From b6713a6d9291558e7a7f09e7b26daf0721592a11 Mon Sep 17 00:00:00 2001 From: Florent Yvon Date: Tue, 8 Oct 2024 17:19:31 +0100 Subject: [PATCH 1/6] Added 2021 paper to requested PGS Catalog citation --- catalog/context_processors.py | 3 +- catalog/templates/catalog/docs/about.html | 15 +++++++--- catalog/templates/catalog/docs/faq.html | 21 ++++++++----- pgs_web/constants.py | 36 +++++++++++++++-------- rest_api/views.py | 2 +- 5 files changed, 51 insertions(+), 26 deletions(-) diff --git a/catalog/context_processors.py b/catalog/context_processors.py index 8d265d00..84fa8687 100644 --- 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_CITATION[0], + 'pgs_citations': constants.PGS_CITATION, '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 index 11669ddd..b4458be4 100644 --- a/catalog/templates/catalog/docs/about.html +++ b/catalog/templates/catalog/docs/about.html @@ -90,12 +90,19 @@

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 publication: +

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:

-

{{ pgs_citation.authors }}

-

{{ pgs_citation.title }}

-

{{ pgs_citation.journal }}doi: {{ pgs_citation.doi }} ({{ pgs_citation.year }}).

+ {% for c in pgs_citations %} +
+

{{ c.authors }}

+

{{ c.title }}

+

{{ c.journal }}doi: {{ c.doi }} ({{ c.year }}).

+
+ {% if not forloop.last %} +
+ {% endif %} + {% endfor %}

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).

diff --git a/catalog/templates/catalog/docs/faq.html b/catalog/templates/catalog/docs/faq.html index 6ca62cdf..b8d7d4fd 100644 --- a/catalog/templates/catalog/docs/faq.html +++ b/catalog/templates/catalog/docs/faq.html @@ -77,14 +77,21 @@

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 publication: +

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 below flagship publications:

-
-

{{ pgs_citation.authors }}

-

{{ pgs_citation.title }}

-

{{ pgs_citation.journal }}doi: {{ pgs_citation.doi }} ({{ pgs_citation.year }}).

-
-
+
+ {% for c in pgs_citations %} +
+

{{ c.authors }}

+

{{ c.title }}

+

{{ c.journal }}doi: {{ c.doi }} ({{ c.year }}).

+
+ {% if not forloop.last %} +
+ {% endif %} + {% endfor %} +
+

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).

