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Regenerated downstream products using "make". Fixes OBOFoundry#165 
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‎_config.yml

+27-11
Original file line numberDiff line numberDiff line change
@@ -123,9 +123,7 @@ ontologies:
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title: Ontology for Biomedical Investigations
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tracker: http://purl.obofoundry.org/obo/obi/tracker
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- browsers:
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- {label: Aber-OWL, title: Aber-OWL Ontology Browser, url: 'http://aber-owl.net/ontology/PATO'}
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- {label: BioPortal, title: BioPortal Ontology Browser, url: 'https://bioportal.bioontology.org/ontologies/PATO'}
128-
- {label: OntoBee, title: OntoBee Browser, url: 'http://www.ontobee.org/browser/index.php?o=PATO'}
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build: {infallible: 1, method: obo2owl, source_url: 'https://raw.githubusercontent.com/pato-ontology/pato/master/pato.obo'}
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contact: {email: [email protected], label: George Gkoutos}
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description: An ontology of phenotypic qualities (properties, attributes or characteristics)
@@ -256,7 +254,7 @@ ontologies:
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products:
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- {id: aero.owl, ontology_purl: 'http://purl.obolibrary.org/obo/aero.owl'}
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title: Adverse Event Reporting Ontology
259-
- build: {method: obo2owl, source_url: 'http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/ascomycete_phenotype.obo'}
257+
- build: {method: obo2owl, source_url: 'https://raw.githubusercontent.com/obophenotype/ascomycete-phenotype-ontology/master/apo.obo'}
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contact: {email: [email protected], label: Maria Costanza}
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description: A structured controlled vocabulary for the phenotypes of Ascomycete
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fungi
@@ -267,6 +265,7 @@ ontologies:
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ontology_purl: http://purl.obolibrary.org/obo/apo.owl
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products:
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- {id: apo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/apo.owl'}
268+
- {id: apo.obo, ontology_purl: 'http://purl.obolibrary.org/obo/apo.obo'}
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taxon: {id: 'NCBITaxon:4890', label: Ascomycota}
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title: Ascomycete phenotype ontology
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- contact: {email: [email protected], label: Jie Zheng}
@@ -1305,9 +1304,7 @@ ontologies:
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termgenie: http://mp.termgenie.org
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title: Mammalian phenotype
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tracker: https://github.com/obophenotype/mammalian-phenotype-ontology/issues
1308-
- browsers:
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- {label: Aber-OWL, title: Aber-OWL Ontology Repository, url: 'http://aber-owl.net/ontology/MPATH'}
1310-
build: {method: obo2owl, source_url: 'https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo'}
1307+
- build: {method: obo2owl, source_url: 'https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo'}
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contact: {email: [email protected], label: Paul Schofield}
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description: A structured controlled vocabulary of mutant and transgenic mouse pathology
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phenotypes
@@ -1356,9 +1353,7 @@ ontologies:
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- {id: ms.owl, ontology_purl: 'http://purl.obolibrary.org/obo/ms.owl'}
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title: Mass spectrometry ontology
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- browsers:
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- {label: Aber-OWL, title: Aber-OWL Ontology Browser, url: 'http://aber-owl.net/ontology/NBO'}
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- {label: BioPortal, title: BioPortal Ontology Browser, url: 'https://bioportal.bioontology.org/ontologies/NBO'}
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- {label: OntoBee, title: OntoBee Ontology Browser, url: 'http://www.ontobee.org/browser/index.php?o=NBO'}
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build: {checkout: 'git clone https://github.com/bio-ontology-research-group/behavior-ontology.git',
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method: vcs, path: ., system: git}
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contact: {email: [email protected], label: George Gkoutos}
@@ -1408,6 +1403,22 @@ ontologies:
