diff --git a/_config.yml b/_config.yml
index f300c7fbd..e09593c85 100644
--- 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: hastings@ebi.ac.uk, label: Janna Hastings}
- description: A structured classification of chemical compounds of biological relevance.
+ contact: {email: gowen@ebi.ac.uk, 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: carrine.blank@umontana.edu, 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: vdritsou@imbb.forth.gr, 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: PS@mole.bio.cam.ac.uk, 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: pns12@cam.ac.uk, 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: bpeters@liai.org, 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'}
@@ -1348,18 +1366,24 @@ 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: geg18@aber.ac.uk, 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: g.gkoutos@gmail.com, 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'}
@@ -1367,7 +1391,7 @@ ontologies:
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: ncicb@pop.nci.nih.gov}
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: geg18@aber.ac.uk, 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: g.gkoutos@gmail.com, 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: lynn.schriml@gmail.com, 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: dsonensh@odu.edu, label: Daniel Sonenshine}
description: 'The anatomy of the Tick, Families: Ixodidae, Argassidae'
@@ -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: lynn.schriml@gmail.com, 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: peteremidford@yahoo.com, 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: geg18@aber.ac.uk, label: George Gkoutos}
+ contact: {email: g.gkoutos@gmail.com, 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
index 19aad5441..6785f74d0 100644
--- 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
diff --git a/registry/ontologies.jsonld b/registry/ontologies.jsonld
index 4b7776bde..3f76f6494 100644
--- a/registry/ontologies.jsonld
+++ b/registry/ontologies.jsonld
@@ -411,10 +411,10 @@
"source_url": "http://build.berkeleybop.org/job/build-chebi/lastSuccessfulBuild/artifact/*zip*/archive.zip"
},
"contact": {
- "email": "hastings@ebi.ac.uk",
- "label": "Janna Hastings"
+ "email": "gowen@ebi.ac.uk",
+ "label": "Gareth Owen"
},
- "description": "A structured classification of chemical compounds of biological relevance.",
+ "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",
@@ -432,7 +432,7 @@
"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"
},
@@ -1215,6 +1215,7 @@
"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/"
},
"ontology_purl": "http://purl.obolibrary.org/obo/eo.owl",
@@ -2417,6 +2418,24 @@
"title": "MIAPA Ontology",
"tracker": "https://github.com/miapa/miapa/issues"
},
+ {
+ "contact": {
+ "email": "carrine.blank@umontana.edu",
+ "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": "vdritsou@imbb.forth.gr",
@@ -2657,12 +2676,19 @@
"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": "http://mpath.googlecode.com/svn/trunk/mpath.obo"
+ "source_url": "https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo"
},
"contact": {
- "email": "PS@mole.bio.cam.ac.uk",
+ "email": "pns12@cam.ac.uk",
"label": "Paul Schofield"
},
"description": "A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes",
@@ -2670,6 +2696,11 @@
"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": [
{
@@ -2681,7 +2712,8 @@
"id": "NCBITaxon:10088",
"label": "Mus"
},
- "title": "Mouse pathology"
+ "title": "Mouse pathology",
+ "tracker": "https://github.com/PaulNSchofield/mpath/issues"
},
{
"contact": {
@@ -2694,6 +2726,7 @@
"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/"
},
"ontology_purl": "http://purl.obolibrary.org/obo/mro.owl",
@@ -2746,19 +2779,42 @@