diff --git a/pgs_web/constants.py b/pgs_web/constants.py index 45ca746b..ee34cc4e 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_CITATION = [ + { '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_CITATION[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_CITATION[0]['year'], + 'doi': PGS_CITATION[0]['doi'], + 'PMID': PGS_CITATION[0]['PMID'], + 'journal': PGS_CITATION[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_CITATION[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_CITATION[1]['year'], + 'doi': PGS_CITATION[1]['doi'], + 'PMID': PGS_CITATION[1]['PMID'], + 'journal': PGS_CITATION[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_CITATION[0]['doi'], 'EPMC_REST_SEARCH' : 'https://www.ebi.ac.uk/europepmc/webservices/rest/search' } diff --git a/rest_api/views.py b/rest_api/views.py index b93ccc52..f5342c99 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_CITATION[0], 'pgs_catalog_publications': constants.PGS_PUBLICATIONS, 'ensembl_version': constants.ENSEMBL_VERSION, 'terms_of_use': constants.USEFUL_URLS['TERMS_OF_USE'] From 2fc9ff8fe98f1716ea2c628733d8e08445b23f07 Mon Sep 17 00:00:00 2001 From: Florent Yvon Date: Tue, 8 Oct 2024 17:20:05 +0100 Subject: [PATCH 2/6] Updated examples with latest publications and release numbers --- .../rest_api/openapi/openapi-schema.yml | 98 ++++++++++++------- 1 file changed, 64 insertions(+), 34 deletions(-) diff --git a/rest_api/static/rest_api/openapi/openapi-schema.yml b/rest_api/static/rest_api/openapi/openapi-schema.yml index 928175da..ec17399a 100644 --- a/rest_api/static/rest_api/openapi/openapi-schema.yml +++ b/rest_api/static/rest_api/openapi/openapi-schema.yml @@ -568,6 +568,34 @@ components: format: date example: "2015-04-08" + PGSCatalogPublication: + type: object + properties: + title: + type: string + description: "Title of the publication" + 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/s41588-024-01937-x' + PMID: + type: number + description: "PubMed ID" + example: 39327485 + authors: + type: string + description: "Publication first author(s)" + example: 'Lambert et al' + journal: + type: string + description: "Name of the journal" + example: 'Nature Genetics' + year: + type: number + description: "Year of publication" + example: 2024 + Publication_extended: description: "Based on the **Publication** object, with the addition of the '**authors**' and the '**associated_pgs_ids**'." allOf: @@ -2359,19 +2387,19 @@ 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 +2407,15 @@ 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 +2423,7 @@ paths: journal: type: string description: "Name of the journal" - example: 'medRxiv (Preprint)' + example: 'Nature Genetics' year: type: number description: "Year of publication" @@ -2404,32 +2432,34 @@ paths: type: array description: "List of all PGS Catalog publications" items: - type: object - properties: - title: - type: string - description: "Title of the publication" - example: 'The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation' - doi: - type: string - description: "doi of the publication" - example: '10.1038/s41588-021-00783-5' - PMID: - type: number - description: "PubMed ID" - example: 33692568 - authors: - type: string - description: "Publication first author(s)" - example: 'Lambert et al' - journal: - type: string - description: "Name of the journal" - example: 'Nature Genetics' - year: - type: number - description: "Year of publication" - example: 2021 + $ref: '#/components/schemas/PGSCatalogPublication' + example: [ + { + "title": "Enhancing the Polygenic Score Catalog with tools for score calculation and ancestry normalization", + "doi": "10.1038/s41588-024-01937-x", + "PMID": 39327485, + "authors": "Lambert et al", + "journal": "Nature Genetics", + "year": 2024 + }, + { + "title": "The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource", + "authors": "Sollis et al", + "year": 2023, + "doi": "10.1093/nar/gkac1010", + "PMID": 36350656, + "journal": "Nucleic Acids Research 51(D1):D977-D985" + }, + { + "title": "The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation", + "authors": "Lambert et al", + "year": 2021, + "doi": "10.1038/s41588-021-00783-5", + "PMID": 33692568, + "journal": "Nature Genetics volume 53, pages420–425" + } + + ] ensembl_version: type: number description: "Ensembl version used to generate the Harmonized Scoring files" From c0641e8f2845b95995ba73e7f1965cec39d8b043 Mon Sep 17 00:00:00 2001 From: Florent Yvon Date: Tue, 8 Oct 2024 17:27:51 +0100 Subject: [PATCH 3/6] Using plural to clarify constants.PGS_CITATION type change to list --- catalog/context_processors.py | 4 ++-- catalog/tests/test_models.py | 2 +- pgs_web/constants.py | 24 ++++++++++++------------ release/scripts/EuropePMCLinkage.py | 2 +- rest_api/views.py | 2 +- 5 files changed, 17 insertions(+), 17 deletions(-) diff --git a/catalog/context_processors.py b/catalog/context_processors.py index 84fa8687..7c197e65 100644 --- a/catalog/context_processors.py +++ b/catalog/context_processors.py @@ -46,8 +46,8 @@ def pgs_search_examples(request): def pgs_info(request): return { - 'pgs_citation': constants.PGS_CITATION[0], - 'pgs_citations': 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/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 ee34cc4e..372911c5 100644 --- a/pgs_web/constants.py +++ b/pgs_web/constants.py @@ -1,6 +1,6 @@ # 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', @@ -21,12 +21,12 @@ PGS_PUBLICATIONS = [ { - 'title': PGS_CITATION[0]['title'], + 'title': PGS_CITATIONS[0]['title'], 'authors': 'Lambert, Wingfield et al', - 'year': PGS_CITATION[0]['year'], - 'doi': PGS_CITATION[0]['doi'], - 'PMID': PGS_CITATION[0]['PMID'], - 'journal': PGS_CITATION[0]['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', @@ -37,12 +37,12 @@ 'journal': 'Nucleic Acids Research 51(D1):D977-D985' }, { - 'title': PGS_CITATION[1]['title'], + 'title': PGS_CITATIONS[1]['title'], 'authors': 'Lambert et al', - 'year': PGS_CITATION[1]['year'], - 'doi': PGS_CITATION[1]['doi'], - 'PMID': PGS_CITATION[1]['PMID'], - 'journal': PGS_CITATION[1]['journal'] + 'year': PGS_CITATIONS[1]['year'], + 'doi': PGS_CITATIONS[1]['doi'], + 'PMID': PGS_CITATIONS[1]['PMID'], + 'journal': PGS_CITATIONS[1]['journal'] } ] @@ -65,7 +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[0]['doi'], + 'CATALOG_PUBLICATION_URL' : 'https://doi.org/' + PGS_CITATIONS[0]['doi'], 'EPMC_REST_SEARCH' : 'https://www.ebi.ac.uk/europepmc/webservices/rest/search' } 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/views.py b/rest_api/views.py index f5342c99..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[0], + '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'] From 951c137e9fd4490a912dcc3aa7376a2da4303a9e Mon Sep 17 00:00:00 2001 From: Florent Yvon Date: Tue, 8 Oct 2024 18:19:31 +0100 Subject: [PATCH 4/6] Rolled back to 1 example of PGSCatalog publications --- .../rest_api/openapi/openapi-schema.yml | 82 ++++++------------- 1 file changed, 26 insertions(+), 56 deletions(-) diff --git a/rest_api/static/rest_api/openapi/openapi-schema.yml b/rest_api/static/rest_api/openapi/openapi-schema.yml index ec17399a..af6c2228 100644 --- a/rest_api/static/rest_api/openapi/openapi-schema.yml +++ b/rest_api/static/rest_api/openapi/openapi-schema.yml @@ -568,34 +568,6 @@ components: format: date example: "2015-04-08" - PGSCatalogPublication: - type: object - properties: - title: - type: string - description: "Title of the publication" - 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/s41588-024-01937-x' - PMID: - type: number - description: "PubMed ID" - example: 39327485 - authors: - type: string - description: "Publication first author(s)" - example: 'Lambert et al' - journal: - type: string - description: "Name of the journal" - example: 'Nature Genetics' - year: - type: number - description: "Year of publication" - example: 2024 - Publication_extended: description: "Based on the **Publication** object, with the addition of the '**authors**' and the '**associated_pgs_ids**'." allOf: @@ -2432,34 +2404,32 @@ paths: type: array description: "List of all PGS Catalog publications" items: - $ref: '#/components/schemas/PGSCatalogPublication' - example: [ - { - "title": "Enhancing the Polygenic Score Catalog with tools for score calculation and ancestry normalization", - "doi": "10.1038/s41588-024-01937-x", - "PMID": 39327485, - "authors": "Lambert et al", - "journal": "Nature Genetics", - "year": 2024 - }, - { - "title": "The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource", - "authors": "Sollis et al", - "year": 2023, - "doi": "10.1093/nar/gkac1010", - "PMID": 36350656, - "journal": "Nucleic Acids Research 51(D1):D977-D985" - }, - { - "title": "The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation", - "authors": "Lambert et al", - "year": 2021, - "doi": "10.1038/s41588-021-00783-5", - "PMID": 33692568, - "journal": "Nature Genetics volume 53, pages420–425" - } - - ] + type: object + properties: + title: + type: string + description: "Title of the publication" + 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/s41588-024-01937-x' + PMID: + type: number + description: "PubMed ID" + example: 39327485 + authors: + type: string + description: "Publication first author(s)" + example: 'Lambert et al' + journal: + type: string + description: "Name of the journal" + example: 'Nature Genetics' + year: + type: number + description: "Year of publication" + example: 2024 ensembl_version: type: number description: "Ensembl version used to generate the Harmonized Scoring files" From 131bcffbf87196babcbb6317aa6d22c6d1f74c6e Mon Sep 17 00:00:00 2001 From: Florent Yvon Date: Thu, 17 Oct 2024 14:57:33 +0100 Subject: [PATCH 5/6] Now citing the 2 last PGS Catalog papers --- catalog/templates/catalog/docs/about.html | 21 +----------------- catalog/templates/catalog/docs/faq.html | 22 +------------------ .../templates/catalog/includes/citation.html | 20 +++++++++++++++++ 3 files changed, 22 insertions(+), 41 deletions(-) create mode 100644 catalog/templates/catalog/includes/citation.html diff --git a/catalog/templates/catalog/docs/about.html b/catalog/templates/catalog/docs/about.html index b4458be4..8c071997 100644 --- a/catalog/templates/catalog/docs/about.html +++ b/catalog/templates/catalog/docs/about.html @@ -86,26 +86,7 @@

