Merge pull request PGScatalog#390 from fyvon/improve/about_citation

Added previous publication for PGS-Catalog citation and updated acknowledgements
HDRUK · Oct 18, 2024 · 0dca9c6 · 0dca9c6
2 parents f5d1330 + 1e09244
commit 0dca9c6
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Showing 9 changed files with 63 additions and 56 deletions.
diff --git a/catalog/context_processors.py b/catalog/context_processors.py
@@ -46,7 +46,8 @@ def pgs_search_examples(request):
 
 def pgs_info(request):
     return {
-        'pgs_citation': constants.PGS_CITATION,
+        'pgs_citation': constants.PGS_CITATIONS[0],
+        'pgs_citations': constants.PGS_CITATIONS,
         'pgs_publications': constants.PGS_PUBLICATIONS,
         'pgs_table_helper': constants.TABLE_HELPER,
         'ensembl_version': constants.ENSEMBL_VERSION

diff --git a/catalog/templates/catalog/docs/about.html b/catalog/templates/catalog/docs/about.html
@@ -86,19 +86,7 @@ <h3 id="project">The PGS Catalog Project</h3>
         </p>
 
     <h4 id="citation">Citation</h4>
-    <p>The PGS Catalog development is led by <a href="{{ ebi_url }}/about/people/samuel-lambert">Samuel Lambert</a>
-        under the supervision of <a href="https://www.inouyelab.org/home/people">Michael Inouye</a> (<a href="https://sysgenresearch.org/">University of Cambridge & Baker Institute</a>)
-        in collaboration with <a href="{{ hdr_uk_cam_url }}">Health Data Research - UK</a> (Laurent Gil)
-        and the <a href="{{ ebi_url }}/gwas/">EBI Samples, Phenotypes and Ontologies team / NHGRI-EBI GWAS Catalog</a> (Helen Parkinson, Aoife McMahon, Laura Harris).</p>
-    <p>The Catalog is under active development, and we continue to add new features and curate new data. If you use the Catalog or Calculator in your research we ask that you cite our recent publication:
-    <div class="clearfix mb-3">
-      <div class="highlight_content">
-        <p>{{ pgs_citation.authors }}</p>
-        <p><u>{{ pgs_citation.title }}</u></p>
-        <p><span class="with_sep_right"><i>{{ pgs_citation.journal }}</i></span>doi: <a href="https://doi.org/{{ pgs_citation.doi }}">{{ pgs_citation.doi }}</a> ({{ pgs_citation.year }}).</p>
-      </div>
-    </div>
-    <p>Individual PGS obtained from the database should also be cited appropriately, and used in accordance with any licensing restrictions set by the authors (see our <a href="{{ terms_of_use }}">Terms of Use</a> for more information).</p>
+    {% include "catalog/includes/citation.html" %}
     <div class="more more-section">
         <h6 class="more-section-title">All PGS Catalog Publications:</h6>
         <span class="moreellipses"></span>

diff --git a/catalog/templates/catalog/docs/faq.html b/catalog/templates/catalog/docs/faq.html
@@ -73,20 +73,7 @@ <h3 class="mt-5" id="access_how">How to access PGS Catalog data?</h3>
 
 
       <h3 class="mt-5" id="cite_how">How to cite the PGS Catalog?</h3>
-      <p>The PGS Catalog development is led by <a href="{{ ebi_url }}/about/people/samuel-lambert">Samuel Lambert</a>
-          under the supervision of <a href="https://www.inouyelab.org/home/people">Michael Inouye</a> (<a href="https://sysgenresearch.org/">University of Cambridge & Baker Institute</a>)
-          in collaboration with <a href="{{ hdr_uk_cam_url }}">Health Data Research - UK</a> (Laurent Gil)
-          and the <a href="{{ ebi_url }}/gwas/">NHGRI-EBI GWAS Catalog</a> (Aoife McMahon & Laura Harris).</p>
-      <p>The Catalog is under active development, and we continue to add new features and curate new data. If you use the Catalog in your research we ask that you cite our recent publication:
-      <div class="clearfix mb-3">
-        <div class="highlight_content">
-          <p>{{ pgs_citation.authors }}</p>
-          <p><u>{{ pgs_citation.title }}</u></p>
-          <p><span class="with_sep_right"><i>{{ pgs_citation.journal }}</i></span>doi: <a href="https://doi.org/{{ pgs_citation.doi }}">{{ pgs_citation.doi }}</a> ({{ pgs_citation.year }}).</p>
-        </div>
-      </div>
-      <p>Individual PGS obtained from the database should also be cited appropriately, and used in accordance with any licensing restrictions set by the authors (see our <a href="{{ terms_of_use }}">Terms of Use</a> for more information).</p>
-
+      {% include "catalog/includes/citation.html" %}
 