"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": "svn co http://behavior-ontology.googlecode.com/svn/trunk",
+ "checkout": "git clone https://github.com/bio-ontology-research-group/behavior-ontology.git",
"method": "vcs",
- "system": "svn"
+ "path": ".",
+ "system": "git"
},
"contact": {
- "email": "geg18@aber.ac.uk",
+ "email": "g.gkoutos@gmail.com",
"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": [
{
@@ -2767,7 +2823,7 @@
}
],
"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": [
@@ -2790,7 +2846,7 @@
"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": [
{
@@ -2816,11 +2872,13 @@
{
"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"
},
{
@@ -3298,13 +3356,30 @@
"title": "Plant Anatomy Ontology"
},
{
+ "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": "geg18@aber.ac.uk",
+ "email": "g.gkoutos@gmail.com",
"label": "George Gkoutos"
},
"description": "An ontology of phenotypic qualities (properties, attributes or characteristics)",
@@ -3319,6 +3394,11 @@
}
],
"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": [
{
@@ -3447,7 +3527,8 @@
"layout": "ontology_detail",
"license": {
"label": "CC-BY",
- "url": "https://creativecommons.org/licenses/by/3.0/"
+ "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",
@@ -4033,8 +4114,9 @@
},
{
"build": {
+ "infallible": 1,
"method": "obo2owl",
- "source_url": "http://gemina.svn.sourceforge.net/viewvc/gemina/trunk/Gemina/ontologies/gemina_symptom.obo"
+ "source_url": "https://sourceforge.net/p/diseaseontology/code/HEAD/tree/Symptom_Ontology/symptom_ontology.obo"
},
"contact": {
"email": "lynn.schriml@gmail.com",
@@ -4065,7 +4147,8 @@
"id": "NCBITaxon:9606",
"label": "Homo sapiens"
},
- "title": "Symptom Ontology"
+ "title": "Symptom Ontology",
+ "tracker": "http://sourceforge.net/tracker/?func=add&group_id=79168&atid=555739"
},
{
"build": {
@@ -4220,6 +4303,7 @@
"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/"
},
"ontology_purl": "http://purl.obolibrary.org/obo/to.owl",
@@ -4245,8 +4329,9 @@
},
{
"build": {
+ "infallible": 1,
"method": "obo2owl",
- "source_url": "http://gemina.cvs.sourceforge.net/*checkout*/gemina/Gemina/ontologies/transmission_process.obo"
+ "source_url": "https://sourceforge.net/p/diseaseontology/code/HEAD/tree/Transmission_Process_Ontology/transmission_process_ontology.obo"
},
"contact": {
"email": "lynn.schriml@gmail.com",
@@ -4274,7 +4359,7 @@
}
],
"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": {
@@ -4510,7 +4595,7 @@
"source_url": "https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"
},
"contact": {
- "email": "geg18@aber.ac.uk",
+ "email": "g.gkoutos@gmail.com",
"label": "George Gkoutos"
},
"description": "Metrical units for use in conjunction with PATO",
@@ -4519,6 +4604,11 @@
"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": [
{
@@ -4882,6 +4972,11 @@
"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": [
{
@@ -4918,6 +5013,11 @@
"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/registry/ontologies.ttl b/registry/ontologies.ttl
index 0b7debaae..a9493af4b 100644
--- a/registry/ontologies.ttl
+++ b/registry/ontologies.ttl
@@ -497,6 +497,12 @@
"http://purl.obolibrary.org/obo/cl/cl-basic.obo" .
+
+
+ "OntoBee" ;
+
+ "OntoBee Browser" .
+
;
@@ -773,7 +779,8 @@
- "CC-BY" .
+ "CC-BY" ;
+ .
@@ -972,6 +979,8 @@
"http://purl.obolibrary.org/obo/trans.obo" .
+
+ , , ;
[
"obo2owl" ;
@@ -982,6 +991,8 @@
"An ontology of phenotypic qualities (properties, attributes or characteristics)" ;
"Phenotypic quality" ;
+
+ ;
"phenotype" ;
@@ -992,7 +1003,7 @@
[
"George Gkoutos" ;
- "geg18@aber.ac.uk"
+ "g.gkoutos@gmail.com"
] ;
, ;
@@ -1029,16 +1040,16 @@
.
-
-
- "http://purl.obolibrary.org/obo/gaz.obo" .
-
"OBO Format version of Main release" ;
"http://purl.obolibrary.org/obo/ncbitaxon.obo" .
+
+
+ "http://purl.obolibrary.org/obo/gaz.obo" .
