From b6c78bc803ffc0f24f2241be1bce61dc374bc83d Mon Sep 17 00:00:00 2001
From: James Stevenson <james.sharpsteen@gmail.com>
Date: Mon, 25 Nov 2024 10:54:30 -0500
Subject: [PATCH] feat: add NCBO BioPortal link (#2654)

---
 _layouts/ontology_detail.html    | 29 ++++++++++++++++-------------
 _plugins/bioportal_identifier.rb | 28 ++++++++++++++++++++++++++++
 2 files changed, 44 insertions(+), 13 deletions(-)
 create mode 100644 _plugins/bioportal_identifier.rb

diff --git a/_layouts/ontology_detail.html b/_layouts/ontology_detail.html
index ce3ce1289..8bdc6d2f3 100644
--- a/_layouts/ontology_detail.html
+++ b/_layouts/ontology_detail.html
@@ -55,31 +55,34 @@ <h1>
     <div class="card" style="margin-bottom: 1.5em;">
       <div class="card-body">
         <!-- TODO: each ontology should configure which browsers to be exposed in -->
-        <a href="https://ontobee.org/ontology/{{page.id}}" class="btn btn-outline-primary">
+        <a href="https://ontobee.org/ontology/{{page.id}}" class="btn btn-outline-primary" target="_blank" rel="noopener">
           OntoBee
         </a>
         {% if page.aberowl_id %}
-        <a href="http://aber-owl.net/ontology/{{page.aberowl_id | upcase}}" class="btn btn-outline-primary">
-          AberOWL
-        </a>
+          <a href="http://aber-owl.net/ontology/{{page.aberowl_id | upcase}}" class="btn btn-outline-primary" target="_blank" rel="noopener">
+            AberOWL
+          </a>
         {% else %}
-        <a href="http://aber-owl.net/ontology/{{page.id | upcase}}" class="btn btn-outline-primary">
-          AberOWL
-        </a>
+          <a href="http://aber-owl.net/ontology/{{page.id | upcase}}" class="btn btn-outline-primary" target="_blank" rel="noopener">
+            AberOWL
+          </a>
         {% endif %}
-        <a href="http://www.ebi.ac.uk/ols/ontologies/{{page.id}}" class="btn btn-outline-primary">
+        <a href="http://www.ebi.ac.uk/ols/ontologies/{{page.id}}" class="btn btn-outline-primary" target="_blank" rel="noopener">
           OLS
         </a>
-        {% for b in page.browsers %}
-        <a href="{{b.url}}" class="btn btn-outline-primary">
-          {{b.label}}
+        <a href="https://bioportal.bioontology.org/ontologies/{{ page.id | make_bioportal_id }}" class="btn btn-outline-primary" target="_blank" rel="noopener">
+          BioPortal
         </a>
+        {% for b in page.browsers %}
+          <a href="{{b.url}}" class="btn btn-outline-primary" target="_blank" rel="noopener">
+            {{b.label}}
+          </a>
         {% endfor %}
-        <a href="https://bioregistry.io/metaregistry/obofoundry/{{page.id}}" class="btn btn-outline-primary">
+        <a href="https://bioregistry.io/metaregistry/obofoundry/{{page.id}}" class="btn btn-outline-primary" target="_blank" rel="noopener">
          Bioregistry
         </a>
         {% if stripped_content_size > 0 %}
-        <p class="card-text">{{ content }}</p>
+          <p class="card-text">{{ content }}</p>
         {% endif %}
       </div>
     </div>
diff --git a/_plugins/bioportal_identifier.rb b/_plugins/bioportal_identifier.rb
new file mode 100644
index 000000000..7c37d23e9
--- /dev/null
+++ b/_plugins/bioportal_identifier.rb
@@ -0,0 +1,28 @@
+module CustomFilter
+  def make_bioportal_id(obo_id)
+    return obo_id unless obo_id.is_a?(String)
+
+    # ID requirements should be locked down moving forward, so additions to this table
+    # should be rare
+    special_cases = {
+      'fbbt' => 'FB-BT',
+      'ro' => 'OBOREL',
+      'apollo_sv' => 'APOLLO-SV',
+      'trans' => 'PTRANS',
+      'wbls' => 'WB-LS',
+      'fbdv' => 'FB-DV',
+      'wbbt' => 'WB-BT',
+      'wbphenotype' => 'WB-PHENOTYPE',
+      'to' => 'PTO',
+      'fbcv' => 'FB-CV',
+      'mod' => 'PSIMOD',
+      'pso' => 'PLANTSO'
+    }
+
+    return special_cases[obo_id] if special_cases.key? obo_id
+
+    obo_id == obo_id.downcase ? obo_id.upcase : obo_id
+  end
+end
+
+Liquid::Template.register_filter(CustomFilter)