The PGS Catalog development is led by Samuel Lambert - 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 publication: -
{{ pgs_citation.authors }}
-{{ pgs_citation.title }}
-{{ pgs_citation.journal }}doi: {{ pgs_citation.doi }} ({{ pgs_citation.year }}).
-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 Terms of Use for more information).
+ {% include "catalog/includes/citation.html" %}The PGS Catalog development is led by Samuel Lambert - 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 publication: -
{{ pgs_citation.authors }}
-{{ pgs_citation.title }}
-{{ pgs_citation.journal }}doi: {{ pgs_citation.doi }} ({{ pgs_citation.year }}).
-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 Terms of Use for more information).
- + {% include "catalog/includes/citation.html" %}diff --git a/catalog/templates/catalog/includes/citation.html b/catalog/templates/catalog/includes/citation.html new file mode 100644 index 00000000..6510b189 --- /dev/null +++ b/catalog/templates/catalog/includes/citation.html @@ -0,0 +1,20 @@ +
The PGS Catalog development is led by Samuel Lambert + 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 below flagship publications: +
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 Terms of Use for more information).
\ No newline at end of file diff --git a/catalog/tests/test_models.py b/catalog/tests/test_models.py index 3ef8d374..dd5e4692 100644 --- 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 index 45ca746b..427b3107 100644 --- 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 index aae65cc0..af22ff5a 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_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 index 928175da..af6c2228 100644 --- a/rest_api/static/rest_api/openapi/openapi-schema.yml +++ b/rest_api/static/rest_api/openapi/openapi-schema.yml @@ -2359,19 +2359,19 @@ 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" @@ -2379,15 +2379,15 @@ paths: 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" @@ -2395,7 +2395,7 @@ paths: 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 index b93ccc52..943ef83f 100644 --- 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']