regenerated registry

OBOFoundry · May 13, 2016 · dd5ef3e · dd5ef3e
1 parent 15669ad
commit dd5ef3e
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Showing 6 changed files with 202 additions and 122 deletions.
diff --git a/Makefile b/Makefile
@@ -108,6 +108,7 @@ 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:

diff --git a/_config.yml b/_config.yml
@@ -468,10 +468,7 @@ ontologies:
   termgenie: http://cl.termgenie.org
   title: Cell Ontology
   tracker: https://github.com/obophenotype/cell-ontology/issues
-- build: {checkout: 'svn --ignore-externals co http://clo-ontology.googlecode.com/svn/trunk/src/ontology',
-    method: vcs, post_processing_command: owltools --use-catalog clo.owl --merge-imports-closure
-      --ni -o -f obo --no-check clo.obo, system: svn}
-  contact: {email: Sirarat.Sarntivijai@fda.hhs.gov, label: Sirarat Sarntivijai}
+- contact: {email: Sirarat.Sarntivijai@fda.hhs.gov, label: Sirarat Sarntivijai}
   dependencies:
   - {id: uberon}
   - {id: cl}
@@ -482,6 +479,8 @@ ontologies:
   homepage: http://www.clo-ontology.org
   id: clo
   layout: ontology_detail
+  license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
+    url: 'http://creativecommons.org/licenses/by/3.0/'}
   ontology_purl: http://purl.obolibrary.org/obo/clo.owl
   products:
   - {id: clo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/clo.owl'}
@@ -803,6 +802,7 @@ ontologies:
   page: http://ctdbase.org/downloads/#exposures
   products:
   - {id: exo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/exo.owl'}
+  - {id: exo.obo, ontology_purl: 'http://purl.obolibrary.org/obo/exo.obo'}
   title: Exposure ontology
 - build: {insert_ontology_id: true, method: obo2owl, source_url: 'http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/microbial_gross_anatomy/fungi/fungal_anatomy.obo'}
   contact: {email: maria@genome.stanford.edu, label: Maria Costanzo}
@@ -909,7 +909,8 @@ ontologies:
   products:
   - {id: fix.owl, ontology_purl: 'http://purl.obolibrary.org/obo/fix.owl'}
   title: Physico-chemical methods and properties
-- contact: {email: robert.hoehndorf@kaust.edu.sa, label: Robert Hoehndorf}
+- build: {method: owl2obo, source_url: 'https://github.com/flora-phenotype-ontology/flopoontology/raw/master/ontology/flopo.owl'}
+  contact: {email: robert.hoehndorf@kaust.edu.sa, label: Robert Hoehndorf}
   description: Traits and phenotypes of flowering plants occurring in digitized Floras
   domain: phenotype
   homepage: https://github.com/flora-phenotype-ontology/flopoontology
@@ -1227,6 +1228,7 @@ ontologies:
   page: https://rawgit.com/MICommunity/psidev/master/psi/mi/xml/doc/user/index.html
   products:
   - {id: mi.owl, ontology_purl: 'http://purl.obolibrary.org/obo/mi.owl'}
+  - {id: mi.obo, ontology_purl: 'http://purl.obolibrary.org/obo/mi.obo'}
   title: Molecular interactions
 - contact: {email: hlapp@drycafe.net, label: Hilamr Lapp}
   description: An application ontology to formalize annotation of phylogenetic data.
@@ -1378,8 +1380,9 @@ ontologies:
   - {id: mro.owl, ontology_purl: 'http://purl.obolibrary.org/obo/mro.owl'}
   title: MHC Restriction Ontology
   tracker: https://github.com/IEDB/MRO/issues
-- build: {method: obo2owl, source_url: 'https://raw.githubusercontent.com/MICommunity/psidev/master/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo'}
+- build: {method: obo2owl, source_url: 'https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo'}
   contact: {email: gerhard.mayer@rub.de, label: Gerhard Mayer}
+  createdWith: http://oboedit.org
   dependencies:
   - {id: pato}
   - {id: uo}
@@ -1388,15 +1391,20 @@ ontologies:
   domain: MS experiments
   homepage: http://www.psidev.info/groups/controlled-vocabularies
   id: ms
-  integration_server: https://raw.githubusercontent.com/MICommunity/psidev/master/psi/psi-ms/mzML/controlledVocabulary/
-  label: Mass spectrometry ontology
+  integration_server: https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master
+  label: MS
   layout: ontology_detail
+  license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
+    url: 'https://creativecommons.org/licenses/by/3.0/'}
   mailing_list: psidev-ms-vocab@lists.sourceforge.net
   ontology_purl: http://purl.obolibrary.org/obo/ms.owl
   page: http://www.psidev.info/groups/controlled-vocabularies
   products:
   - {id: ms.obo, ontology_purl: 'http://purl.obolibrary.org/obo/ms.obo'}
   - {id: ms.owl, ontology_purl: 'http://purl.obolibrary.org/obo/ms.owl'}
+  publications:
+  - {id: 'http://www.ncbi.nlm.nih.gov/pubmed/23482073', title: The HUPO proteomics
+      standards initiative- mass spectrometry controlled vocabulary.}
   title: Mass spectrometry ontology
 - browsers:
   - {label: BioPortal, title: BioPortal Ontology Browser, url: 'https://bioportal.bioontology.org/ontologies/NBO'}
@@ -1717,6 +1725,9 @@ ontologies:
   ontology_purl: http://purl.obolibrary.org/obo/poro.owl
   products:
   - {id: poro.owl, ontology_purl: 'http://purl.obolibrary.org/obo/poro.owl'}
+  publications:
+  - {id: 'http://dx.doi.org/10.1186/2041-1480-5-39', title: 'The Porifera Ontology
+      (PORO): enhancing sponge systematics with an anatomy ontology'}
   taxon: {id: 'NCBITaxon:6040', label: Porifera}
   title: Porifera Ontology
   tracker: https://github.com/obophenotype/porifera-ontology/issues

