added metadata

ontology/bfo.md

@@ -11,6 +11,7 @@ page: http://ifomis.org/bfo/
 products: 
   - id: bfo.owl
 title: Basic Formal Ontology
+depicted_by: https://code.google.com/p/bfo/logo?cct=1426583016
 ---
 
 BFO grows out of a philosophical orientation which overlaps with that of DOLCE and SUMO. Unlike these, however, it is narrowly focused on the task of providing a genuine upper ontology which can be used in support of domain ontologies developed for scientific research, as for example in biomedicine within the framework of the OBO Foundry. Thus BFO does not contain physical, chemical, biological or other terms which would properly fall within the special sciences domains. BFO is the upper level ontology upon which OBO Foundry ontologies are built.

ontology/bto.md

@@ -7,10 +7,17 @@ contact:
 description: A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.
 domain: anatomy
 homepage: http://www.brenda-enzymes.info
-page: http://www.brenda-enzymes.info
+page: https://en.wikipedia.org/wiki/BRENDA_tissue_ontology
+publications:
+  - id: https://www.ncbi.nlm.nih.gov/pubmed/21030441
+    title: "The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources"
 products: 
   - id: bto.owl
+license:
+  url: http://www.brenda-enzymes.org/copy.php
+  label: BRENDA license
+  alert: Restricted
 title: BRENDA tissue / enzyme source
 ---
 
-A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.
+A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.

ontology/cteno.md

@@ -14,6 +14,13 @@ taxon:
   id: NCBITaxon:10197
   label: Ctenophore
 tracker: https://github.com/obophenotype/ctenophore-ontology/issues
+license:
+  url: https://creativecommons.org/licenses/by/3.0/
+  label: CC-BY
 ---
 
-An anatomical and developmental ontology for ctenophores (Comb Jellies)
+An anatomical and developmental ontology for ctenophores (Comb Jellies).
+
+<img alt="Haeckel Ctenophorae" src="https://upload.wikimedia.org/wikipedia/commons/thumb/4/42/Haeckel_Ctenophorae.jpg/440px-Haeckel_Ctenophorae.jpg"/>
+
+This ontology is available as a standalone artefact, and is also available as part of Uberon composite-metaozoan

ontology/ddanat.md

@@ -7,6 +7,7 @@ contact:
 description: A structured controlled vocabulary of the anatomy of the slime-mould <i>Dictyostelium discoideum</i>.
 domain: anatomy
 homepage: http://dictybase.org/
+twitter: dictybase
 products: 
   - id: ddanat.owl
 taxon: 
@@ -16,4 +17,4 @@ title: Dictyostelium discoideum anatomy
 tracker: http://sourceforge.net/tracker/?group_id=76834&atid=974664
 ---
 
-A structured controlled vocabulary of the anatomy of the slime-mould <i>Dictyostelium discoideum</i>.
+A structured controlled vocabulary of the anatomy of the slime-mould <i>Dictyostelium discoideum</i>.

ontology/doid.md

@@ -5,11 +5,19 @@ contact:
   email: [email protected]
   label: Lynn Schriml
 description: Creating a comprehensive hierarchical controlled vocabulary for human disease representation.
+twitter: diseaseontology
 domain: health
 homepage: http://diseaseontology.sourceforge.net/
 page: http://diseaseontology.sourceforge.net/
 products: 
   - id: doid.owl
+browsers:
+  - label: DO
+    title: DO Browser
+    url: http://www.disease-ontology.org/
+  - label: Monarch
+    title: Monarch Phenotype Page
+    url: http://monarchinitiative.org/phenotype/DOID:4
 taxon: 
   id: NCBITaxon:9606
   label: Homo sapiens
@@ -18,3 +26,5 @@ tracker: http://sourceforge.net/tracker/?func=add&group_id=79168&atid=555739
 ---
 