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layout: ontology_detail
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title: NCI Thesaurus
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uri_prefix: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#
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- browsers: null
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contact: {email: [email protected], label: Jingshan Huang}
1408+
description: An ontology for non-coding RNA, both of biological origin, and engineered.
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domain: experiments
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homepage: http://omnisearch.soc.southalabama.edu/OntologyFile.aspx
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id: ncro
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layout: ontology_detail
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license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
1414+
url: 'http://creativecommons.org/licenses/by/4.0/'}
1415+
mailing_list: [email protected]
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ontology_purl: http://purl.obolibrary.org/obo/ncro.owl
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products:
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- {id: ncro/dev/ncro.owl, ontology_purl: 'http://purl.obolibrary.org/obo/ncro/dev/ncro.owl',
1419+
title: NCRO development version}
1420+
title: non-coding RNA Ontology
1421+
tracker: https://github.com/OmniSearch/NCRO-Ontology-Files/issues
14111422
- build: {method: owl2obo, source_url: 'http://svn.code.sf.net/p/oae/code/trunk/src/ontology/oae.owl'}
14121423
contact: {email: [email protected], label: Yongqunh He}
14131424
description: A biomedical ontology in the domain of adverse events
@@ -1667,8 +1678,8 @@ ontologies:
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- {id: rnao.owl, ontology_purl: 'http://purl.obolibrary.org/obo/rnao.owl'}
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- {id: rnao.obo, ontology_purl: 'http://purl.obolibrary.org/obo/rnao.obo'}
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title: RNA ontology
1670-
- build: {checkout: 'svn co http://obo-relations.googlecode.com/svn/trunk/src/ontology',
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infallible: 1, method: vcs, system: svn}
1681+
- build: {checkout: 'git clone https://github.com/oborel/obo-relations.git', infallible: 1,
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method: vcs, system: git}
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canonical: ro.owl
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contact: {email: [email protected], label: Chris Mungall}
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description: Relationship types shared across multiple ontologies
@@ -1677,6 +1688,7 @@ ontologies:
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id: ro
16781689
jobs:
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- {id: 'http://build.berkeleybop.org/job/build-ro', type: DryRunBuild}
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- {id: 'https://travis-ci.org/oborel/obo-relations', type: travis-ci}
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layout: ontology_detail
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license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
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url: 'http://creativecommons.org/licenses/by/3.0/'}
@@ -1890,7 +1902,10 @@ ontologies:
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- {id: tgma.owl, ontology_purl: 'http://purl.obolibrary.org/obo/tgma.owl'}
18911903
taxon: {id: 'NCBITaxon:44484', label: Anopheles}
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title: Mosquito gross anatomy
1893-
- build: {infallible: 1, method: obo2owl, source_url: 'https://raw.githubusercontent.com/Planteome/plant-trait-ontology/master/to-release-files/plant-trait-ontology.obo'}
1905+
- browsers:
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- {label: Planteome, title: Planteome browser, url: 'http://dev.planteome.org/amigo/term/TO:0000387'}
1907+
build: {checkout: 'git clone https://github.com/Planteome/plant-trait-ontology.git',
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infallible: 1, method: vcs, path: ., system: git}
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contact: {email: [email protected], label: Pankaj Jaiswal}
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description: A controlled vocabulary of describe phenotypic traits in plants.
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domain: phenotype
@@ -1903,6 +1918,7 @@ ontologies:
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page: http://planteome.org/amigo/cgi-bin/crop_amigo/term_details?term=TO:0000387&session_id=815amigo1442021959
19041919
products:
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- {id: to.owl, ontology_purl: 'http://purl.obolibrary.org/obo/to.owl'}
1921+
- {id: to.obo, ontology_purl: 'http://purl.obolibrary.org/obo/to.obo'}
19061922
publications:
19071923
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/22847540', title: Ontologies as integrative
19081924
tools for plant science.}

