add funcitonality for reviews to be entered on the ontology's .md fil…

…e; completed reviews are then read from the ontology .md files
ptgolden · Apr 8, 2020 · dedbd88 · dedbd88
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diff --git a/_config.yml b/_config.yml
@@ -38,6 +38,11 @@ ontologies:
     ontology_purl: http://purl.obolibrary.org/obo/bfo.owl
   - id: bfo.obo
     ontology_purl: http://purl.obolibrary.org/obo/bfo.obo
+  review:
+    date: 2016
+    document:
+      label: PDF
+      link: https://drive.google.com/open?id=0B81h9ah4tAM_RnNTRUZnVGRyWXM
   title: Basic Formal Ontology
   tracker: https://github.com/BFO-ontology/BFO/issues
   usages:
@@ -56,9 +61,9 @@ ontologies:
     method: obo2owl
     source_url: ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo
   contact:
-    email: gowen@ebi.ac.uk
-    github: G-Owen
-    label: Gareth Owen
+    email: amalik@ebi.ac.uk
+    github: amalik01
+    label: Adnan Malik
   depicted_by: https://www.ebi.ac.uk/chebi/images/ChEBI_logo.png
   description: A structured classification of molecular entities of biological interest
     focusing on 'small' chemical compounds.
@@ -90,6 +95,8 @@ ontologies:
   publications:
   - id: http://europepmc.org/article/MED/26467479
     title: 'ChEBI in 2016: Improved services and an expanding collection of metabolites.'
+  review:
+    date: 2010
   title: Chemical Entities of Biological Interest
   tracker: https://github.com/ebi-chebi/ChEBI/issues
   twitter: chebit
@@ -144,6 +151,11 @@ ontologies:
   - id: http://www.ncbi.nlm.nih.gov/pubmed/?term=25348409
     title: 'Disease Ontology 2015 update: an expanded and updated database of human
       diseases for linking biomedical knowledge through disease data'
+  review:
+    date: 2015
+    document:
+      label: PDF
+      link: https://drive.google.com/open?id=0B8vqEgF1N0NIZ082U2JETHlSTGs
   taxon:
     id: NCBITaxon:9606
     label: Homo sapiens
@@ -253,6 +265,8 @@ ontologies:
     ontology_purl: http://purl.obolibrary.org/obo/go/snapshot/go.obo
     page: http://geneontology.org/page/download-ontology
     title: GO (OBO Format edition), daily snapshot release
+  review:
+    date: 2010
   taxon:
     id: NCBITaxon:1
     label: All life
@@ -306,6 +320,11 @@ ontologies:
     id: obi/obi_core.owl
     ontology_purl: http://purl.obolibrary.org/obo/obi/obi_core.owl
     title: OBI Core
+  review:
+    date: 2013
+    document:
+      label: PDF
+      link: https://drive.google.com/open?id=0B8vqEgF1N0NIMFlSM3RvdUxGTnc
   title: Ontology for Biomedical Investigations
   tracker: http://purl.obolibrary.org/obo/obi/tracker
   usages:
@@ -363,6 +382,8 @@ ontologies:
     id: pato/pato-base.owl
     ontology_purl: http://purl.obolibrary.org/obo/pato/pato-base.owl
   repository: https://github.com/pato-ontology/pato/
+  review:
+    date: 2010
   title: Phenotype And Trait Ontology
   tracker: https://github.com/pato-ontology/pato/issues
   usages:
@@ -416,6 +437,11 @@ ontologies:
   - id: https://doi.org/10.1093/nar/gkx1152
     title: 'The Planteome database: an integrated resource for reference ontologies,
       plant genomics and phenomics.'
+  review:
+    date: 2013
+    document:
+      label: PDF
+      link: https://drive.google.com/open?id=0B8vqEgF1N0NIV1o0N21UOHlLSmc
   taxon:
     id: NCBITaxon:33090
     label: Viridiplantae
@@ -485,6 +511,8 @@ ontologies:
   publications:
   - id: https://proconsortium.org/pro_dsmnt.shtml#publication
     title: Publications & Dissemination
+  review:
+    date: 2010
   title: PRotein Ontology (PRO)
   tracker: https://github.com/PROconsortium/PRoteinOntology/issues
 - activity_status: active
@@ -518,6 +546,8 @@ ontologies:
   - id: http://www.ncbi.nlm.nih.gov/pubmed/24139024
     title: 'Enhanced XAO: the ontology of Xenopus anatomy and development underpins
       more accurate annotation of gene expression and queries on Xenbase.'
+  review:
+    date: 2010
   taxon:
     id: NCBITaxon:8353
     label: Xenopus
@@ -554,6 +584,8 @@ ontologies:
   - id: http://www.ncbi.nlm.nih.gov/pubmed/24568621
     title: 'The zebrafish anatomy and stage ontologies: representing the anatomy and
       development of Danio rerio.'
+  review:
+    date: 2010
   taxon:
     id: NCBITaxon:7954
     label: Danio
@@ -590,6 +622,7 @@ ontologies:
   - id: aeo.owl
     ontology_purl: http://purl.obolibrary.org/obo/aeo.owl
   title: Anatomical Entity Ontology
+  tracker: https://github.com/obophenotype/human-developmental-anatomy-ontology/issues
 - activity_status: active
   build:
     checkout: git clone  https://github.com/AgriculturalSemantics/agro.git
@@ -1688,6 +1721,7 @@ ontologies:
   depicted_by: https://raw.githubusercontent.com/EuPathDB/communitysite/master/assets/images/VEuPathDB-logo-s.png
   description: An ontology is developed to support Eukaryotic Pathogen, Host & Vector
     Genomics Resource (VEuPathDB; https://veupathdb.org).
+  domain: functional genomics, population biology, clinical epidemiology, and microbiomes
   homepage: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology
   id: eupath
   layout: ontology_detail
@@ -1701,6 +1735,19 @@ ontologies:
     ontology_purl: http://purl.obolibrary.org/obo/eupath.owl
   title: VEuPathDB ontology
   tracker: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues
+  usages:
+  - description: The VEuPathDB ontology is used in the VEuPathDB (Eukaryotic Pathogen,
+      Vector & Host Informatics Resources) covers both functional genomics and population
+      biology.
+    type: annotation and query
+    user: https://veupathdb.org
+  - description: The VEuPathDB ontology is used in the clinical epidemiology resources.
+    type: annotation and query
+    user: https://clinepidb.org
+  - description: The VEuPathDB ontology is used in the MicrobiomeDB, a systems biology
+      platform for integrating, mining and analyzing microbiome experiments.
+    type: annotation and query
+    user: https://microbiomedb.org
 - activity_status: active
   build:
     method: obo2owl
@@ -2182,13 +2229,16 @@ ontologies:
     url: https://creativecommons.org/licenses/by/4.0/
   ontology_purl: http://purl.obolibrary.org/obo/gno.owl
   products:
-  - id: gno.owl
+  - description: Glycan Naming Ontology, OWL format
+    id: gno.owl
     ontology_purl: http://purl.obolibrary.org/obo/gno.owl
-  - id: gno.obo
+  - description: Glycan Naming Ontology, OBO format
+    id: gno.obo
     ontology_purl: http://purl.obolibrary.org/obo/gno.obo
-  - id: gno.json
+  - description: Glycan Naming Ontology, JSON format
+    id: gno.json
     ontology_purl: http://purl.obolibrary.org/obo/gno.json
-  title: Glycan Naming Ontology
+  title: Glycan Naming Ontology (GNOme)
   tracker: https://github.com/glygen-glycan-data/GNOme/issues
 - activity_status: active
   contact:

diff --git a/_layouts/ontology_detail.html b/_layouts/ontology_detail.html
@@ -148,7 +148,25 @@ <h2>Products</h2>
             {% endif %}
           </dd>
 
-
+					{% if page.review %}
+					<dt>Review Date</dt>
+					<dd>
+						{% if page.review.date %}
+						{{page.review.date}}
+						{% else %}
+						n/a
+						{% endif %}
+					</dd>
+					<dt>Review Document</dt>
+					<dd>
+						{% if page.review.document %}
+					  <a href="{{page.review.document.link}}">{{page.review.document.label}}</a>
+						{% else %}
+						n/a
+						{% endif %}
+					<dd>
+					{% endif %}
+
           <dt>Homepage</dt>
           <dd>
             <a href="{{page.homepage}}">{{page.homepage}}</a>
@@ -179,7 +197,7 @@ <h2>Products</h2>
           <dd>
             <a href="/domain/{{page.domain}}.html">{{page.domain}}</a>
           </dd>
-
+					
           {% if page.mailing_list %}
           <dt>Mail List</dt>
           <dd>

diff --git a/docs/CompletedReviews.md b/docs/CompletedReviews.md
@@ -9,66 +9,13 @@ This page lists OBO Foundry ontologies that have gone through the current [revie
 