       <h3 class="mt-5" id="submit_how">How to submit data to the PGS Catalog?</h3>
       <p>

diff --git a/catalog/templates/catalog/includes/citation.html b/catalog/templates/catalog/includes/citation.html
@@ -0,0 +1,20 @@
+<p>The PGS Catalog development is led by <a href="{{ ebi_url }}/about/people/samuel-lambert">Samuel Lambert</a>
+    under the supervision of <a href="https://www.inouyelab.org/home/people">Michael Inouye</a> (<a href="https://sysgenresearch.org/">University of Cambridge & Baker Institute</a>)
+    in collaboration with <a href="{{ hdr_uk_cam_url }}">Health Data Research - UK</a> (Laurent Gil)
+    and the <a href="{{ ebi_url }}/gwas/">EBI Samples, Phenotypes and Ontologies team / NHGRI-EBI GWAS Catalog</a> (Helen Parkinson, Aoife McMahon, Laura Harris).</p>
+<p>The Catalog is under active development, and we continue to add new features and curate new data. If you use the Catalog or Calculator in your research we ask that you cite our below flagship publications:
+<div class="clearfix mb-3">
+      <div class="highlight_content">
+          {% for c in pgs_citations %}
+              <div>
+                <p>{{ c.authors }}</p>
+                <p><u>{{ c.title }}</u></p>
+                <p><span class="with_sep_right"><i>{{ c.journal }}</i></span>doi: <a href="https://doi.org/{{ c.doi }}">{{ c.doi }}</a> ({{ c.year }}).</p>
+              </div>
+          {% if not forloop.last %}
+              <hr>
+          {% endif %}
+          {% endfor %}
+      </div>
+</div>
+<p>Individual PGS obtained from the database should also be cited appropriately, and used in accordance with any licensing restrictions set by the authors (see our <a href="{{ terms_of_use }}">Terms of Use</a> for more information).</p>
diff --git a/catalog/tests/test_models.py b/catalog/tests/test_models.py
@@ -1155,7 +1155,7 @@ def create_retired(self, data_id, pub_doi, retirement_notes):
 
     def test_retired_score(self):
         score_id = 'PGS000999'
-        score_doi = constants.PGS_CITATION['doi']
+        score_doi = constants.PGS_CITATIONS[0]['doi']
         score_notes = 'This score has been retired'
         retired_score = self.create_retired(score_id, score_doi, score_notes)
         # Instance

diff --git a/pgs_web/constants.py b/pgs_web/constants.py
@@ -1,22 +1,32 @@
 # Module storing constants used across the website
 
-PGS_CITATION = {
+PGS_CITATIONS = [
+    {
     'title': 'Enhancing the Polygenic Score Catalog with tools for score calculation and ancestry normalization',
     'doi': '10.1038/s41588-024-01937-x',
     'PMID': 39327485,
     'authors': 'Samuel A. Lambert, Benjamin Wingfield, Joel T. Gibson, Laurent Gil, Santhi Ramachandran, Florent Yvon, Shirin Saverimuttu, Emily Tinsley, Elizabeth Lewis, Scott C. Ritchie, Jingqin Wu, Rodrigo Canovas, Aoife McMahon, Laura W. Harris, Helen Parkinson, Michael Inouye',
     'journal': 'Nature Genetics', # TODO: Update volume/page when printed
     'year': 2024
-}
+    },
+    {
+    'title': 'The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation',
+    'doi': '10.1038/s41588-021-00783-5',
+    'PMID': 33692568,
+    'authors': 'Samuel A. Lambert, Laurent Gil, Simon Jupp, Scott C. Ritchie, Yu Xu, Annalisa Buniello, Aoife McMahon, Gad Abraham, Michael Chapman, Helen Parkinson, John Danesh, Jacqueline A. L. MacArthur, Michael Inouye ',
+    'journal': 'Nature Genetics volume 53, pages420–425',
+    'year': 2021
+    }
+]
 
 PGS_PUBLICATIONS = [
     {
-        'title': PGS_CITATION['title'],
+        'title': PGS_CITATIONS[0]['title'],
         'authors': 'Lambert, Wingfield et al',
-        'year': PGS_CITATION['year'],
-        'doi': PGS_CITATION['doi'],
-        'PMID': PGS_CITATION['PMID'],
-        'journal': PGS_CITATION['journal']
+        'year': PGS_CITATIONS[0]['year'],
+        'doi': PGS_CITATIONS[0]['doi'],
+        'PMID': PGS_CITATIONS[0]['PMID'],
+        'journal': PGS_CITATIONS[0]['journal']
     },
     {
         'title': 'The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource',
@@ -27,12 +37,12 @@
         'journal': 'Nucleic Acids Research 51(D1):D977-D985'
     },
     {
-        'title': 'The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation',
+        'title': PGS_CITATIONS[1]['title'],
         'authors': 'Lambert et al',
-        'year': 2021,
-        'doi': '10.1038/s41588-021-00783-5',
-        'PMID': 33692568,
-        'journal': 'Nature Genetics volume 53, pages420–425'
+        'year': PGS_CITATIONS[1]['year'],
+        'doi': PGS_CITATIONS[1]['doi'],
+        'PMID': PGS_CITATIONS[1]['PMID'],
+        'journal': PGS_CITATIONS[1]['journal']
     }
 ]
 
