diff --git a/_config.yml b/_config.yml index 2c13ecb47..a531ef64f 100644 --- a/_config.yml +++ b/_config.yml @@ -83,6 +83,10 @@ ontologies: layout: ontology_detail products: - {id: bspo.owl} + publications: + - {id: 'http://www.ncbi.nlm.nih.gov/pubmed/25140222', title: 'Nose to tail, roots + to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial + Ontology.'} title: Biological Spatial Ontology tracker: https://github.com/obophenotype/biological-spatial-ontology/issues - contact: {email: a.chang@tu-bs.de, label: Antje Chang} @@ -253,10 +257,8 @@ ontologies: - {id: dpo.owl} title: Drosophila Phenotype Ontology - contact: {email: hoganwr@gmail.com, label: William Hogan} - description: We built this ontology primarily to support comparative effectiveness - researchers studying claims data. They need to be able to query U.S. National - Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), - physiological effect (diuresis), and therapeutic intent (anti-hypertensive). + description: An ontology to support comparative effectiveness researchers studying + claims data. domain: health homepage: http://code.google.com/p/dr-on id: dron @@ -1062,6 +1064,7 @@ ontologies: title: RNA ontology - canonical: ro.owl domain: relations + homepage: https://code.google.com/p/obo-relations/issues id: ro jobs: - {id: 'http://build.berkeleybop.org/job/build-ro', type: DryRunBuild} @@ -1072,7 +1075,7 @@ ontologies: - {id: ro.obo} - {id: ro/ro-interaction.owl} title: Relations Ontology - tracker: https://code.google.com/p/obo-relations/issues/list + tracker: https://github.com/oborel/obo-relations/issues - contact: {email: rnigam@mcw.edu, label: Rajni Nigam} description: Ontology of rat strains homepage: http://rgd.mcw.edu/ @@ -1121,18 +1124,21 @@ ontologies: title: Social Insect Behavior Ontology tracker: https://github.com/obophenotype/sibo/issues - contact: {email: song-devel@lists.sourceforge.net, label: SONG developers} - description: The Sequence Ontology provides a structured controlled vocabulary for - sequence annotation, for the exchange of annotation data and for the description - of sequence objects in databases. SOFA - is a minimal version of SO for use in data exchange. + description: A structured controlled vocabulary for sequence annotation, for the + exchange of annotation data and for the description of sequence objects in databases. domain: biological sequence - homepage: http://song.sourceforge.net/ + homepage: https://github.com/The-Sequence-Ontology/SO-Ontologies id: so layout: ontology_detail products: - {id: so.owl} + publications: + - {id: 'http://www.ncbi.nlm.nih.gov/pubmed/20226267', title: Evolution of the Sequence + Ontology terms and relationships.} + - {id: 'http://www.ncbi.nlm.nih.gov/pubmed/15892872', title: 'The Sequence Ontology: + a tool for the unification of genome annotations.'} title: Sequence types and features - tracker: http://sourceforge.net/tracker/?group_id=72703&atid=810408 + tracker: https://github.com/The-Sequence-Ontology/SO-Ontologies/issues - contact: {email: ramirez@macn.gov.ar, label: Martin Ramirez} description: An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, @@ -1185,12 +1191,14 @@ ontologies: domain: anatomy homepage: https://www.nescent.org/phenoscape/Main_Page id: tao + is_obsolete: true layout: ontology_detail products: - {id: tao.owl} + replaced_by: uberon taxon: {id: 'NCBITaxon:32443', label: Teleostei} title: Teleost Anatomy Ontology - tracker: http://sourceforge.net/tracker/?group_id=76834&atid=994764 + tracker: https://github.com/obophenotype/uberon/issues?q=is%3Aissue+label%3ATAO - contact: {email: peteremidford@yahoo.com, label: Peter Midford} description: A vocabulary of taxonomic ranks intended to replace the sets of rank terms found in the Teleost Taxonomy Ontology, the OBO translation of the NCBI @@ -1356,17 +1364,19 @@ ontologies: title: Vaccine ontology tracker: http://sourceforge.net/tracker/?atid=1127137&group_id=255029&func=browse - contact: {email: wasila.dahdul@usd.edu, label: Wasila Dahdul} - description: 'Vertebrate skeletal anatomy ontology. ' + description: Vertebrate skeletal anatomy ontology. domain: anatomy homepage: https://www.nescent.org/phenoscape/Main_Page id: vsao + is_obsolete: true layout: ontology_detail page: https://www.phenoscape.org/wiki/Skeletal_Anatomy_Jamboree products: - {id: vsao.owl} + replaced_by: uberon taxon: {id: 'NCBITaxon:7742', label: Vertebrata} - title: Vertebrate Skeletal Anatomy Ontology - tracker: https://sourceforge.net/tracker/?group_id=76834&atid=2257941 + title: Vertebrate Skeletal Anatomy Ontology- + tracker: https://github.com/obophenotype/uberon/issues?q=is%3Aissue+label%3AVSAO - id: vto layout: ontology_detail products: diff --git a/_includes/navbar.html b/_includes/navbar.html index 5b6ad550f..f68b1219c 100644 --- a/_includes/navbar.html +++ b/_includes/navbar.html @@ -12,7 +12,7 @@ - + @@ -21,8 +21,39 @@ - diff --git a/_includes/ontology_table.html b/_includes/ontology_table.html index 5bf9d7701..80a3d81b8 100644 --- a/_includes/ontology_table.html +++ b/_includes/ontology_table.html @@ -34,11 +34,13 @@ + {% if ont.contact %} + {% endif %} @@ -49,6 +51,14 @@ + + + + + + {% if ont.in_foundry %} diff --git a/_layouts/ontology_detail.html b/_layouts/ontology_detail.html index 729c377e7..11b911147 100644 --- a/_layouts/ontology_detail.html +++ b/_layouts/ontology_detail.html @@ -16,22 +16,22 @@