‎ontology/ro.md

+2-2
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@@ -3,8 +3,8 @@ layout: ontology_detail
33
id: ro
44
title: Relations Ontology
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build:
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checkout: svn co http://obo-relations.googlecode.com/svn/trunk/src/ontology
7-
system: svn
6+
checkout: git clone https://github.com/oborel/obo-relations.git
7+
system: git
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method: vcs
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infallible: 1
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canonical: ro.owl

‎registry/ontologies.jsonld

+54-32
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@@ -238,20 +238,10 @@
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},
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{
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"browsers": [
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{
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"label": "Aber-OWL",
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"title": "Aber-OWL Ontology Browser",
244-
"url": "http://aber-owl.net/ontology/PATO"
245-
},
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{
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"label": "BioPortal",
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"title": "BioPortal Ontology Browser",
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"url": "https://bioportal.bioontology.org/ontologies/PATO"
250-
},
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{
252-
"label": "OntoBee",
253-
"title": "OntoBee Browser",
254-
"url": "http://www.ontobee.org/browser/index.php?o=PATO"
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}
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],
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"build": {
@@ -517,7 +507,7 @@
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{
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"build": {
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"method": "obo2owl",
520-
"source_url": "http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/ascomycete_phenotype.obo"
510+
"source_url": "https://raw.githubusercontent.com/obophenotype/ascomycete-phenotype-ontology/master/apo.obo"
521511
},
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"contact": {
523513
"email": "[email protected]",
@@ -533,6 +523,10 @@
533523
{
534524
"id": "apo.owl",
535525
"ontology_purl": "http://purl.obolibrary.org/obo/apo.owl"
526+
},
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{
528+
"id": "apo.obo",
529+
"ontology_purl": "http://purl.obolibrary.org/obo/apo.obo"
536530
}
537531
],
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"taxon": {
@@ -2678,13 +2672,6 @@
26782672
"tracker": "https://github.com/obophenotype/mammalian-phenotype-ontology/issues"
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},
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{
2681-
"browsers": [
2682-
{
2683-
"label": "Aber-OWL",
2684-
"title": "Aber-OWL Ontology Repository",
2685-
"url": "http://aber-owl.net/ontology/MPATH"
2686-
}
2687-
],
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"build": {
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"method": "obo2owl",
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"source_url": "https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo"
@@ -2782,20 +2769,10 @@
27822769
},
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{
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"browsers": [
2785-
{
2786-
"label": "Aber-OWL",
2787-
"title": "Aber-OWL Ontology Browser",
2788-
"url": "http://aber-owl.net/ontology/NBO"
2789-
},
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{
27912773
"label": "BioPortal",
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"title": "BioPortal Ontology Browser",
27932775
"url": "https://bioportal.bioontology.org/ontologies/NBO"
2794-
},
2795-
{
2796-
"label": "OntoBee",
2797-
"title": "OntoBee Ontology Browser",
2798-
"url": "http://www.ontobee.org/browser/index.php?o=NBO"
27992776
}
28002777
],
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"build": {
@@ -2895,6 +2872,34 @@
28952872
"title": "NCI Thesaurus",
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"uri_prefix": "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#"
28972874
},
2875+
{
2876+
"browsers": null,
2877+
"contact": {
2878+
"email": "[email protected]",
2879+
"label": "Jingshan Huang"
2880+
},
2881+
"description": "An ontology for non-coding RNA, both of biological origin, and engineered.",
2882+
"domain": "experiments",
2883+
"homepage": "http://omnisearch.soc.southalabama.edu/OntologyFile.aspx",
2884+
"id": "ncro",
2885+
"layout": "ontology_detail",
2886+
"license": {
2887+
"label": "CC-BY",
2888+
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
2889+
"url": "http://creativecommons.org/licenses/by/4.0/"
2890+
},
2891+
"mailing_list": "[email protected]",
2892+
"ontology_purl": "http://purl.obolibrary.org/obo/ncro.owl",
2893+
"products": [
2894+
{
2895+
"id": "ncro/dev/ncro.owl",
2896+
"ontology_purl": "http://purl.obolibrary.org/obo/ncro/dev/ncro.owl",
2897+
"title": "NCRO development version"
2898+
}
2899+
],
2900+
"title": "non-coding RNA Ontology",
2901+
"tracker": "https://github.com/OmniSearch/NCRO-Ontology-Files/issues"
2902+
},
28982903
{
28992904
"build": {
29002905
"method": "owl2obo",
@@ -3416,10 +3421,10 @@
34163421
},
34173422
{
34183423
"build": {
3419-
"checkout": "svn co http://obo-relations.googlecode.com/svn/trunk/src/ontology",
3424+
"checkout": "git clone https://github.com/oborel/obo-relations.git",
34203425
"infallible": 1,
34213426
"method": "vcs",
3422-
"system": "svn"
3427+
"system": "git"
34233428
},
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"canonical": "ro.owl",
34253430
"contact": {
@@ -3434,6 +3439,10 @@
34343439
{
34353440
"id": "http://build.berkeleybop.org/job/build-ro",
34363441
"type": "DryRunBuild"
3442+
},
3443+
{
3444+
"id": "https://travis-ci.org/oborel/obo-relations",
3445+
"type": "travis-ci"
34373446
}
34383447
],
34393448
"layout": "ontology_detail",
@@ -3862,10 +3871,19 @@
38623871
"title": "Mosquito gross anatomy"
38633872
},
38643873
{
3874+
"browsers": [
3875+
{
3876+
"label": "Planteome",
3877+
"title": "Planteome browser",
3878+
"url": "http://dev.planteome.org/amigo/term/TO:0000387"
3879+
}
3880+
],
38653881
"build": {
3882+
"checkout": "git clone https://github.com/Planteome/plant-trait-ontology.git",
38663883
"infallible": 1,
3867-
"method": "obo2owl",
3868-
"source_url": "https://raw.githubusercontent.com/Planteome/plant-trait-ontology/master/to-release-files/plant-trait-ontology.obo"
3884+
"method": "vcs",
3885+
"path": ".",
3886+
"system": "git"
38693887
},
38703888
"contact": {
38713889
"email": "[email protected]",
@@ -3887,6 +3905,10 @@
38873905
{
38883906
"id": "to.owl",
38893907
"ontology_purl": "http://purl.obolibrary.org/obo/to.owl"
3908+
},
3909+
{
3910+
"id": "to.obo",
3911+
"ontology_purl": "http://purl.obolibrary.org/obo/to.obo"
38903912
}
38913913
],
38923914
"publications": [

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