 Creating a comprehensive hierarchical controlled vocabulary for human disease representation.
+
+<img src="http://www.disease-ontology.org/media/images/DO_logo.jpg"/>

ontology/go.md

@@ -32,10 +32,21 @@ dependencies:
    connects:
      - id: nifstd
      - id: go
+browsers:
+  - label: AmiGO
+    title: Gene Ontology AmiGO 2 Browser
+    url: http://amigo.geneontology.org/amigo/term/GO:0008150#display-lineage-tab
 products:
  - id: go.owl
  - id: go/extensions/go-plus.owl
    title: GO-Plus
+   description: The core ontology plus axioms connecting to select external ontologies
+ - id: go/extensions/go-taxon-groupings.owl
+   title: GO Taxon Groupings
+   description: Classes added to ncbitaxon for groupings such as prokaryotes
+license:
+  url: https://creativecommons.org/licenses/by/3.0/
+  label: CC-BY
 depicted_by: http://geneontology.org/sites/default/files/go-logo-icon.mini__0.png
 ---
 

ontology/hp.md

@@ -4,6 +4,7 @@ id: hp
 alternativePrefix: HPO
 description: A structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease.
 domain: phenotype
+twitter: hp_ontology
 homepage: http://www.human-phenotype-ontology.org/
 contact: 
   email: [email protected]
@@ -16,7 +17,14 @@ taxon:
   label: Homo sapiens
 title: human phenotype ontology
 tracker: https://sourceforge.net/p/obo/human-phenotype-requests/
-termgenie: http://hp.termgenie,org
+termgenie: http://hp.termgenie.org
+browsers:
+  - label: HPO
+    title: Charite HPO Browser
+    url: http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000118
+  - label: Monarch
+    title: Monarch Phenotype Page
+    url: http://monarchinitiative.org/phenotype/HP:0000118
 publications:
   - id: http://www.ncbi.nlm.nih.gov/pubmed/18950739
     title: "The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease."

ontology/mp.md

@@ -11,11 +11,18 @@ domain: phenotype
 products: 
   - id: mp.owl
   - id: mp.obo
+browsers:
+  - label: MGI
+    title: MGI MP Browser
+    url: http://www.informatics.jax.org/searches/MP_form.shtml
+  - label: Monarch
+    title: Monarch Phenotype Page
+    url: http://monarchinitiative.org/phenotype/MP:0000001
 taxon: 
   id: NCBITaxon:10088
   label: Mus
 tracker: https://sourceforge.net/p/obo/mammalian-phenotype-requests/
 termgenie: http://mp.termgenie.org
 ---
 
-The Mammalian Phenotype Ontology is under development as a community effort to provide standard terms for annotating mammalian phenotypic data.
+The Mammalian Phenotype Ontology is under development as a community effort to provide standard terms for annotating mammalian phenotypic data.

ontology/ncbitaxon.md

@@ -13,6 +13,10 @@ createdWith: http://owltools.googlecode.com/
 domain: taxonomy
 homepage: http://www.obofoundry.org/wiki/index.php/NCBITaxon:Main_Page
 page: http://www.ncbi.nlm.nih.gov/taxonomy
+browsers:
+  - label: NCBI
+    title: NCBI Taxonomy Browser
+    url: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi
 jobs:
   - id: http://build.berkeleybop.org/job/build-ncbitaxon/
     type: ReleaseBuild
@@ -22,11 +26,11 @@ products:
     title: taxslim
 ---
 
-The NCBITaxon ontology is an automatic translation of the NCBI taxonomy database into obo/owl.
+The NCBITaxon ontology is an automatic translation of the [NCBI taxonomy database](http://www.ncbi.nlm.nih.gov/taxonomy) into obo/owl.
 
 The translation treats each taxon as an obo/owl class whose instances (for most branches of the ontology) would be individual organisms. For example:
 
-  'Craig Venter' instance_of NCBITaxon_9606 (Homo sapiens)
+    'Craig Venter' instance_of NCBITaxon_9606 (Homo sapiens)
 
 The translation faithfully reproduces all of the content of the source database, even where this contravenes OBO guidelines. For example:
 
@@ -39,15 +43,29 @@ The translation faithfully reproduces all of the content of the source database,
 
 The purls for this ontology are:
 
- * http://purl.obolibrary.org/obo/ncbitaxon.owl (official purl)
+ * http://purl.obolibrary.org/obo/ncbitaxon.owl (official purl for *ontology*)
  * http://purl.obolibrary.org/obo/ncbitaxon.obo (obo-format version)
 
 The PURLs should be resolvable in OntoBee. E.g.
 
