Add badge for preferred citations (#2070)

* Add badge for preferred citations This PR adds a "preferred" citation field as suggested in #2063 (comment) and adds a nice display badge to match it so we can remove more redundant information from ECO and FBbt. This PR also removes some redundant information from ECO and FBbt. * Revert ECO change * Add test for only one preferred citation Co-authored-by: Nico Matentzoglu <[email protected]>
OBOFoundry · Aug 30, 2022 · 10dd17d · 10dd17d
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Showing 5 changed files with 17 additions and 7 deletions.
diff --git a/_layouts/ontology_detail.html b/_layouts/ontology_detail.html
@@ -93,6 +93,9 @@ <h3 class="panel-title">Publications</h3>
         {% for p in page.publications %}
         <div class="list-group-item">
           <a href="{{p.id}}">{{p.title}}</a>
+          {% if p.preferred %}
+          <span class="badge">Preferred</span>
+          {% endif %}
         </div>
         {% endfor %}
       </div>

diff --git a/ontology/eco.md b/ontology/eco.md
@@ -31,6 +31,7 @@ products:
 publications:
 - id: https://www.ncbi.nlm.nih.gov/pubmed/30407590
   title: 'ECO, the Evidence & Conclusion Ontology: community standard for evidence information.'
+  preferred: true
 - id: https://www.ncbi.nlm.nih.gov/pubmed/25052702
   title: Standardized description of scientific evidence using the Evidence Ontology (ECO)
 repository: https://github.com/evidenceontology/evidenceontology
@@ -65,6 +66,4 @@ For **advice on requesting new terms**, please see **[the Evidence & Conclusion
 
 For **further information** visit the **[Evidence & Conclusion Ontology website](http://www.evidenceontology.org/)**.
 
-Please **cite** the following paper: [Giglio M, Tauber R, Nadendla S, Munro J, Olley D, Ball S, Mitraka E, Schriml LM, Gaudet P, Hobbs ET, Erill I, Siegele DA, Hu JC, Mungall C, Chibucos MC. **ECO, the Evidence & Conclusion Ontology: community standard for evidence information**. Nucleic Acids Res. 2019 Jan 8;47(D1):D1186-D1194.](https://www.ncbi.nlm.nih.gov/pubmed/30407590)
-
 This work is made possible by **[award number 1458400](http://www.nsf.gov/awardsearch/showAward?AWD_ID=1458400)** from the **US National Science Foundation's Division of Biological Infrastructure**.
diff --git a/ontology/fbbt.md b/ontology/fbbt.md
@@ -37,6 +37,7 @@ products:
 publications:
 - id: https://www.ncbi.nlm.nih.gov/pubmed/24139062
   title: The Drosophila anatomy ontology
+  preferred: true
 - id: https://www.ncbi.nlm.nih.gov/pubmed/22402613
   title: A strategy for building neuroanatomy ontologies
 - id: https://www.ncbi.nlm.nih.gov/pubmed/22180411
@@ -65,8 +66,3 @@ usages:
   user: http://flybase.org
 activity_status: active
 ---
-
-An ontology representing the gross anatomy of Drosophila melanogaster.
-
-FBbt can be cited as:
-_Costa M., Reeve S., Grumbling G., Osumi-Sutherland D._ (2013) The Drosophila anatomy ontology. [Journal of Biomedical Semantics __4__(32).](https://doi.org/10.1186/2041-1480-4-32)
diff --git a/tests/test_integrity.py b/tests/test_integrity.py
@@ -84,6 +84,15 @@ def test_dependencies(self):
     def test_publications(self):
         """Test publications information."""
         for ontology, data in sorted(self.ontologies.items()):
+            self.assertIn(
+                sum(
+                    publication.get("preferred", False)
+                    for publication in data.get("publications", [])
+                ),
+                {0, 1},
+                msg=f"Only one publication can be marked as preferred for {ontology}.",
+            )
+
             for i, publication in enumerate(data.get("publications", [])):
                 identifier = publication["id"]
                 if ontology == "agro" and identifier.startswith("http://ceur-ws.org/"):

diff --git a/util/schema/registry_schema.json b/util/schema/registry_schema.json
@@ -341,6 +341,9 @@
           },
           "title": {
             "type": "string"
+          },
+          "preferred": {
+            "type": "boolean"
           }
         },
         "required": [