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

pporrasebi · Nov 19, 2015 · cc6c831 · cc6c831
1 parent ee22e3f
commit cc6c831
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Showing 6 changed files with 262 additions and 186 deletions.
diff --git 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: [email protected], 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: [email protected], 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: [email protected], 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: [email protected], 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: [email protected], 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: [email protected], 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: [email protected]
+  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: [email protected], 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: [email protected], 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: [email protected], 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
@@ -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
@@ -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": "[email protected]",
@@ -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": "[email protected]",
+                "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": "[email protected]",
+            "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": "[email protected]",
@@ -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": [