- * http://purl.obolibrary.org/obo/NCBITaxon_9606 (Homo sapiens)
+ * [http://purl.obolibrary.org/obo/NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) (Homo sapiens)
  * http://purl.obolibrary.org/obo/NCBITaxon_7711 (Chordates)
  * http://purl.obolibrary.org/obo/NCBITaxon_7227 (Danio rerio)
 
+## Releases
+
+Releases of the obo/owl happen when the [Continuous Integration
+Job](http://build.berkeleybop.org/job/build-ncbitaxon/) is manually
+triggered. Currently this must be done by an OBO administrator. There
+is currently no fixed cycle, and this is generally done on demand. The
+team that informally handles this are:
+
+ * James Overton, IEBD/OBO
+ * Heiko Dietze, LBNL/GO
+ * Frederic Bastian, BgeeDb/Uberon
+ * Chris Mungall, LBNL/GO/Monarch/Uberon/OBO
+ * Peter Midford, Phenoscape
+
 ## Extensions
 
 The GO uses an extension of NCBITaxon for grouping purposes. See:
@@ -60,27 +78,38 @@ this ontology includes new classes in the NCBITaxon_Union namespace. These class
 
 One of the main uses for the NCBITaxon ontology is to define taxon constraints in a multi-species ontology. For details, see:
 
- * Waclaw Kusnierczyk (2008) [http://dx.doi.org/10.1016/j.jbi.2007.07.007 Taxonomy-based partitioning of the Gene Ontology], ''Journal of Biomedical Informatics''
- * Deegan Née Clark, J. I., Dimmer, E. C., and Mungall, C. J. (2010). [http://www.biomedcentral.com/1471-2105/11/530 Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development]. ''BMC Bioinformatics 11, 530''
- * [http://douroucouli.wordpress.com/2012/04/24/taxon-constraints-in-owl/ Taxon constraints in OWL]
-
+ * Waclaw Kusnierczyk (2008) [Taxonomy-based partitioning of the Gene Ontology](http://dx.doi.org/10.1016/j.jbi.2007.07.007), *Journal of Biomedical Informatics*
+ * Deegan Née Clark, J. I., Dimmer, E. C., and Mungall, C. J. (2010). [Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development](http://www.biomedcentral.com/1471-2105/11/530). *BMC Bioinformatics 11, 530**
+ * [Taxon constraints in OWL](http://douroucouli.wordpress.com/2012/04/24/taxon-constraints-in-owl) (blog post)
+ * [Taxon constraints in Uberon](https://github.com/obophenotype/uberon/wiki/Taxon-constraints)
+ * [A Taxonomy for Immunologists](http://ceur-ws.org/Vol-1060/icbo2013_submission_76.pdf) **ICBO 2013**
 
 ## Mailing Lists
 
  * https://lists.sourceforge.net/lists/listinfo/obo-taxonomy
  * http://groups.google.com/group/obo-taxonomy
 
-## Citing the NCBITaxon ontology ==
+## Tracker
+
+Note that this differs from other OBO ontologies in that it is a
+translation of a database produced external to OBO. If you wish to
+suggest actual taxonomy changes to the database, contact NCBI.
+
+The NCBI staff are very responsive and helpful, [as this post from the Bgee team shows](https://bgeedb.wordpress.com/2013/05/29/new-taxon-dipnotetrapodomorpha-in-ncbi-taxonomy/)
+
+If you wish to suggest changes to the *translation* then contact the
+maintainer or the mail list above.
+
+## Citing the NCBITaxon ontology
 
 before citing, ask yourself what the artefact you wish to cite is:
 
- * The NCBI taxonomy ''database''
+ * The NCBI taxonomy **database**
  * The OBO/OWL rendering of the NCBI taxonomy database
 
