo" }, "contact": { "email": "maria@genome.stanford.edu", @@ -533,6 +523,10 @@ { "id": "apo.owl", "ontology_purl": "http://purl.obolibrary.org/obo/apo.owl" + }, + { + "id": "apo.obo", + "ontology_purl": "http://purl.obolibrary.org/obo/apo.obo" } ], "taxon": { @@ -2678,13 +2672,6 @@ "tracker": "https://github.com/obophenotype/mammalian-phenotype-ontology/issues" }, { - "browsers": [ - { - "label": "Aber-OWL", - "title": "Aber-OWL Ontology Repository", - "url": "http://aber-owl.net/ontology/MPATH" - } - ], "build": { "method": "obo2owl", "source_url": "https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo" @@ -2782,20 +2769,10 @@ }, { "browsers": [ - { - "label": "Aber-OWL", - "title": "Aber-OWL Ontology Browser", - "url": "http://aber-owl.net/ontology/NBO" - }, { "label": "BioPortal", "title": "BioPortal Ontology Browser", "url": "https://bioportal.bioontology.org/ontologies/NBO" - }, - { - "label": "OntoBee", - "title": "OntoBee Ontology Browser", - "url": "http://www.ontobee.org/browser/index.php?o=NBO" } ], "build": { @@ -2895,6 +2872,34 @@ "title": "NCI Thesaurus", "uri_prefix": "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#" }, + { + "browsers": null, + "contact": { + "email": "huang@southalabama.edu", + "label": "Jingshan Huang" + }, + "description": "An ontology for non-coding RNA, both of biological origin, and engineered.", + "domain": "experiments", + "homepage": "http://omnisearch.soc.southalabama.edu/OntologyFile.aspx", + "id": "ncro", + "layout": "ontology_detail", + "license": { + "label": "CC-BY", + "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png", + "url": "http://creativecommons.org/licenses/by/4.0/" + }, + "mailing_list": "ncro-devel@googlegroups.com", + "ontology_purl": "http://purl.obolibrary.org/obo/ncro.owl", + "products": [ + { + "id": "ncro/dev/ncro.owl", + "ontology_purl": "http://purl.obolibrary.org/obo/ncro/dev/ncro.owl", + "title": "NCRO development version" + } + ], + "title": "non-coding RNA Ontology", + "tracker": "https://github.com/OmniSearch/NCRO-Ontology-Files/issues" + }, { "build": { "method": "owl2obo", @@ -3416,10 +3421,10 @@ }, { "build": { - "checkout": "svn co http://obo-relations.googlecode.com/svn/trunk/src/ontology", + "checkout": "git clone https://github.com/oborel/obo-relations.git", "infallible": 1, "method": "vcs", - "system": "svn" + "system": "git" }, "canonical": "ro.owl", "contact": { @@ -3434,6 +3439,10 @@ { "id": "http://build.berkeleybop.org/job/build-ro", "type": "DryRunBuild" + }, + { + "id": "https://travis-ci.org/oborel/obo-relations", + "type": "travis-ci" } ], "layout": "ontology_detail", @@ -3862,10 +3871,19 @@ "title": "Mosquito gross anatomy" }, { + "browsers": [ + { + "label": "Planteome", + "title": "Planteome browser", + "url": "http://dev.planteome.org/amigo/term/TO:0000387" + } + ], "build": { + "checkout": "git clone https://github.com/Planteome/plant-trait-ontology.git", "infallible": 1, - "method": "obo2owl", - "source_url": "https://raw.githubusercontent.com/Planteome/plant-trait-ontology/master/to-release-files/plant-trait-ontology.obo" + "method": "vcs", + "path": ".", + "system": "git" }, "contact": { "email": "jaiswalp@science.oregonstate.edu", @@ -3887,6 +3905,10 @@ { "id": "to.owl", "ontology_purl": "http://purl.obolibrary.org/obo/to.owl" + }, + { + "id": "to.obo", + "ontology_purl": "http://purl.obolibrary.org/obo/to.obo" } ], "publications": [ diff --git a/registry/ontologies.ttl b/registry/ontologies.ttl index c81bde165..eb1a03202 100644 --- a/registry/ontologies.ttl +++ b/registry/ontologies.ttl @@ -98,37 +98,13 @@ "NCBI Taxonomy Browser" . - + - "http://purl.obolibrary.org/obo/aero.owl" . + "http://purl.obolibrary.org/obo/apo.obo" . - - - [ - "owl2obo" ; - - "http://purl.obolibrary.org/obo/aero.owl" - ] ; - - "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events" ; - - "Adverse Event Reporting Ontology" ; - - ; - - "health" ; + - "http://purl.obolibrary.org/obo/aero.owl" ; - - [ - "Melanie Courtot" ; - - "mcourtot@gmail.com" - ] ; - - ; - - . + "http://purl.obolibrary.org/obo/aero.owl" . @@ -164,6 +140,34 @@ . + + + [ + "owl2obo" ; + + "http://purl.obolibrary.org/obo/aero.owl" + ] ; + + "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events" ; + + "Adverse Event Reporting Ontology" ; + + ; + + "health" ; + + "http://purl.obolibrary.org/obo/aero.owl" ; + + [ + "Melanie Courtot" ; + + "mcourtot@gmail.com" + ] ; + + ; + + . + "http://purl.obolibrary.org/obo/olatdv.owl" . @@ -499,12 +503,6 @@ "http://purl.obolibrary.org/obo/cl/cl-basic.obo" . - - - "OntoBee" ; - - "OntoBee Browser" . - ; @@ -982,7 +980,7 @@ - , , ; + ; [ "obo2owl" ; @@ -1223,6 +1221,12 @@ . + + + "NCRO development version" ; + + "http://purl.obolibrary.org/obo/ncro/dev/ncro.owl" . + ; @@ -1453,14 +1457,14 @@ "http://purl.obolibrary.org/obo/obi.owl" . - - - "http://purl.obolibrary.org/obo/sep.owl" . - "The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments." . + + + "http://purl.obolibrary.org/obo/sep.owl" . + [ @@ -1483,13 +1487,7 @@ . - - - "http://purl.obolibrary.org/obo/fbdv/fbbt-simple.obo" . - - - ; [ "obo2owl" ; @@ -1521,6 +1519,10 @@ . + + + "http://purl.obolibrary.org/obo/fbdv/fbbt-simple.obo" . + [ @@ -1641,6 +1643,12 @@ "http://purl.obolibrary.org/obo/fbbt.owl" . + + + "Planteome" ; + + "Planteome browser" . + "Saccharomyces cerevisiae" . @@ -1856,11 +1864,13 @@ . + + ; - [ - "obo2owl" ; - - "https://raw.githubusercontent.com/Planteome/plant-trait-ontology/master/to-release-files/plant-trait-ontology.obo" + [ + "git clone https://github.com/Planteome/plant-trait-ontology.git" ; + + "vcs" ] ; ; @@ -1885,7 +1895,7 @@ "jaiswalp@science.oregonstate.edu" ] ; - ; + , ; ; @@ -2175,11 +2185,9 @@ "Zea" . - - - "Aber-OWL" ; - - "Aber-OWL Ontology Browser" . + + + "http://purl.obolibrary.org/obo/to.obo" . @@ -2754,6 +2762,32 @@ "http://purl.obolibrary.org/obo/idomal.owl" . + + + "An ontology for non-coding RNA, both of biological origin, and engineered." ; + + "non-coding RNA Ontology" ; + + ; + + "experiments" ; + + "https://github.com/OmniSearch/NCRO-Ontology-Files/issues" ; + + "ncro-devel@googlegroups.com" ; + + "http://purl.obolibrary.org/obo/ncro.owl" ; + + [ + "Jingshan Huang" ; + + "huang@southalabama.edu" + ] ; + + ; + + . + "The environment ontology: contextualising biological and biomedical entities" . @@ -2884,7 +2918,7 @@ - , , ; + ; [ "git clone https://github.com/bio-ontology-research-group/behavior-ontology.git" ; @@ -2952,12 +2986,6 @@ "http://purl.obolibrary.org/obo/poro.owl" . - - - "Aber-OWL" ; - - "Aber-OWL Ontology Repository" . - [ @@ -3344,34 +3372,6 @@ "http://purl.obolibrary.org/obo/tgma.owl" . - - - [ - "obo2owl" ; - - "https://raw.githubusercontent.com/xenopus-anatomy/xao/master/xenopus_anatomy.obo" - ] ; - - ; - - "Anatomy and development of the African clawed frog (Xenopus laevis)." ; - - "Xenopus anatomy and development" ; - - ; - - , ; - - "anatomy" ; - - "https://github.com/xenopus-anatomy/xao/issues" ; - - "http://purl.obolibrary.org/obo/xao.owl" ; - - ; - - . - [ @@ -3400,31 +3400,33 @@ . - + + + [ + "obo2owl" ; + + "https://raw.githubusercontent.com/xenopus-anatomy/xao/master/xenopus_anatomy.obo" + ] ; + + ; - "A formal ontology of genes and genomes of biological organisms." ; + "Anatomy and development of the African clawed frog (Xenopus laevis)." ; - "The Ontology of Genes and Genomes" ; + "Xenopus anatomy and development" ; ; + + , ; + + "anatomy" ; - "https://code.google.com/p/ogg/issues/list" ; + "https://github.com/xenopus-anatomy/xao/issues" ; - "http://purl.obolibrary.org/obo/ogg.owl" ; - - [ - "Yongqun Oliver He" ; - - "yongqunh@med.umich.edu" - ] ; + "http://purl.obolibrary.org/obo/xao.owl" ; - ; + ; - . - - - - "http://purl.obolibrary.org/obo/pco.owl" . + . @@ -3462,6 +3464,32 @@ . + + + "A formal ontology of genes and genomes of biological organisms." ; + + "The Ontology of Genes and Genomes" ; + + ; + + "https://code.google.com/p/ogg/issues/list" ; + + "http://purl.obolibrary.org/obo/ogg.owl" ; + + [ + "Yongqun Oliver He" ; + + "yongqunh@med.umich.edu" + ] ; + + ; + + . + + + + "http://purl.obolibrary.org/obo/pco.owl" . + "FB" ; @@ -3608,6 +3636,11 @@ "http://purl.obolibrary.org/obo/iao/dev/iao.owl" . + + + "CC-BY" ; + . + [ @@ -3761,7 +3794,7 @@ [ "obo2owl" ; - "http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/ascomycete_phenotype.obo" + "https://raw.githubusercontent.com/obophenotype/ascomycete-phenotype-ontology/master/apo.obo" ] ; ; @@ -3780,7 +3813,7 @@ "maria@genome.stanford.edu" ] ; - ; + , ; . @@ -4354,7 +4387,7 @@ [ - "svn co http://obo-relations.googlecode.com/svn/trunk/src/ontology" ; + "git clone https://github.com/oborel/obo-relations.git" ; "vcs" ] ; @@ -4538,12 +4571,6 @@ . - - - "OntoBee" ; - - "OntoBee Ontology Browser" . - "Oryzias" . @@ -4828,14 +4855,14 @@ "http://purl.obolibrary.org/obo/ehdaa2.owl" . - - - "The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease." . - "http://purl.obolibrary.org/obo/bfo.owl" . + + + "The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease." . + [ @@ -5151,12 +5178,6 @@ "http://purl.obolibrary.org/obo/fbdv.owl" . - - - "Aber-OWL" ; - - "Aber-OWL Ontology Browser" . - "Relation Ontology in obo format" ; @@ -5377,10 +5398,6 @@ . - - - "http://purl.obolibrary.org/obo/zfs.owl" . - "Vertebrate Taxonomy Ontology" ; @@ -5391,6 +5408,10 @@ . + + + "http://purl.obolibrary.org/obo/zfs.owl" . + "http://purl.obolibrary.org/obo/hao.owl" . diff --git a/registry/ontologies.yml b/registry/ontologies.yml index 745a3b31f..e04eeb6e9 100644 --- a/registry/ontologies.yml +++ b/registry/ontologies.yml @@ -115,9 +115,7 @@ ontologies: title: Ontology for Biomedical Investigations tracker: http://purl.obofoundry.org/obo/obi/tracker - browsers: - - {label: Aber-OWL, title: Aber-OWL Ontology Browser, url: 'http://aber-owl.net/ontology/PATO'} - {label: BioPortal, title: BioPortal Ontology Browser, url: 'https://bioportal.bioontology.org/ontologies/PATO'} - - {label: OntoBee, title: OntoBee