From 66240f56b83056f5804642f1bc8ede2acf8fd658 Mon Sep 17 00:00:00 2001 From: Florent Yvon Date: Tue, 1 Oct 2024 12:24:44 +0100 Subject: [PATCH 1/3] Updated citation with latest published PGS Catalog paper --- pgs_web/constants.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pgs_web/constants.py b/pgs_web/constants.py index 4ddcad21..45ca746b 100644 --- a/pgs_web/constants.py +++ b/pgs_web/constants.py @@ -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 } From 5e05e46b34bd8a590394cd61e5fb7f5f7eaf82d4 Mon Sep 17 00:00:00 2001 From: Florent Yvon Date: Tue, 1 Oct 2024 14:01:30 +0100 Subject: [PATCH 2/3] Replaced "preprint" with "publication" for PGSCatalog paper mentions --- catalog/templates/catalog/docs/about.html | 2 +- catalog/templates/catalog/docs/faq.html | 2 +- catalog/templates/catalog/index.html | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/catalog/templates/catalog/docs/about.html b/catalog/templates/catalog/docs/about.html index c0320425..11669ddd 100644 --- a/catalog/templates/catalog/docs/about.html +++ b/catalog/templates/catalog/docs/about.html @@ -90,7 +90,7 @@

Citation

under the supervision of Michael Inouye (University of Cambridge & Baker Institute) in collaboration with Health Data Research - UK (Laurent Gil) and the EBI Samples, Phenotypes and Ontologies team / NHGRI-EBI GWAS Catalog (Helen Parkinson, Aoife McMahon, Laura Harris).

-

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: +

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:

{{ pgs_citation.authors }}

diff --git a/catalog/templates/catalog/docs/faq.html b/catalog/templates/catalog/docs/faq.html index 72608a60..6ca62cdf 100644 --- a/catalog/templates/catalog/docs/faq.html +++ b/catalog/templates/catalog/docs/faq.html @@ -77,7 +77,7 @@

How to cite the PGS Catalog?

under the supervision of Michael Inouye (University of Cambridge & Baker Institute) in collaboration with Health Data Research - UK (Laurent Gil) and the NHGRI-EBI GWAS Catalog (Aoife McMahon & Laura Harris).

-

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: +

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:

{{ pgs_citation.authors }}

diff --git a/catalog/templates/catalog/index.html b/catalog/templates/catalog/index.html index afaead8d..5299054f 100644 --- a/catalog/templates/catalog/index.html +++ b/catalog/templates/catalog/index.html @@ -124,7 +124,7 @@
An open database of polygenic scores and the relevant metadata Each PGS in the Catalog 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.

- More about the PGS Catalog project, descriptions of the data, and publication eligibility criteria can be found in our documentation and recent preprint. + More about the PGS Catalog project, descriptions of the data, and publication eligibility criteria can be found in our documentation and recent publication.

From bacea902784adbb9ffb2d1cebe386ebe31bbf8dc Mon Sep 17 00:00:00 2001 From: Florent Yvon Date: Tue, 1 Oct 2024 14:20:28 +0100 Subject: [PATCH 3/3] Using last now-published PGS publication PMID in EPMC link file --- release/scripts/EuropePMCLinkage.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/release/scripts/EuropePMCLinkage.py b/release/scripts/EuropePMCLinkage.py index f265e3ba..aae65cc0 100644 --- 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_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