additional info for some ontologies, adding ontobee links and search

pporrasebi · Jul 29, 2015 · 2fa05d9 · 2fa05d9
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diff --git 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: [email protected], label: Antje Chang}
@@ -253,10 +257,8 @@ ontologies:
   - {id: dpo.owl}
   title: Drosophila Phenotype Ontology
 - contact: {email: [email protected], 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: [email protected], 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: [email protected], 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. <a href="http://obo.cvs.sourceforge.net/*checkout*/song/ontology/sofa.obo">SOFA</a>
-    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: [email protected], 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: [email protected], 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: [email protected], 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
@@ -12,7 +12,7 @@
       <!-- TODO: copy source -->
       <!-- see also: http://stackoverflow.com/questions/18474564/bootstrap-3-navbar-with-logo -->
       <a class="navbar-brand" href="#">
-        <img style="max-width:100px; margin-top: -7px;" src="http://obofoundry.org/images/foundrylogo.gif"/>
+        <img style="max-width:50px; margin-top: -7px;" src="http://obofoundry.org/images/foundrylogo.gif"/>
       </a>
     </div>
 
@@ -21,8 +21,39 @@
       <ul class="nav navbar-nav">
         <li class="active"><a href="#">Link <span class="sr-only">(current)</span></a></li>
         <li><a href="#">Link</a></li>
+
+        <li class="dropdown">
+          <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">About <span class="caret"></span></a>
+          <ul class="dropdown-menu">
+            <li><a href="coordination.html">Coordination</a></li>
+            <li><a href="related.html">Related</a></li>
+            <li><a href="faq.html">FAQ</a></li>
+            <li><a href="https://github.com/OBOFoundry">GitHub Organization</a></li>
+            <li><a href="https://github.com/OBOFoundry/OBOFoundry.github.io">GitHub project</a></li>
+          </ul>
+        </li>
+
         <li class="dropdown">
-          <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Dropdown <span class="caret"></span></a>
+          <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Ontologies <span class="caret"></span></a>
+          <ul class="dropdown-menu">
+            <li><a href="id-policy.html">ID Policy</a></li>
+            <li><a href="literature.html">Literature</a></li>
+            <li><a href="https://github.com/OBOFoundry/OBOFoundry.github.io/tree/master/ontology">Ontology Metadata</a></li>
+            <li><a href="https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/registry/ontologies.yml">Ontology YAML</a></li>
+          </ul>
+        </li>
+
+        <li class="dropdown">
+          <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Resources <span class="caret"></span></a>
+          <ul class="dropdown-menu">
+            <li><a href="id-policy.html">ID Policy</a></li>
+            <li><a href="faq.html">FAQ</a></li>
+            <li><a href="literature.html">Literature</a></li>
+          </ul>
+        </li>
+
+        <li class="dropdown">
+          <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Participate <span class="caret"></span></a>
           <ul class="dropdown-menu">
             <li><a href="id-policy.html">ID Policy</a></li>
             <li><a href="faq.html">FAQ</a></li>
@@ -33,10 +64,11 @@
             <li><a href="#">One more separated link</a></li>
           </ul>
         </li>
+
       </ul>
-      <form class="navbar-form navbar-left" role="search" action="http://www.ontobee.org/browser/index.php" method="get">
+      <form class="navbar-form navbar-left" role="search" action="http://www.ontobee.org/browser/search.php" method="get">
         <div class="form-group">
-          <input type="text" class="form-control" placeholder="Search Ontobee">
+          <input name="keywords" type="text" class="form-control" placeholder="Search Ontobee">
         </div>
         <button type="submit" class="btn btn-default">Submit</button>
       </form>

diff --git a/_includes/ontology_table.html b/_includes/ontology_table.html
@@ -34,11 +34,13 @@
       </td>
 