+
a ;
@@ -1124,7 +1135,7 @@
[
"obo2owl" ;
- "http://gemina.svn.sourceforge.net/viewvc/gemina/trunk/Gemina/ontologies/gemina_symptom.obo"
+ "https://sourceforge.net/p/diseaseontology/code/HEAD/tree/Symptom_Ontology/symptom_ontology.obo"
] ;
;
@@ -1136,6 +1147,8 @@
;
"disease" ;
+
+ "http://sourceforge.net/tracker/?func=add&group_id=79168&atid=555739" ;
"http://purl.obolibrary.org/obo/symp.owl" ;
@@ -1263,6 +1276,8 @@
"Developmental stages of the Zebrafish" ;
"Zebrafish developmental stages" ;
+
+ ;
"anatomy" ;
@@ -1294,7 +1309,7 @@
"Plant Ontology" ;
- ;
+ ;
, ;
@@ -1465,11 +1480,13 @@
.
+
+ ;
[
"obo2owl" ;
- "http://mpath.googlecode.com/svn/trunk/mpath.obo"
+ "https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo"
] ;
;
@@ -1477,15 +1494,19 @@
"A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes" ;
"Mouse pathology" ;
+
+ ;
"health" ;
+
+ "https://github.com/PaulNSchofield/mpath/issues" ;
"http://purl.obolibrary.org/obo/mpath.owl" ;
[
"Paul Schofield" ;
- "PS@mole.bio.cam.ac.uk"
+ "pns12@cam.ac.uk"
] ;
;
@@ -1570,6 +1591,24 @@
.
+
+
+ "An ontology of prokaryotic phenotypic and metabolic characters" ;
+
+ "prokaryotic phenotypic and metabolic characters" ;
+
+ ;
+
+ "phenotype" ;
+
+ [
+ "Carrine Blank" ;
+
+ "carrine.blank@umontana.edu"
+ ] ;
+
+ .
+
"Metazoa" .
@@ -1678,9 +1717,9 @@
"http://build.berkeleybop.org/job/build-chebi/lastSuccessfulBuild/artifact/*zip*/archive.zip"
] ;
- "A structured classification of chemical compounds of biological relevance." ;
+ "A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds." ;
- "Chemical entities of biological interest" ;
+ "Chemical Entities of Biological Interest" ;
"biochemistry" ;
@@ -1689,9 +1728,9 @@
"http://purl.obolibrary.org/obo/chebi.owl" ;
[
- "Janna Hastings" ;
+ "Gareth Owen" ;
- "hastings@ebi.ac.uk"
+ "gowen@ebi.ac.uk"
] ;
, ;
@@ -1738,14 +1777,14 @@
"http://purl.obolibrary.org/obo/obib.owl" .
-
-
- "The plant ontology as a tool for comparative plant anatomy and genomic analyses." .
-
"http://purl.obolibrary.org/obo/chebi.owl" .
+
+
+ "The plant ontology as a tool for comparative plant anatomy and genomic analyses." .
+
[
@@ -1810,6 +1849,12 @@
.
+
+
+ "FB" ;
+
+ "FlyBase Browser" .
+
[
@@ -1846,12 +1891,6 @@
.
-
-
- "FB" ;
-
- "FlyBase Browser" .
-
[
@@ -2130,6 +2169,12 @@
"Zea" .
+
+
+ "Aber-OWL" ;
+
+ "Aber-OWL Ontology Browser" .
+
"The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data." .
@@ -2324,7 +2369,9 @@
"taxslim" ;
- "http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl" .
+ "http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl" ;
+
+ .
@@ -2777,6 +2824,12 @@
"http://purl.obolibrary.org/obo/tao.owl" .
+
+
+ "BioPortal" ;
+
+ "BioPortal Ontology Browser" .