 
 <style type="text/css">
-.tg  {border-collapse:collapse;border-spacing:0;border-color:#ccc;}
-.tg td{font-family:Arial, sans-serif;font-size:14px;padding:10px 5px;border-style:solid;border-width:1px;overflow:hidden;word-break:normal;border-color:#ccc;color:#333;background-color:#fff;}
-.tg th{font-family:Arial, sans-serif;font-size:14px;font-weight:normal;padding:10px 5px;border-style:solid;border-width:1px;overflow:hidden;word-break:normal;border-color:#ccc;color:#333;background-color:#f0f0f0;}
-.tg .tg-yp4a{border-color:#333333;vertical-align:top}
-.tg .tg-lbaf{font-weight:bold;border-color:#333333;vertical-align:top}
+  .tg  {border-collapse:collapse;border-spacing:0;border-color:#ccc;}
+  .tg td{font-family:Arial, sans-serif;font-size:14px;padding:10px 5px;border-style:solid;border-width:1px;overflow:hidden;word-break:normal;border-color:#ccc;color:#333;background-color:#fff;}
+  .tg th{font-family:Arial, sans-serif;font-size:14px;font-weight:normal;padding:10px 5px;border-style:solid;border-width:1px;overflow:hidden;word-break:normal;border-color:#ccc;color:#333;background-color:#f0f0f0;}
+  .tg .tg-yp4a{border-color:#333333;vertical-align:top}
+  .tg .tg-lbaf{font-weight:bold;border-color:#333333;vertical-align:top}
 </style>
-<table class="tg">
-  <tr>
-    <th class="tg-lbaf">Ontology Name</th>
-    <th class="tg-lbaf">Date</th>
-    <th class="tg-lbaf">Review</th>
-  </tr>
-  <tr>
-    <td class="tg-yp4a"><a href="http://www.obofoundry.org/ontology/bfo">Basic Formal Ontology</a></td>
-    <td class="tg-yp4a">2016</td>
-    <td class="tg-yp4a"><a href="https://drive.google.com/open?id=0B81h9ah4tAM_RnNTRUZnVGRyWXM">PDF</a></td>
-  </tr>
-  <tr>
-    <td class="tg-yp4a"><a href="http://www.obofoundry.org/ontology/doid">Human Disease Ontology</a></td>
-    <td class="tg-yp4a">2015</td>
-    <td class="tg-yp4a"><a href="https://drive.google.com/open?id=0B8vqEgF1N0NIZ082U2JETHlSTGs">PDF</a></td>
-  </tr>
-  <tr>
-    <td class="tg-yp4a"><a href="http://obofoundry.org/ontology/obi">Ontology of Biomedical Investigations</a></td>
-    <td class="tg-yp4a">2013</td>
-    <td class="tg-yp4a"><a href="https://drive.google.com/open?id=0B8vqEgF1N0NIMFlSM3RvdUxGTnc">PDF</a></td>
-  </tr>
-  <tr>
-    <td class="tg-yp4a"><a href="http://obofoundry.org/ontology/po">Plant Ontology</a></td>
-    <td class="tg-yp4a">2013</td>
-    <td class="tg-yp4a"><a href="https://drive.google.com/open?id=0B8vqEgF1N0NIV1o0N21UOHlLSmc">PDF</a></td>
-  </tr>
-  <tr>
-    <td class="tg-yp4a"><a href="http://www.obofoundry.org/ontology/chebi">Chemical Entities of Biological Interest</a></td>
-    <td class="tg-yp4a">2010</td>
-    <td class="tg-yp4a">n/a</td>
-  </tr>
-  <tr>
-    <td class="tg-yp4a"><a href="http://www.obofoundry.org/ontology/go">Gene Ontology</a></td>
-    <td class="tg-yp4a">2010</td>
-    <td class="tg-yp4a">n/a</td>
-  </tr>
-  <tr>
-    <td class="tg-yp4a"><a href="http://www.obofoundry.org/ontology/pato">Phenotype And Trait Ontology</a></td>
-    <td class="tg-yp4a">2010</td>
-    <td class="tg-yp4a">n/a</td>
-  </tr>
-  <tr>
-    <td class="tg-yp4a"><a href="http://www.obofoundry.org/ontology/pr">Protein Ontology</a></td>
-    <td class="tg-yp4a">2010</td>
-    <td class="tg-yp4a">n/a</td>
-  </tr>
-  <tr>
-    <td class="tg-yp4a"><a href="http://www.obofoundry.org/ontology/xao">Xenopus anatomy and development</a></td>
-    <td class="tg-yp4a">2010</td>
-    <td class="tg-yp4a">n/a</td>
-  </tr>
-  <tr>
-    <td class="tg-yp4a"><a href="http://www.obofoundry.org/ontology/zfa">Zebrafish anatomy and development</a></td>
-    <td class="tg-yp4a">2010</td>
-    <td class="tg-yp4a">n/a</td>
-  </tr>
-</table>
+
+
+{% include review_table.html %}
+
diff --git a/ontology/bfo.md b/ontology/bfo.md
@@ -18,6 +18,11 @@ license:
   url: http://creativecommons.org/licenses/by/4.0/
   label: CC-BY
 title: Basic Formal Ontology
+review:
+  date: 2016
+  document:
+    label: PDF
+    link: https://drive.google.com/open?id=0B81h9ah4tAM_RnNTRUZnVGRyWXM
 depicted_by: https://avatars2.githubusercontent.com/u/12972134?v=3&s=200
 browsers:
   # Ontobee link is generated by default