The PGS Catalog Project

Citation

-

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: -

-
- {% for c in pgs_citations %} -
-

{{ c.authors }}

-

{{ c.title }}

-

{{ c.journal }}doi: {{ c.doi }} ({{ c.year }}).

-
- {% if not forloop.last %} -
- {% endif %} - {% endfor %} -
-
-

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" %}
All PGS Catalog Publications:
diff --git a/catalog/templates/catalog/docs/faq.html b/catalog/templates/catalog/docs/faq.html index b8d7d4fd..60988e00 100644 --- a/catalog/templates/catalog/docs/faq.html +++ b/catalog/templates/catalog/docs/faq.html @@ -73,27 +73,7 @@

How to access PGS Catalog data?

How to cite the PGS Catalog?

-

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 below flagship publications: -

-
- {% for c in pgs_citations %} -
-

{{ c.authors }}

-

{{ c.title }}

-

{{ c.journal }}doi: {{ c.doi }} ({{ c.year }}).

-
- {% if not forloop.last %} -
- {% endif %} - {% endfor %} -
-
-

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" %}

How to submit data to the PGS Catalog?

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: +

+
+ {% for c in pgs_citations %} +
+

{{ c.authors }}

+

{{ c.title }}

+

{{ c.journal }}doi: {{ c.doi }} ({{ c.year }}).

+
+ {% if not forloop.last %} +
+ {% endif %} + {% endfor %} +
+
+

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 From 1e09244e9a684f712f2e83b5fb119d887934cd20 Mon Sep 17 00:00:00 2001 From: Florent Yvon Date: Thu, 17 Oct 2024 17:02:10 +0100 Subject: [PATCH 6/6] Updated PGS contributors --- pgs_web/constants.py | 1 + 1 file changed, 1 insertion(+) diff --git a/pgs_web/constants.py b/pgs_web/constants.py index 372911c5..427b3107 100644 --- a/pgs_web/constants.py +++ b/pgs_web/constants.py @@ -173,6 +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']},