Browser, url: 'http://www.ontobee.org/browser/index.php?o=PATO'} build: {infallible: 1, method: obo2owl, source_url: 'https://raw.githubusercontent.com/pato-ontology/pato/master/pato.obo'} contact: {email: g.gkoutos@gmail.com, label: George Gkoutos} description: An ontology of phenotypic qualities (properties, attributes or characteristics) @@ -248,7 +246,7 @@ ontologies: products: - {id: aero.owl, ontology_purl: 'http://purl.obolibrary.org/obo/aero.owl'} title: Adverse Event Reporting Ontology -- build: {method: obo2owl, source_url: 'http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/ascomycete_phenotype.obo'} +- build: {method: obo2owl, source_url: 'https://raw.githubusercontent.com/obophenotype/ascomycete-phenotype-ontology/master/apo.obo'} contact: {email: maria@genome.stanford.edu, label: Maria Costanza} description: A structured controlled vocabulary for the phenotypes of Ascomycete fungi @@ -259,6 +257,7 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/apo.owl products: - {id: apo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/apo.owl'} + - {id: apo.obo, ontology_purl: 'http://purl.obolibrary.org/obo/apo.obo'} taxon: {id: 'NCBITaxon:4890', label: Ascomycota} title: Ascomycete phenotype ontology - contact: {email: jiezheng@upenn.edu, label: Jie Zheng} @@ -1297,9 +1296,7 @@ ontologies: termgenie: http://mp.termgenie.org title: Mammalian phenotype tracker: https://github.com/obophenotype/mammalian-phenotype-ontology/issues -- browsers: - - {label: Aber-OWL, title: Aber-OWL Ontology Repository, url: 'http://aber-owl.net/ontology/MPATH'} - build: {method: obo2owl, source_url: 'https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo'} +- build: {method: obo2owl, source_url: 'https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo'} contact: {email: pns12@cam.ac.uk, label: Paul Schofield} description: A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes @@ -1348,9 +1345,7 @@ ontologies: - {id: ms.owl, ontology_purl: 'http://purl.obolibrary.org/obo/ms.owl'} title: Mass spectrometry ontology - browsers: - - {label: Aber-OWL, title: Aber-OWL Ontology Browser, url: 'http://aber-owl.net/ontology/NBO'} - {label: BioPortal, title: BioPortal Ontology Browser, url: 'https://bioportal.bioontology.org/ontologies/NBO'} - - {label: OntoBee, title: OntoBee Ontology Browser, url: 'http://www.ontobee.org/browser/index.php?o=NBO'} build: {checkout: 'git clone https://github.com/bio-ontology-research-group/behavior-ontology.git', method: vcs, path: ., system: git} contact: {email: g.gkoutos@gmail.com, label: George Gkoutos} @@ -1400,6 +1395,22 @@ ontologies: layout: ontology_detail title: NCI Thesaurus uri_prefix: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl# +- browsers: null + contact: {email: huang@southalabama.edu, label: Jingshan Huang} + description: An ontology for non-coding RNA, both of biological origin, and engineered. + domain: experiments + homepage: http://omnisearch.soc.southalabama.edu/OntologyFile.aspx + id: ncro + layout: ontology_detail + license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png', + url: 'http://creativecommons.org/licenses/by/4.0/'} + mailing_list: ncro-devel@googlegroups.com + ontology_purl: http://purl.obolibrary.org/obo/ncro.owl + products: + - {id: ncro/dev/ncro.owl, ontology_purl: 