{{page.description}}

- Source for this entry: -
- - - - - - - -
- + {% if page.is_obsolete %} +
+ + {% for repl in page.replaced_by %} + + {% endfor %} +
+ {% endif %} +
@@ -107,8 +107,24 @@

+ + +
+ + + + + + + +

+ + + + + {{ content }}
diff --git a/index.html b/index.html index 98cf2a5f6..cdaec6f2f 100644 --- a/index.html +++ b/index.html @@ -11,10 +11,11 @@

The OBO Foundry

-
- yadda + +

Foundry

diff --git a/logos/envo.png b/logos/envo.png new file mode 100644 index 000000000..d1691e613 Binary files /dev/null and b/logos/envo.png differ diff --git a/ontology/bspo.md b/ontology/bspo.md index aff463b42..aad502107 100644 --- a/ontology/bspo.md +++ b/ontology/bspo.md @@ -11,6 +11,9 @@ products: - id: bspo.owl title: Biological Spatial Ontology tracker: https://github.com/obophenotype/biological-spatial-ontology/issues +publications: + - id: http://www.ncbi.nlm.nih.gov/pubmed/25140222 + title: "Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology." --- An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies. diff --git a/ontology/dron.md b/ontology/dron.md index c40575a55..252889d7e 100644 --- a/ontology/dron.md +++ b/ontology/dron.md @@ -4,7 +4,7 @@ id: dron contact: email: hoganwr@gmail.com label: William Hogan -description: We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), physiological effect (diuresis), and therapeutic intent (anti-hypertensive). +description: An ontology to support comparative effectiveness researchers studying claims data. domain: health homepage: http://code.google.com/p/dr-on products: @@ -13,4 +13,4 @@ title: The Drug Ontology tracker: https://code.google.com/p/dr-on/issues/list --- -We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), physiological effect (diuresis), and therapeutic intent (anti-hypertensive). \ No newline at end of file +We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), physiological effect (diuresis), and therapeutic intent (anti-hypertensive). diff --git a/ontology/envo.md b/ontology/envo.md index 5850646d2..7eefd26ab 100644 --- a/ontology/envo.md +++ b/ontology/envo.md @@ -15,11 +15,15 @@ products: - id: envo.owl title: Environment Ontology tracker: https://github.com/EnvironmentOntology/envo/issues/ + --- EnvO is a community ontology for the concise, controlled description of environments. + + Envo can be cited as: -Buttigieg, P. L., Morrison, N., Smith, B., Mungall, C. J., & Lewis, S. E. (2013). The environment ontology: contextualising biological and biomedical entities. Journal of Biomedical Semantics, 4(1), 43. doi:10.1186/2041-1480-4-43 +Buttigieg, P. L., Morrison, N., Smith, B., Mungall, C. J., & Lewis, S. E. (2013). The environment ontology: contextualising biological and biomedical entities. Journal of Biomedical Semantics, 4(1), 43. doi:10.1186/2041-1480-4-43 + diff --git a/ontology/hp.md b/ontology/hp.md index 11aacdbe1..acbf5abdf 100644 --- a/ontology/hp.md +++ b/ontology/hp.md @@ -2,7 +2,7 @@ layout: ontology_detail id: hp alternativePrefix: HPO -description: The Human Phenotype Ontology is being developed to provide a structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease. Our goal is to provide resource for the computational analysis of the human phenome, with a current focus on monogenic diseases listed in the Online Mendelian Inheritance in Man (OMIM) database, for which annotations are also provided. +description: A structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease. domain: phenotype homepage: http://www.human-phenotype-ontology.org/ contact: @@ -17,6 +17,19 @@ taxon: title: human phenotype ontology tracker: https://sourceforge.net/p/obo/human-phenotype-requests/ termgenie: http://hp.termgenie,org +publications: + - id: http://www.ncbi.nlm.nih.gov/pubmed/18950739 + title: "The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease." + - id: http://www.ncbi.nlm.nih.gov/pubmed/26119816 + title: "The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease." + - id: http://www.ncbi.nlm.nih.gov/pubmed/24217912 + title: "The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data." --- -The Human Phenotype Ontology is being developed to provide a structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease. Our goal is to provide resource for the computational analysis of the human phenome, with a current focus on monogenic diseases listed in the Online Mendelian Inheritance in Man (OMIM) database, for which annotations are also provided. \ No newline at end of file + + +The Human Phenotype Ontology is being developed to provide a structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease. Our goal is to provide resource for the computational analysis of the human