       <td>
+        {% if ont.contact %}
         <a href="mailto:{{ont.contact.id}}">
           <button type="button" class="btn btn-default" aria-label="Left Align">
             <span class="glyphicon glyphicon-envelope" aria-hidden="true"></span>
           </button>
         </a>
+        {% endif %}
       </td>
 
       <td>
@@ -49,6 +51,14 @@
         </a>
       </td>
 
+      <td>
+        <a href="http://www.ontobee.org/browser/index.php?o={{ont.id}}">
+          <button type="button" class="btn btn-default" aria-label="Left Align">
+            <span class="glyphicon glyphicon-eye-open" aria-hidden="true"></span>
+          </button>
+        </a>
+      </td>
+
       <td>
         {% if ont.in_foundry %}
         <a href="link-to-foundry-principles">

diff --git a/_layouts/ontology_detail.html b/_layouts/ontology_detail.html
@@ -16,22 +16,22 @@ <h1>
       {{page.description}}
     </p>
     </div>
-    Source for this entry:
-    <div class="btn-group" role="group" aria-label="Source">
-      <a href="https://github.com/OBOFoundry/OBOFoundry.github.io/master/ontology/{{page.id}}.md">
-        <button type="button" class="btn btn-default">View</button>
-      </a>
-      <a href="https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/{{page.id}}.md">
-        <button type="button" class="btn btn-default">Edit</button>
-      </a>
-      <button type="button" class="btn btn-default">Help</button>
-    </div>
-    <button>
-
-    </button>
 
   </div>
 
+  {% if page.is_obsolete %}
+  <div>
+    <div class="alert alert-danger" role="alert">
+      This ontology is deprecated!
+    </div>
+    {% for repl in page.replaced_by %}
+    <div class="alert alert-info" role="alert">
+      Consider using: <a href="{{repl}}.html">{{repl}}</a>
+    </div>
+    {% endfor %}
+  </div>
+  {% endif %}
+
   <div class="col-md-12">
 
     <div class="row">
@@ -107,8 +107,24 @@ <h1>
 
 
         </dl>
+
+
+        <div class="btn-group" role="group" aria-label="Source">
+          <a href="https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/ontology/{{page.id}}.md">
+            <button type="button" class="btn btn-default">View</button>
+          </a>
+          <a href="https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/{{page.id}}.md">
+            <button type="button" class="btn btn-default">Edit</button>
+          </a>
+          <!-- <button type="button" class="btn btn-default">Help</button> -->
+        </div>
       </div>
       <div class="col-md-9">
+        <!-- TODO: each ontology should configure which browsers to be exposed in -->
+        <a href="http://www.ontobee.org/browser/index.php?o={{page.id}}">
+          <button type="button" class="btn btn-default">OntoBee</button>
+        </a>
+
         {{ content }}
 
         <div>

diff --git a/index.html b/index.html
@@ -11,10 +11,11 @@
       <h1>The OBO Foundry</h1>
     </div>
 
-    <div class="jumbotron">
-      yadda
+    <div class="alert alert-info" role="alert">
+      This site is in development! Check the <a href="https://github.com/OBOFoundry/OBOFoundry.github.io">GitHub project</a> for more info.
     </div>
 
+
   <div class="col-md-12">
     <h2>Foundry</h2>
     <div class="row">

diff --git a/logos/envo.png b/logos/envo.png
diff --git 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
@@ -4,7 +4,7 @@ id: dron
 contact: 
   email: [email protected]
   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).
+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
@@ -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.
 
+<img src="/logos/envo.png"/>
+
 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). <b>The environment ontology: contextualising biological and biomedical entities</b>. <i>Journal of Biomedical Semantics, 4(1), 43</i>. <a href="http://www.dx.doi.org/10.1186/2041-1480-4-43">doi:10.1186/2041-1480-4-43</a>
+
 
diff --git 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.
+<img src="http://www.human-phenotype-ontology.org/contao/tl_files/simplifyblue/images/HPO-logo.png"/>
+
+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
@@ -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.