fix: use direct liquid assign expressions and remove redundant biopor…

…tal browser links
OBOFoundry · Nov 25, 2024 · 26b93f9 · 26b93f9
1 parent b6c78bc
commit 26b93f9
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Showing 13 changed files with 27 additions and 69 deletions.
diff --git a/_layouts/ontology_detail.html b/_layouts/ontology_detail.html
@@ -70,7 +70,33 @@ <h1>
         <a href="http://www.ebi.ac.uk/ols/ontologies/{{page.id}}" class="btn btn-outline-primary" target="_blank" rel="noopener">
           OLS
         </a>
-        <a href="https://bioportal.bioontology.org/ontologies/{{ page.id | make_bioportal_id }}" class="btn btn-outline-primary" target="_blank" rel="noopener">
+        {% assign bioportal_id = page.id | upcase %}
+        {% if bioportal_id == 'FBBT' %}
+            {% assign bioportal_id = 'FB-BT' %}
+        {% elsif bioportal_id == 'ro' %}
+            {% assign bioportal_id = 'OBOREL' %}
+        {% elsif bioportal_id == 'apollo_sv' %}
+            {% assign bioportal_id = 'APOLLO-SV' %}
+        {% elsif bioportal_id == 'trans' %}
+            {% assign bioportal_id = 'PTRANS' %}
+        {% elsif bioportal_id == 'wbls' %}
+            {% assign bioportal_id = 'WB-LS' %}
+        {% elsif bioportal_id == 'fbdv' %}
+            {% assign bioportal_id = 'FB-DV' %}
+        {% elsif bioportal_id == 'wbbt' %}
+            {% assign bioportal_id = 'WB-BT' %}
+        {% elsif bioportal_id == 'wbphenotype' %}
+            {% assign bioportal_id = 'WB-PHENOTYPE' %}
+        {% elsif bioportal_id == 'to' %}
+            {% assign bioportal_id = 'PTO' %}
+        {% elsif bioportal_id == 'fbcv' %}
+            {% assign bioportal_id = 'FB-CV' %}
+        {% elsif bioportal_id == 'umod' %}
+            {% assign bioportal_id = 'PSIMOD' %}
+        {% elsif bioportal_id == 'pso' %}
+            {% assign bioportal_id = 'PLANTSO' %}
+        {% endif %}
+        <a href="https://bioportal.bioontology.org/ontologies/{{ bioportal_id }}" class="btn btn-outline-primary" target="_blank" rel="noopener">
           BioPortal
         </a>
         {% for b in page.browsers %}

diff --git a/_plugins/bioportal_identifier.rb b/_plugins/bioportal_identifier.rb
diff --git a/ontology/bfo.md b/ontology/bfo.md
@@ -2,10 +2,6 @@
 layout: ontology_detail
 id: bfo
 title: Basic Formal Ontology
-browsers:
-- title: BioPortal Browser
-  label: BioPortal
-  url: http://bioportal.bioontology.org/ontologies/BFO?p=classes
 contact:
   email: [email protected]
   github: phismith

diff --git a/ontology/fbbt.md b/ontology/fbbt.md
@@ -9,9 +9,6 @@ browsers:
 - title: Virtual Fly Brain
   label: VFB
   url: http://www.virtualflybrain.org/site/stacks/index.htm?add=FBbt:00007401
-- title: BioPortal Browser
-  label: BioPortal
-  url: http://bioportal.bioontology.org/ontologies/FB-BT?p=classes
 build:
   checkout: git clone https://github.com/FlyBase/drosophila-anatomy-developmental-ontology.git
   path: .

diff --git a/ontology/kisao.md b/ontology/kisao.md
@@ -6,9 +6,6 @@ browsers:
 - title: Ontology Lookup Service
   label: OLS
   url: https://www.ebi.ac.uk/ols/ontologies/kisao
-- title: BioPortal
-  label: BioPortal
-  url: https://bioportal.bioontology.org/ontologies/KISAO
 - title: OntoBee
   label: OntoBee
   url: https://www.ontobee.org/ontology/KISAO

diff --git a/ontology/nbo.md b/ontology/nbo.md
@@ -2,10 +2,6 @@
 layout: ontology_detail
 id: nbo
 title: Neuro Behavior Ontology
-browsers:
-- title: BioPortal Ontology Browser
-  label: BioPortal
-  url: https://bioportal.bioontology.org/ontologies/NBO
 build:
   method: owl2obo
   source_url: https://raw.githubusercontent.com/obo-behavior/behavior-ontology/master/nbo.owl

diff --git a/ontology/obi.md b/ontology/obi.md
@@ -2,10 +2,6 @@
 layout: ontology_detail
 id: obi
 title: Ontology for Biomedical Investigations
-browsers:
-- title: BioPortal Browser
-  label: BioPortal
-  url: http://bioportal.bioontology.org/ontologies/OBI?p=classes
 build:
   source_url: http://purl.obofoundry.org/obo/obi/repository/trunk/src/ontology/branches/
 contact:

diff --git a/ontology/occo.md b/ontology/occo.md
@@ -2,10 +2,6 @@
 layout: ontology_detail
 id: occo
 title: Occupation Ontology
-browsers:
-- title: BioPortal Ontology Browser
-  label: BioPortal
-  url: https://bioportal.bioontology.org/ontologies/OCCO?p=classes
 contact:
   email: [email protected]
   github: zhengj2007

diff --git a/ontology/ontoneo.md b/ontology/ontoneo.md
@@ -2,10 +2,6 @@
 layout: ontology_detail
 id: ontoneo
 title: Obstetric and Neonatal Ontology
-browsers:
-- title: BioPortal Browser
-  label: BioPortal
-  url: https://bioportal.bioontology.org/ontologies/ONTONEO
 build:
   source_url: http://purl.obolibrary.org/obo/ontoneo/ontoneo.owl
 contact:

diff --git a/ontology/pato.md b/ontology/pato.md
@@ -2,10 +2,6 @@
 layout: ontology_detail
 id: pato
 title: Phenotype And Trait Ontology
-browsers:
-- title: BioPortal Ontology Browser
-  label: BioPortal
-  url: https://bioportal.bioontology.org/ontologies/PATO
 contact:
   email: [email protected]
   github: gkoutos

diff --git a/ontology/pr.md b/ontology/pr.md
@@ -3,9 +3,6 @@ layout: ontology_detail
 id: pr
 title: PRotein Ontology (PRO)
 browsers:
-- title: BioPortal Browser
-  label: BioPortal
-  url: http://bioportal.bioontology.org/ontologies/PR?p=classes&conceptid=http://purl.obolibrary.org/obo/PR_000000001
 - title: PRO Home
   label: PRO
   url: http://proconsortium.org

diff --git a/ontology/slso.md b/ontology/slso.md
@@ -2,10 +2,6 @@
 layout: ontology_detail
 id: slso
 title: Space Life Sciences Ontology
-browsers:
-- title: BioPortal Ontology Browser
-  label: BioPortal
-  url: https://bioportal.bioontology.org/ontologies/SLSO
 contact:
   email: [email protected]
   github: DanBerrios

diff --git a/ontology/txpo.md b/ontology/txpo.md
@@ -3,9 +3,6 @@ layout: ontology_detail
 id: txpo
 title: Toxic Process Ontology
 browsers:
-- title: BioPortal Browser
-  label: BioPortal
-  url: http://bioportal.bioontology.org/ontologies/TXPO?p=classes
 - title: TOXPILOT
   label: TOXPILOT
   url: https://toxpilot.nibiohn.go.jp/