phenome, with a current focus on monogenic diseases listed in the Online Mendelian Inheritance in Man (OMIM) database, for which annotations are also provided. + +The HPO can be browsed using: + + * [HPO Browser](http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000118) diff --git a/ontology/ro.md b/ontology/ro.md index 67dfdb084..75c8b9ddb 100644 --- a/ontology/ro.md +++ b/ontology/ro.md @@ -3,7 +3,8 @@ layout: ontology_detail id: ro title: Relations Ontology canonical: ro.owl -tracker: https://code.google.com/p/obo-relations/issues/list +homepage: https://code.google.com/p/obo-relations/issues +tracker: https://github.com/oborel/obo-relations/issues mailing_list: https://lists.sourceforge.net/lists/listinfo/obo-relations domain: relations jobs: @@ -15,3 +16,17 @@ products: - id: ro/ro-interaction.owl --- +# Summary + +RO is a collection of relations intended primarily for standardization across ontologies in the [OBO Foundry](http://obofoundry.org) and wider OBO library. It incorporates [ROCore](https://github.com/oborel/obo-relations/wiki/ROCore) upper-level relations such as [part of](http://purl.obolibrary.org/obo/BFO_0000050) as well as biology-specific relationship types such as [develops from](http://purl.obolibrary.org/obo/RO_0002202). + +See the site [Menu](https://github.com/oborel/obo-relations/wiki/Menu) for more info + +# Download + +Use the following URIs to download this ontology: + + * http://purl.obolibrary.org/obo/ro.owl + * http://purl.obolibrary.org/obo/ro.obo + +Note that the source ontology is OWL - the [OBO](https://github.com/oborel/obo-relations/wiki/OBOFormatUsersGuide) version may have less axioms. Another difference between the two formats is that the OWL makes use of imports, whereas everything is combined into one with the obo file. diff --git a/ontology/so.md b/ontology/so.md index e9080d480..3043ff6e8 100644 --- a/ontology/so.md +++ b/ontology/so.md @@ -4,13 +4,18 @@ id: so contact: email: song-devel@lists.sourceforge.net label: SONG developers -description: The Sequence Ontology provides a structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases. SOFA is a minimal version of SO for use in data exchange. +description: A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases. domain: biological sequence -homepage: http://song.sourceforge.net/ +homepage: https://github.com/The-Sequence-Ontology/SO-Ontologies products: - id: so.owl title: Sequence types and features -tracker: http://sourceforge.net/tracker/?group_id=72703&atid=810408 +tracker: https://github.com/The-Sequence-Ontology/SO-Ontologies/issues +publications: + - id: http://www.ncbi.nlm.nih.gov/pubmed/20226267 + title: Evolution of the Sequence Ontology terms and relationships. + - id: http://www.ncbi.nlm.nih.gov/pubmed/15892872 + title: "The Sequence Ontology: a tool for the unification of genome annotations." --- -The Sequence Ontology provides a structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases. SOFA is a minimal version of SO for use in data exchange. \ No newline at end of file +The Sequence Ontology provides a structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases. SOFA is a minimal version of SO for use in data exchange. diff --git a/ontology/tao.md b/ontology/tao.md index a26c55707..a7b2f078b 100644 --- a/ontology/tao.md +++ b/ontology/tao.md @@ -13,7 +13,9 @@ taxon: id: NCBITaxon:32443 label: Teleostei title: Teleost Anatomy Ontology -tracker: http://sourceforge.net/tracker/?group_id=76834&atid=994764 +tracker: https://github.com/obophenotype/uberon/issues?q=is%3Aissue+label%3ATAO +is_obsolete: true +replaced_by: uberon --- -Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa \ No newline at end of file +Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa diff --git a/ontology/vsao.md b/ontology/vsao.md index 2fc5d7d4e..8173aa615 100644 --- a/ontology/vsao.md +++ b/ontology/vsao.md @@ -4,7 +4,7 @@ id: vsao contact: email: wasila.dahdul@usd.edu label: Wasila Dahdul -description: "Vertebrate skeletal anatomy ontology. " +description: Vertebrate skeletal anatomy ontology. domain: anatomy homepage: https://www.nescent.org/phenoscape/Main_Page page: https://www.phenoscape.org/wiki/Skeletal_Anatomy_Jamboree @@ -13,8 +13,10 @@ products: taxon: id: NCBITaxon:7742 label: Vertebrata -title: Vertebrate Skeletal Anatomy Ontology -tracker: https://sourceforge.net/tracker/?group_id=76834&atid=2257941 +title: Vertebrate Skeletal Anatomy Ontology- +tracker: https://github.com/obophenotype/uberon/issues?q=is%3Aissue+label%3AVSAO +is_obsolete: true +replaced_by: uberon --- -Vertebrate skeletal anatomy ontology. \ No newline at end of file +Vertebrate skeletal anatomy ontology.