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[pull] master from PGScatalog:master #145

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Oct 4, 2024
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[pull] master from PGScatalog:master #145

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66240f5
Updated citation with latest published PGS Catalog paper
fyvon Oct 1, 2024
5e05e46
Replaced "preprint" with "publication" for PGSCatalog paper mentions
fyvon Oct 1, 2024
bacea90
Using last now-published PGS publication PMID in EPMC link file
fyvon Oct 1, 2024
f49b046
Merge pull request #389 from fyvon/update/citation_2024
fyvon Oct 1, 2024
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2 changes: 1 addition & 1 deletion catalog/templates/catalog/docs/about.html
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Expand Up @@ -90,7 +90,7 @@ <h4 id="citation">Citation</h4>
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 preprint:
<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>
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2 changes: 1 addition & 1 deletion catalog/templates/catalog/docs/faq.html
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Expand Up @@ -77,7 +77,7 @@ <h3 class="mt-5" id="cite_how">How to cite the PGS Catalog?</h3>
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 preprint:
<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>
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2 changes: 1 addition & 1 deletion catalog/templates/catalog/index.html
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Expand Up @@ -124,7 +124,7 @@ <h5 class="mt-0">An open database of polygenic scores and the relevant metadata
Each <b>PGS</b> in the <b>Catalog</b> is consistently annotated with relevant metadata; including scoring files (variants, effect alleles/weights), annotations of how the PGS was developed and applied, and evaluations of their predictive performance.
</p>
<p class="mb-0">
More about the PGS Catalog project, descriptions of the data, and publication eligibility criteria can be found in our <a href="/about"><b>documentation</b></a> and recent <a href="{{catalog_publication_url}}"><b>preprint</b></a>.
More about the PGS Catalog project, descriptions of the data, and publication eligibility criteria can be found in our <a href="/about"><b>documentation</b></a> and recent <a href="{{catalog_publication_url}}"><b>publication</b></a>.
</p>
</div>
</div>
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8 changes: 4 additions & 4 deletions pgs_web/constants.py
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@@ -1,11 +1,11 @@
# Module storing constants used across the website

PGS_CITATION = {
'title': 'The Polygenic Score Catalog: new functionality and tools to enable FAIR research',
'doi': '10.1101/2024.05.29.24307783',
'PMID': None, # To be updated when 2024 is published. (+ Update europePMCLinkage)
'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': 'medRxiv (Preprint)',
'journal': 'Nature Genetics', # TODO: Update volume/page when printed
'year': 2024
}

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2 changes: 1 addition & 1 deletion release/scripts/EuropePMCLinkage.py
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Expand Up @@ -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_PUBLICATIONS[-1]['PMID'] # to be restored with constants.CITATION when preprint gets published
pmid = constants.PGS_CITATION['PMID']
self.create_xml_link(title,url,source,pmid)

# Add PGS Publications
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