@@ -55,7 +65,7 @@
     'TERMS_OF_USE'      : 'https://www.ebi.ac.uk/about/terms-of-use',
     'TEMPLATEGoogleDoc_URL' : 'https://docs.google.com/spreadsheets/d/1UEGH0NNuQ8ifbsxIhe8HbnG9XYjsIwSF/edit?usp=sharing',
     'CurationGoogleDoc_URL' : 'https://drive.google.com/file/d/1QYdKBnEqAmhSZIuMux7ifpT3ZBk9gupT/view',
-    'CATALOG_PUBLICATION_URL' : 'https://doi.org/'+PGS_CITATION['doi'],
+    'CATALOG_PUBLICATION_URL' : 'https://doi.org/' + PGS_CITATIONS[0]['doi'],
     'EPMC_REST_SEARCH'  : 'https://www.ebi.ac.uk/europepmc/webservices/rest/search'
 }
 
@@ -163,6 +173,7 @@
     {'name': 'Laurent Gil','group': ['hdruk']},
     {'name': 'Benjamin Wingfield','group': ['ebi']},
     {'name': 'Florent Yvon','group': ['inouye']},
+    {'name': 'Joel Gibson','group': ['curators','inouye']},
     {'name': 'Aoife McMahon', 'group': ['curators','nhgri-ebi']},
     {'name': 'Santhi Ramachandran','group': ['nhgri-ebi']},
     {'name': 'Elizabeth Lewis','group': ['nhgri-ebi']},

diff --git a/release/scripts/EuropePMCLinkage.py b/release/scripts/EuropePMCLinkage.py
@@ -47,7 +47,7 @@ def generate_xml_file(self):
         title = 'Link to the Polygenic Score (PGS) Catalog resource'
         url = self.pgs_url
         source = 'MED'
-        pmid = constants.PGS_CITATION['PMID']
+        pmid = constants.PGS_CITATIONS[0]['PMID']
         self.create_xml_link(title,url,source,pmid)
 
         # Add PGS Publications

diff --git a/rest_api/static/rest_api/openapi/openapi-schema.yml b/rest_api/static/rest_api/openapi/openapi-schema.yml
@@ -2359,43 +2359,43 @@ paths:
                         type: string
                         description: "Date of the latest PGS release (format YYYY-MM-DD)"
                         format: date
-                        example: "2021-02-23"
+                        example: "2024-10-08"
                       scores:
                         type: number
                         description: "Number of Scores in the Catalog"
-                        example: 738
+                        example: 5001
                       traits:
                         type: number
                         description: "Number of Traits in the Catalog"
-                        example: 202
+                        example: 654
                       publications:
                         type: number
                         description: "Number of Publications in the Catalog"
-                        example: 144
+                        example: 673
                   citation:
                     type: object
                     description: "Information about the latest PGS Catalog publication"
                     properties:
                       title:
                         type: string
                         description: "Title of the publication"
-                        example: 'The Polygenic Score Catalog: new functionality and tools to enable FAIR research'
+                        example: 'Enhancing the Polygenic Score Catalog with tools for score calculation and ancestry normalization'
                       doi:
                         type: string
                         description: "doi of the publication"
-                        example: '10.1101/2024.05.29.24307783'
+                        example: '10.1038/s41588-024-01937-x'
                       PMID:
                         type: number
                         description: "PubMed ID"
-                        example: null
+                        example: 39327485
                       authors:
                         type: string
                         description: "List of the publication authors"
                         example: 'Samuel A. Lambert, ... , Michael Inouye'
                       journal:
                         type: string
                         description: "Name of the journal"
-                        example: 'medRxiv (Preprint)'
+                        example: 'Nature Genetics'
                       year:
                         type: number
                         description: "Year of publication"
@@ -2409,15 +2409,15 @@ paths:
                         title:
                           type: string
                           description: "Title of the publication"
-                          example: 'The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation'
+                          example: 'Enhancing the Polygenic Score Catalog with tools for score calculation and ancestry normalization'
                         doi:
                           type: string
                           description: "doi of the publication"
-                          example: '10.1038/s41588-021-00783-5'
+                          example: '10.1038/s41588-024-01937-x'
                         PMID:
                           type: number
                           description: "PubMed ID"
-                          example: 33692568
+                          example: 39327485
                         authors:
                           type: string
                           description: "Publication first author(s)"
@@ -2429,7 +2429,7 @@ paths:
                         year:
                           type: number
                           description: "Year of publication"
-                          example: 2021
+                          example: 2024
                   ensembl_version:
                     type: number
                     description: "Ensembl version used to generate the Harmonized Scoring files"

diff --git a/rest_api/views.py b/rest_api/views.py
@@ -687,7 +687,7 @@ def get(self, request):
         data = {
             'rest_api': constants_rest.PGS_REST_API[0],
             'latest_release': latest_release,
-            'citation': constants.PGS_CITATION,
+            'citation': constants.PGS_CITATIONS[0],
             'pgs_catalog_publications': constants.PGS_PUBLICATIONS,
             'ensembl_version': constants.ENSEMBL_VERSION,
             'terms_of_use': constants.USEFUL_URLS['TERMS_OF_USE']