diff --git a/registry/ontologies.jsonld b/registry/ontologies.jsonld
@@ -932,12 +932,6 @@
             "tracker": "https://github.com/obophenotype/cell-ontology/issues"
         },
         {
-            "build": {
-                "checkout": "svn --ignore-externals co http://clo-ontology.googlecode.com/svn/trunk/src/ontology",
-                "method": "vcs",
-                "post_processing_command": "owltools --use-catalog clo.owl --merge-imports-closure --ni -o -f obo --no-check clo.obo",
-                "system": "svn"
-            },
             "contact": {
                 "email": "Sirarat.Sarntivijai@fda.hhs.gov",
                 "label": "Sirarat Sarntivijai"
@@ -960,6 +954,11 @@
             "homepage": "http://www.clo-ontology.org",
             "id": "clo",
             "layout": "ontology_detail",
+            "license": {
+                "label": "CC-BY",
+                "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
+                "url": "http://creativecommons.org/licenses/by/3.0/"
+            },
             "ontology_purl": "http://purl.obolibrary.org/obo/clo.owl",
             "products": [
                 {
@@ -1623,6 +1622,10 @@
                 {
                     "id": "exo.owl",
                     "ontology_purl": "http://purl.obolibrary.org/obo/exo.owl"
+                },
+                {
+                    "id": "exo.obo",
+                    "ontology_purl": "http://purl.obolibrary.org/obo/exo.obo"
                 }
             ],
             "title": "Exposure ontology"
@@ -1864,6 +1867,10 @@
             "title": "Physico-chemical methods and properties"
         },
         {
+            "build": {
+                "method": "owl2obo",
+                "source_url": "https://github.com/flora-phenotype-ontology/flopoontology/raw/master/ontology/flopo.owl"
+            },
             "contact": {
                 "email": "robert.hoehndorf@kaust.edu.sa",
                 "label": "Robert Hoehndorf"
@@ -2515,6 +2522,10 @@
                 {
                     "id": "mi.owl",
                     "ontology_purl": "http://purl.obolibrary.org/obo/mi.owl"
+                },
+                {
+                    "id": "mi.obo",
+                    "ontology_purl": "http://purl.obolibrary.org/obo/mi.obo"
                 }
             ],
             "title": "Molecular interactions"
@@ -2836,12 +2847,13 @@
         {
             "build": {
                 "method": "obo2owl",
-                "source_url": "https://raw.githubusercontent.com/MICommunity/psidev/master/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"
+                "source_url": "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"
             },
             "contact": {
                 "email": "gerhard.mayer@rub.de",
                 "label": "Gerhard Mayer"
             },
+            "createdWith": "http://oboedit.org",
             "dependencies": [
                 {
                     "id": "pato"
@@ -2854,9 +2866,14 @@
             "domain": "MS experiments",
             "homepage": "http://www.psidev.info/groups/controlled-vocabularies",
             "id": "ms",
-            "integration_server": "https://raw.githubusercontent.com/MICommunity/psidev/master/psi/psi-ms/mzML/controlledVocabulary/",
-            "label": "Mass spectrometry ontology",
+            "integration_server": "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master",
+            "label": "MS",
             "layout": "ontology_detail",
+            "license": {
+                "label": "CC-BY",
+                "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
+                "url": "https://creativecommons.org/licenses/by/3.0/"
+            },
             "mailing_list": "psidev-ms-vocab@lists.sourceforge.net",
             "ontology_purl": "http://purl.obolibrary.org/obo/ms.owl",
             "page": "http://www.psidev.info/groups/controlled-vocabularies",
@@ -2870,6 +2887,12 @@
                     "ontology_purl": "http://purl.obolibrary.org/obo/ms.owl"
                 }
             ],
+            "publications": [
+                {
+                    "id": "http://www.ncbi.nlm.nih.gov/pubmed/23482073",
+                    "title": "The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary."
+                }
+            ],
             "title": "Mass spectrometry ontology"
         },
         {
@@ -3503,6 +3526,12 @@
                     "ontology_purl": "http://purl.obolibrary.org/obo/poro.owl"
                 }
             ],
+            "publications": [
+                {
+                    "id": "http://dx.doi.org/10.1186/2041-1480-5-39",
+                    "title": "The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology"
+                }
+            ],
             "taxon": {
                 "id": "NCBITaxon:6040",
                 "label": "Porifera"