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pporrasebi · Oct 21, 2015 · dede109 · dede109
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diff --git a/_config.yml b/_config.yml
@@ -212,8 +212,9 @@ ontologies:
   browsers:
   - {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: archive, path: archive/main, source_url: 'http://build.berkeleybop.org/job/build-chebi/lastSuccessfulBuild/artifact/*zip*/archive.zip'}
-  contact: {email: [email protected], label: Janna Hastings}
-  description: A structured classification of chemical compounds of biological relevance.
+  contact: {email: [email protected], label: Gareth Owen}
+  description: A structured classification of molecular entities of biological interest
+    focusing on 'small' chemical compounds.
   domain: biochemistry
   homepage: http://www.ebi.ac.uk/chebi
   id: chebi
@@ -224,7 +225,7 @@ ontologies:
   products:
   - {id: chebi.owl, ontology_purl: 'http://purl.obolibrary.org/obo/chebi.owl'}
   - {id: chebi.obo, ontology_purl: 'http://purl.obolibrary.org/obo/chebi.obo'}
-  title: Chemical entities of biological interest
+  title: Chemical Entities of Biological Interest
   tracker: https://sourceforge.net/p/chebi/curator-requests/
   twitter: chebit
 - build: {method: owl2obo, source_url: 'http://semanticchemistry.googlecode.com/svn/trunk/ontology/cheminf.owl'}
@@ -603,7 +604,8 @@ ontologies:
   homepage: http://planteome.org/
   id: eo
   layout: ontology_detail
-  license: {label: CC-BY, url: 'https://creativecommons.org/licenses/by/3.0/'}
+  license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
+    url: 'https://creativecommons.org/licenses/by/3.0/'}
   ontology_purl: http://purl.obolibrary.org/obo/eo.owl
   page: http://planteome.org/amigo/cgi-bin/crop_amigo/term_details?term=EO:0007359&session_id=815amigo1442021959
   products:
@@ -1190,6 +1192,16 @@ ontologies:
   - {id: miapa.owl, ontology_purl: 'http://purl.obolibrary.org/obo/miapa.owl'}
   title: MIAPA Ontology
   tracker: https://github.com/miapa/miapa/issues
+- contact: {email: [email protected], label: Carrine Blank}
+  description: An ontology of prokaryotic phenotypic and metabolic characters
+  domain: phenotype
+  homepage: https://github.com/carrineblank/MicrO
+  id: micro
+  issue: https://github.com/carrineblank/MicrO/issues
+  layout: ontology_detail
+  license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
+    url: 'http://creativecommons.org/licenses/by/2.0/'}
+  title: prokaryotic phenotypic and metabolic characters
 - contact: {email: [email protected], label: Vicky Dritsou}
   description: An application ontology for use with miRNA databases.
   homepage: http://code.google.com/p/mirna-ontology/
@@ -1304,25 +1316,31 @@ ontologies:
   termgenie: http://mp.termgenie.org
   title: Mammalian phenotype
   tracker: https://github.com/obophenotype/mammalian-phenotype-ontology/issues
-- build: {method: obo2owl, source_url: 'http://mpath.googlecode.com/svn/trunk/mpath.obo'}
-  contact: {email: [email protected], label: Paul Schofield}
+- 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'}
+  contact: {email: [email protected], label: Paul Schofield}
   description: A structured controlled vocabulary of mutant and transgenic mouse pathology
     phenotypes
   domain: health
   homepage: http://www.pathbase.net
   id: mpath
   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/mpath.owl
   products:
   - {id: mpath.owl, ontology_purl: 'http://purl.obolibrary.org/obo/mpath.owl'}
   taxon: {id: 'NCBITaxon:10088', label: Mus}
   title: Mouse pathology
+  tracker: https://github.com/PaulNSchofield/mpath/issues
 - contact: {email: [email protected], label: Bjoern Peters}
   description: Represents MHC restrictions
   homepage: https://github.com/IEDB/MRO
   id: mro
   layout: ontology_detail
-  license: {label: CC-BY, url: 'https://creativecommons.org/licenses/by/3.0/'}
+  license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
+    url: 'https://creativecommons.org/licenses/by/3.0/'}
   ontology_purl: http://purl.obolibrary.org/obo/mro.owl
   products:
   - {id: mro.owl, ontology_purl: 'http://purl.obolibrary.org/obo/mro.owl'}
@@ -1348,26 +1366,32 @@ ontologies:
   - {id: ms.obo, ontology_purl: 'http://purl.obolibrary.org/obo/ms.obo'}
   - {id: ms.owl, ontology_purl: 'http://purl.obolibrary.org/obo/ms.owl'}
   title: Mass spectrometry ontology
-- build: {checkout: 'svn co http://behavior-ontology.googlecode.com/svn/trunk', method: vcs,
-    system: svn}
-  contact: {email: [email protected], label: George Gkoutos}
+- 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}
   domain: behavior
-  homepage: http://code.google.com/p/behavior-ontology
+  homepage: https://github.com/bio-ontology-research-group/behavior-ontology/wiki
   id: nbo
   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/nbo.owl
   products:
   - {id: nbo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/nbo.owl'}
   title: Neuro Behavior Ontology
-  tracker: http://code.google.com/p/behavior-ontology/issues/list
+  tracker: https://github.com/bio-ontology-research-group/behavior-ontology/issues
 - browsers:
   - {label: NCBI, title: NCBI Taxonomy Browser, url: 'http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi'}
   build: {infallible: 1, method: archive, path: archive, source_url: 'http://build.berkeleybop.org/job/build-ncbitaxon/lastSuccessfulBuild/artifact/*zip*/archive.zip'}
   contact: {email: [email protected], label: obo-taxonomy-list}
   createdWith: http://owltools.googlecode.com/
   description: An ontology representation of the NCBI organismal taxonomy
   domain: taxonomy
-  homepage: http://www.obofoundry.org/wiki/index.php/NCBITaxon:Main_Page
+  homepage: https://github.com/obophenotype/ncbitaxon
   id: ncbitaxon
   jobs:
   - {id: 'http://build.berkeleybop.org/job/build-ncbitaxon/', type: ReleaseBuild}
@@ -1381,9 +1405,11 @@ ontologies:
   - {id: ncbitaxon.obo, ontology_purl: 'http://purl.obolibrary.org/obo/ncbitaxon.obo',
     title: OBO Format version of Main release}
   - {id: ncbitaxon/subsets/taxslim.owl, ontology_purl: 'http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl',
+    page: 'https://github.com/obophenotype/ncbitaxon/blob/master/subsets/README.md',
     title: taxslim}
   source: http://www.ncbi.nlm.nih.gov/taxonomy
   title: NCBI organismal classification
+  tracker: https://github.com/obophenotype/ncbitaxon/issues
   wasDerivedFrom: ftp://ftp.ebi.ac.uk/pub/databases/taxonomy/taxonomy.dat
 - contact: {email: NCICB Support, label: [email protected]}
   description: an ontology-like vocabulary that includes broad coverage of the cancer
@@ -1637,8 +1663,12 @@ ontologies:
   layout: ontology_detail
   taxon: {id: 'NCBITaxon:33090', label: Viridiplantae}
   title: Plant Anatomy Ontology
-- build: {infallible: 1, method: obo2owl, source_url: 'https://raw.githubusercontent.com/pato-ontology/pato/master/pato.obo'}
-  contact: {email: [email protected], label: George Gkoutos}
+- 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)
   domain: phenotype
   homepage: https://github.com/pato-ontology/pato/
@@ -1647,6 +1677,8 @@ ontologies:
   jobs:
   - {id: 'http://build.berkeleybop.org/job/build-pato', type: DryRunBuild}
   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/pato.owl
   products:
   - {id: pato.owl, ontology_purl: 'http://purl.obolibrary.org/obo/pato.owl'}
@@ -1710,7 +1742,8 @@ ontologies:
   id: po
   in_foundry_order: 1
   layout: ontology_detail
-  license: {label: CC-BY, url: 'https://creativecommons.org/licenses/by/3.0/'}
+  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/po.owl
   page: http://www.plantontology.org/amigo/go.cgi
   products:
@@ -2000,7 +2033,7 @@ ontologies:
   products:
   - {id: swo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/swo.owl'}
   title: Software ontology
-- build: {method: obo2owl, source_url: 'http://gemina.svn.sourceforge.net/viewvc/gemina/trunk/Gemina/ontologies/gemina_symptom.obo'}
+- build: {infallible: 1, method: obo2owl, source_url: 'https://sourceforge.net/p/diseaseontology/code/HEAD/tree/Symptom_Ontology/symptom_ontology.obo'}
   contact: {email: [email protected], label: Lynn Schriml}
   description: An ontology of disease symptoms, with symptoms encompasing perceived
     changes in function, sensations or appearance reported by a patient indicative
@@ -2017,6 +2050,7 @@ ontologies:
   - {id: symp.obo, ontology_purl: 'http://purl.obolibrary.org/obo/symp.obo'}
   taxon: {id: 'NCBITaxon:9606', label: Homo sapiens}
   title: Symptom Ontology
+  tracker: http://sourceforge.net/tracker/?func=add&group_id=79168&atid=555739
 - build: {method: obo2owl, source_url: 'http://anobase.vectorbase.org/anatomy/tick_anatomy.obo'}
   contact: {email: [email protected], label: Daniel Sonenshine}
   description: 'The anatomy of the Tick, <i>Families: Ixodidae, Argassidae</i>'
@@ -2088,7 +2122,8 @@ ontologies:
   homepage: http://planteome.org
   id: to
   layout: ontology_detail
-  license: {label: CC-BY, url: 'https://creativecommons.org/licenses/by/3.0/'}
+  license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
+    url: 'https://creativecommons.org/licenses/by/3.0/'}
   ontology_purl: http://purl.obolibrary.org/obo/to.owl
   page: http://planteome.org/amigo/cgi-bin/crop_amigo/term_details?term=TO:0000387&session_id=815amigo1442021959
   products:
@@ -2099,7 +2134,7 @@ ontologies:
   taxon: {id: 'NCBITaxon:33090', label: Viridiplantae}
   title: Plant Trait Ontology
   tracker: https://github.com/Planteome/plant-trait-ontology/issues
-- build: {method: obo2owl, source_url: 'http://gemina.cvs.sourceforge.net/*checkout*/gemina/Gemina/ontologies/transmission_process.obo'}
+- build: {infallible: 1, method: obo2owl, source_url: 'https://sourceforge.net/p/diseaseontology/code/HEAD/tree/Transmission_Process_Ontology/transmission_process_ontology.obo'}
   contact: {email: [email protected], label: Lynn Schriml}
   description: An ontology representing the disease transmission process during which
     the pathogen is transmitted directly or indirectly from its natural reservoir,
@@ -2115,7 +2150,7 @@ ontologies:
   - {id: trans.owl, ontology_purl: 'http://purl.obolibrary.org/obo/trans.owl'}
   - {id: trans.obo, ontology_purl: 'http://purl.obolibrary.org/obo/trans.obo'}
   title: Pathogen Transmission Ontology
-  tracker: http://sourceforge.net/tracker/?&group_id=76834&atid=1037853
+  tracker: http://sourceforge.net/tracker/?func=add&group_id=79168&atid=555739
 - build: {method: obo2owl, source_url: 'http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/taxonomy/teleost_taxonomy.obo'}
   contact: {email: [email protected], label: Peter Midford}
   description: An ontology covering the taxonomy of teleosts (bony fish)
@@ -2218,13 +2253,15 @@ ontologies:
   - {label: GO Database, type: Database, url: 'https://geneontology.org/'}
   wikidata_template: https://en.wikipedia.org/wiki/Template:Uberon
 - build: {method: obo2owl, source_url: 'https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo'}
-  contact: {email: [email protected], label: George Gkoutos}
+  contact: {email: [email protected], label: George Gkoutos}
   description: Metrical units for use in conjunction with PATO
   domain: phenotype
   homepage: https://github.com/bio-ontology-research-group/unit-ontology
   id: uo
   in_foundry: false
   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/uo.owl
   products:
   - {id: uo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/uo.owl'}
@@ -2404,6 +2441,8 @@ ontologies:
   id: zfa
   in_foundry_order: 1
   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/zfa.owl
   products:
   - {id: zfa.owl, ontology_purl: 'http://purl.obolibrary.org/obo/zfa.owl'}
@@ -2421,6 +2460,8 @@ ontologies:
   id: zfs
   in_foundry: false
   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/zfs.owl
   page: https://github.com/obophenotype/developmental-stage-ontologies/wiki/ZFS
   products:

diff --git a/post-templates/YYYY-MM-DD-announce-new-foundry-ontology.md b/post-templates/YYYY-MM-DD-announce-new-foundry-ontology.md
@@ -3,8 +3,8 @@ layout: post
 title:  "$OntologyName is the newest member of the OBO Foundry"
 date:   YYYY-MM-DD
 categories: update
-summary: The OBO Foundry Operations Committee is pleased to announce the inclusion of the $OntologyName ($IDSPACE) as a full member of the the OBO Foundry.
-image: '$OPTIONAL_IMAGE_URL$
+summary: "The OBO Foundry Operations Committee is pleased to announce the inclusion of the $OntologyName ($IDSPACE) as a full member of the the OBO Foundry."
+image: "OPTIONAL-IMAGE-URL"
 tags:
  - announce
  - foundry