+
;
@@ -2800,6 +2853,8 @@
"http://owltools.googlecode.com/" ;
"ftp://ftp.ebi.ac.uk/pub/databases/taxonomy/taxonomy.dat" ;
+
+ "https://github.com/obophenotype/ncbitaxon/issues" ;
"http://purl.obolibrary.org/obo/ncbitaxon.owl" ;
@@ -2811,35 +2866,39 @@
, , ;
- ;
+ ;
.
+
+ , , ;
[
- "svn co http://behavior-ontology.googlecode.com/svn/trunk" ;
+ "git clone https://github.com/bio-ontology-research-group/behavior-ontology.git" ;
"vcs"
] ;
"Neuro Behavior Ontology" ;
+
+ ;
"behavior" ;
- "http://code.google.com/p/behavior-ontology/issues/list" ;
+ "https://github.com/bio-ontology-research-group/behavior-ontology/issues" ;
"http://purl.obolibrary.org/obo/nbo.owl" ;
[
"George Gkoutos" ;
- "geg18@aber.ac.uk"
+ "g.gkoutos@gmail.com"
] ;
;
- .
+ .
@@ -2881,6 +2940,12 @@
"http://purl.obolibrary.org/obo/poro.owl" .
+
+
+ "Aber-OWL" ;
+
+ "Aber-OWL Ontology Repository" .
+
[
@@ -2990,6 +3055,8 @@
"Metrical units for use in conjunction with PATO" ;
"Units of measurement" ;
+
+ ;
"phenotype" ;
@@ -3000,7 +3067,7 @@
[
"George Gkoutos" ;
- "geg18@aber.ac.uk"
+ "g.gkoutos@gmail.com"
] ;
;
@@ -3142,6 +3209,8 @@
"A structured controlled vocabulary of the anatomy and development of the Zebrafish" ;
"Zebrafish anatomy and development" ;
+
+ ;
;
@@ -3583,6 +3652,11 @@
"http://purl.obolibrary.org/obo/dideo.owl" .
+
+
+ "CC-BY" ;
+ .
+
[
@@ -4033,7 +4107,7 @@
[
"obo2owl" ;
- "http://gemina.cvs.sourceforge.net/*checkout*/gemina/Gemina/ontologies/transmission_process.obo"
+ "https://sourceforge.net/p/diseaseontology/code/HEAD/tree/Transmission_Process_Ontology/transmission_process_ontology.obo"
] ;
"An ontology representing the disease transmission process during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host." ;
@@ -4044,7 +4118,7 @@
"disease" ;
- "http://sourceforge.net/tracker/?&group_id=76834&atid=1037853" ;
+ "http://sourceforge.net/tracker/?func=add&group_id=79168&atid=555739" ;
"http://purl.obolibrary.org/obo/trans.owl" ;
@@ -4106,6 +4180,10 @@
"http://purl.obolibrary.org/obo/pato.owl" .
+
+
+ "http://purl.obolibrary.org/obo/fbsp.owl" .
+
a ;
@@ -4117,10 +4195,6 @@
.
-
-
- "http://purl.obolibrary.org/obo/fbsp.owl" .
-
"http://purl.obolibrary.org/obo/nmr.owl" .
@@ -4450,6 +4524,12 @@
.
+
+
+ "OntoBee" ;
+
+ "OntoBee Ontology Browser" .
+
"Oryzias" .
@@ -4648,21 +4728,11 @@
"http://purl.obolibrary.org/obo/fma.owl" .
-
-
- "For the description of covalent bonds in proteins." ;
+
- "Protein covalent bond" ;
-
- "proteins" ;
-
- [
- "John Garavelli" ;
-
- "john.garavelli@ebi.ac.uk"
- ] ;
-
- .
+ "Relation Ontology" ;
+
+ "http://purl.obolibrary.org/obo/ro.owl" .
@@ -4684,11 +4754,21 @@
"bakerc@unb.ca"
] .
-
+
+
+ "For the description of covalent bonds in proteins." ;
- "Relation Ontology" ;
-
- "http://purl.obolibrary.org/obo/ro.owl" .
+ "Protein covalent bond" ;
+
+ "proteins" ;
+