-The latter is a fairly trivial translation of the former. If you are in any way citing the ''contents'' then '''you should cite the database'''. Currently the most up to date reference is:
+The latter is a fairly trivial translation of the former. If you are in any way citing the *contents* then **you should cite the database**. Currently the most up to date reference is:
 
-Federhen, Scott. '''The NCBI taxonomy database.''' ''Nucleic acids research 40.D1 (2012): D136-D143.''
-http://nar.oxfordjournals.org/content/40/D1/D136.short
+ * Federhen, Scott. **The NCBI taxonomy database.** *Nucleic acids research 40.D1 (2012): D136-D143.* [http://nar.oxfordjournals.org/content/40/D1/D136.short](http://nar.oxfordjournals.org/content/40/D1/D136.short)
 
 If you specifically wish to cite the OBO/OWL translation, use the URL for this page
 

ontology/obi.md

@@ -12,7 +12,9 @@ homepage: http://purl.obofoundry.org/obo/obi
 page: http://obi-ontology.org/page/Technical_Reports
 products: 
   - id: obi.owl
-license: https://creativecommons.org/licenses/by/3.0/
+license:
+  url: https://creativecommons.org/licenses/by/3.0/
+  label: CC-BY
 tracker: http://sourceforge.net/p/obi/obi-terms/
 ---
 

ontology/poro.md

@@ -12,6 +12,9 @@ products:
 taxon: 
   id: NCBITaxon:6040
   label: Porifera
+license:
+  url: https://creativecommons.org/licenses/by/3.0/
+  label: CC-BY
 title: Porifera Ontology
 integration_server: http://build.berkeleybop.org/job/build-poro/
 tracker: https://github.com/obophenotype/porifera-ontology/issues

ontology/ro.md

@@ -15,6 +15,9 @@ products:
  - id: ro.owl
  - id: ro.obo
  - id: ro/ro-interaction.owl
+license:
+  url: https://creativecommons.org/licenses/by/3.0/
+  label: CC-BY
 ---
 
 # Summary

ontology/uberon.md

@@ -9,8 +9,12 @@ homepage: http://uberon.org
 page: http://en.wikipedia.org/wiki/Uberon
 twitter: uberanat
 google_plus: "+UberonOrg"
+wikidata_template: https://en.wikipedia.org/wiki/Template:Uberon
 mailing_list: https://lists.sourceforge.net/lists/listinfo/obo-anatomy
 canonical: uberon.owl
+license:
+  url: https://creativecommons.org/licenses/by/3.0/
+  label: CC-BY
 taxon: 
   id: NCBITaxon:33208
   label: Metazoa
@@ -23,7 +27,9 @@ contact:
   label: Chris Mungall
 publications:
   - id: http://www.ncbi.nlm.nih.gov/pubmed/22293552
-    title: Uberon, an integrative multi-species anatomy ontology
+    title: "Uberon, an integrative multi-species anatomy ontology"
+  - id: http://www.ncbi.nlm.nih.gov/pubmed/25009735
+    title: "Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon"
 depicted_by: http://uberon.github.io/images/u-logo.jpg
 exampleClass: UBERON_0002046
 redirects:
@@ -40,6 +46,13 @@ dependencies:
    subset: uberon/chebi_import.owl
  - id: pr
    subset: uberon/pr_import.owl
+browsers:
+  - label: RGD
+    title: Gene Ontology AmiGO 2 Browser
+    url: http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=UBERON:0001062
+  - label: AmiGO (SUBSET)
+    title: Gene Ontology AmiGO 2 Browser
+    url: http://amigo.geneontology.org/amigo/term/UBERON:0001062#display-lineage-tab
 products:
  - id: uberon.owl
    type: owl:Ontology

ontology/vhog.md

@@ -3,5 +3,11 @@ layout: ontology_detail
 id: vhog
 products: 
   - id: vhog.owl
+is_obsolete: true
+replaced_by: uberon
 ---
 
+vHOG has been rolled into Uberon, with homology assertions available on a [separate project on github](https://github.com/BgeeDB/anatomical-similarity-annotations)
+
+<img src="http://bgee.org/img/logo/bgee13_logo.png"/>
+