diff --git a/ontology/chebi.md b/ontology/chebi.md
@@ -4,6 +4,8 @@ id: chebi
 in_foundry_order: 1
 alternatePrefix: ChEBI
 title: Chemical Entities of Biological Interest
+review:
+  date: 2010
 build:
   source_url: ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo
   method: obo2owl

diff --git a/ontology/doid.md b/ontology/doid.md
@@ -26,6 +26,11 @@ taxon:
   id: NCBITaxon:9606 
   label: Homo sapiens
 title: Human Disease Ontology
+review:
+  date: 2015
+  document:
+    label: PDF
+    link: https://drive.google.com/open?id=0B8vqEgF1N0NIZ082U2JETHlSTGs
 build:
   source_url: https://raw.githubusercontent.com/DiseaseOntology/HumanDiseaseOntology/master/src/ontology/doid.obo
   method: obo2owl

diff --git a/ontology/go.md b/ontology/go.md
@@ -12,6 +12,8 @@ license:
 label: GO
 description: An ontology for describing the function of genes and gene products
 title: Gene Ontology
+review:
+  date: 2010
 homepage: http://geneontology.org/
 twitter: news4go
 facebook: https://www.facebook.com/Gene-Ontology-305908656519/ 

diff --git a/ontology/obi.md b/ontology/obi.md
@@ -3,6 +3,11 @@ layout: ontology_detail
 id: obi
 in_foundry_order: 1
 title: Ontology for Biomedical Investigations
+review:
+  date: 2013
+  document:
+    label: PDF
+    link: https://drive.google.com/open?id=0B8vqEgF1N0NIMFlSM3RvdUxGTnc
 description: An integrated ontology for the description of life-science and clinical investigations
 domain: experiments
 homepage: http://obi-ontology.org

diff --git a/ontology/pato.md b/ontology/pato.md
@@ -3,6 +3,8 @@ layout: ontology_detail
 id: pato
 in_foundry_order: 1
 title: Phenotype And Trait Ontology
+review:
+  date: 2010
 build:
   source_url: https://raw.githubusercontent.com/pato-ontology/pato/master/pato.obo
   method: obo2owl

diff --git a/ontology/po.md b/ontology/po.md
@@ -3,6 +3,11 @@ layout: ontology_detail
 id: po
 in_foundry_order: 1
 title: Plant Ontology
+review:
+  date: 2013
+  document:
+    label: PDF
+    link: https://drive.google.com/open?id=0B8vqEgF1N0NIV1o0N21UOHlLSmc
 jobs:
   - id: https://travis-ci.org/Planteome/plant-ontology
     type: travis-ci

diff --git a/ontology/pr.md b/ontology/pr.md
@@ -25,6 +25,8 @@ browsers:
     title: PRO Home
     url: http://proconsortium.org
 title: PRotein Ontology (PRO)
+review:
+  date: 2010
 license:
   url: http://creativecommons.org/licenses/by/4.0/
   label: CC-BY

diff --git a/ontology/xao.md b/ontology/xao.md
@@ -16,6 +16,8 @@ taxon:
   id: NCBITaxon:8353
   label: Xenopus
 title: Xenopus Anatomy Ontology
+review:
+  date: 2010
 build:
   source_url: https://raw.githubusercontent.com/xenopus-anatomy/xao/master/xenopus_anatomy.obo
   method: obo2owl

diff --git a/ontology/zfa.md b/ontology/zfa.md
@@ -16,6 +16,8 @@ taxon:
   id: NCBITaxon:7954
   label: Danio
 title: Zebrafish anatomy and development ontology
+review:
+  date: 2010
 license:
   url: http://creativecommons.org/licenses/by/3.0/
   label: CC-BY