'http://purl.obolibrary.org/obo/ncro/dev/ncro.owl', + title: NCRO development version} + title: non-coding RNA Ontology + tracker: https://github.com/OmniSearch/NCRO-Ontology-Files/issues - build: {method: owl2obo, source_url: 'http://svn.code.sf.net/p/oae/code/trunk/src/ontology/oae.owl'} contact: {email: yongqunh@med.umich.edu, label: Yongqunh He} description: A biomedical ontology in the domain of adverse events @@ -1659,8 +1670,8 @@ ontologies: - {id: rnao.owl, ontology_purl: 'http://purl.obolibrary.org/obo/rnao.owl'} - {id: rnao.obo, ontology_purl: 'http://purl.obolibrary.org/obo/rnao.obo'} title: RNA ontology -- build: {checkout: 'svn co http://obo-relations.googlecode.com/svn/trunk/src/ontology', - infallible: 1, method: vcs, system: svn} +- build: {checkout: 'git clone https://github.com/oborel/obo-relations.git', infallible: 1, + method: vcs, system: git} canonical: ro.owl contact: {email: cjmungall@lbl.gov, label: Chris Mungall} description: Relationship types shared across multiple ontologies @@ -1669,6 +1680,7 @@ ontologies: id: ro jobs: - {id: 'http://build.berkeleybop.org/job/build-ro', type: DryRunBuild} + - {id: 'https://travis-ci.org/oborel/obo-relations', type: travis-ci} layout: ontology_detail license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png', url: 'http://creativecommons.org/licenses/by/3.0/'} @@ -1882,7 +1894,10 @@ ontologies: - {id: tgma.owl, ontology_purl: 'http://purl.obolibrary.org/obo/tgma.owl'} taxon: {id: 'NCBITaxon:44484', label: Anopheles} title: Mosquito gross anatomy -- build: {infallible: 1, method: obo2owl, source_url: 'https://raw.githubusercontent.com/Planteome/plant-trait-ontology/master/to-release-files/plant-trait-ontology.obo'} +- browsers: + - {label: Planteome, title: Planteome browser, url: 'http://dev.planteome.org/amigo/term/TO:0000387'} + build: {checkout: 'git clone https://github.com/Planteome/plant-trait-ontology.git', + infallible: 1, method: vcs, path: ., system: git} contact: {email: jaiswalp@science.oregonstate.edu, label: Pankaj Jaiswal} description: A controlled vocabulary of describe phenotypic traits in plants. domain: phenotype @@ -1895,6 +1910,7 @@ ontologies: page: http://planteome.org/amigo/cgi-bin/crop_amigo/term_details?term=TO:0000387&session_id=815amigo1442021959 products: - {id: to.owl, ontology_purl: 'http://purl.obolibrary.org/obo/to.owl'} + - {id: to.obo, ontology_purl: 'http://purl.obolibrary.org/obo/to.obo'} publications: - {id: 'http://www.ncbi.nlm.nih.gov/pubmed/22847540', title: Ontologies as integrative tools for plant science.} diff --git a/util/processor.py b/util/processor.py index 9b9ba2341..b56656152 100755 --- a/util/processor.py +++ b/util/processor.py @@ -180,6 +180,7 @@ def sparql_compare_ont(obj): run_sparql(obj, 'license', license, "SELECT DISTINCT ?license WHERE {<"+purl+"> ?license}") run_sparql(obj, 'title', obj['title'] if 'title' in obj else '', "SELECT DISTINCT ?title WHERE {<"+purl+"> ?title}") run_sparql(obj, 'description', obj['description'] if 'description' in obj else '', "SELECT DISTINCT ?description WHERE {<"+purl+"> ?description}") + run_sparql(obj, 'homepage', obj['homepage'] if 'homepage' in obj else '', "SELECT DISTINCT ?homepage WHERE {<"+purl+"> ?homepage}") def run_sparql(obj, p, expected_value, q): sparql = SPARQLWrapper("http://sparql.hegroup.org/sparql")