{"id":"https://openalex.org/W4414111067","doi":"https://doi.org/10.1093/bioinformatics/btaf503","title":"<tt>acmgscaler</tt> : an R package and Colab for standardized gene-level variant effect score calibration within the ACMG/AMP framework","display_name":"<tt>acmgscaler</tt> : an R package and Colab for standardized gene-level variant effect score calibration within the ACMG/AMP framework","publication_year":2025,"publication_date":"2025-09-09","ids":{"openalex":"https://openalex.org/W4414111067","doi":"https://doi.org/10.1093/bioinformatics/btaf503","pmid":"https://pubmed.ncbi.nlm.nih.gov/40929116"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf503","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf503","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf503/64237226/btaf503.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf503/64237226/btaf503.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013184525","display_name":"Mihaly Badonyi","orcid":"https://orcid.org/0000-0002-8305-5618"},"institutions":[{"id":"https://openalex.org/I4210158898","display_name":"Institute of Genetics and Cancer","ror":"https://ror.org/05hygey35","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210087105","https://openalex.org/I4210158898","https://openalex.org/I90344618","https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Mihaly Badonyi","raw_affiliation_strings":["MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh , Edinburgh EH4 2XU,","MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh United Kingdom"],"affiliations":[{"raw_affiliation_string":"MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh , Edinburgh EH4 2XU,","institution_ids":["https://openalex.org/I4210158898"]},{"raw_affiliation_string":"MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh United Kingdom","institution_ids":["https://openalex.org/I4210158898"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002238592","display_name":"Joseph A. Marsh","orcid":"https://orcid.org/0000-0003-4132-0628"},"institutions":[{"id":"https://openalex.org/I4210158898","display_name":"Institute of Genetics and Cancer","ror":"https://ror.org/05hygey35","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210087105","https://openalex.org/I4210158898","https://openalex.org/I90344618","https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Joseph A Marsh","raw_affiliation_strings":["MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh , Edinburgh EH4 2XU,","MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh United Kingdom"],"affiliations":[{"raw_affiliation_string":"MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh , Edinburgh EH4 2XU,","institution_ids":["https://openalex.org/I4210158898"]},{"raw_affiliation_string":"MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh United Kingdom","institution_ids":["https://openalex.org/I4210158898"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5013184525"],"corresponding_institution_ids":["https://openalex.org/I4210158898"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":10.2143,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.98372707,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"41","issue":"10","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.9979000091552734,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.9979000091552734,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.9962000250816345,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.8102999925613403},{"id":"https://openalex.org/keywords/calibration","display_name":"Calibration","score":0.717199981212616},{"id":"https://openalex.org/keywords/software-package","display_name":"Software package","score":0.5027999877929688},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.42980000376701355},{"id":"https://openalex.org/keywords/score","display_name":"Score","score":0.30480000376701355}],"concepts":[{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.8102999925613403},{"id":"https://openalex.org/C165838908","wikidata":"https://www.wikidata.org/wiki/Q736777","display_name":"Calibration","level":2,"score":0.717199981212616},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6330999732017517},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.5027999877929688},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.42980000376701355},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36410000920295715},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.35839998722076416},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3400999903678894},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3084000051021576},{"id":"https://openalex.org/C65660741","wikidata":"https://www.wikidata.org/wiki/Q3952743","display_name":"Score","level":2,"score":0.30480000376701355},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.27559998631477356},{"id":"https://openalex.org/C2986587452","wikidata":"https://www.wikidata.org/wiki/Q938438","display_name":"Statistical analysis","level":2,"score":0.25760000944137573}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002138","descriptor_name":"Calibration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002138","descriptor_name":"Calibration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002138","descriptor_name":"Calibration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002138","descriptor_name":"Calibration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btaf503","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf503","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf503/64237226/btaf503.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40929116","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40929116","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pure.ed.ac.uk:openaire/2a3fbdee-27be-4676-b755-feeaa5d4d0ca","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/en/publications/2a3fbdee-27be-4676-b755-feeaa5d4d0ca","pdf_url":null,"source":{"id":"https://openalex.org/S4306400321","display_name":"Edinburgh Research Explorer (University of Edinburgh)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98677209","host_organization_name":"University of Edinburgh","host_organization_lineage":["https://openalex.org/I98677209"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Badonyi, M & Marsh, J A 2025, 'acmgscaler: An R package and Colab for standardised gene-level variant effect score calibration within the ACMG/AMP framework', Bioinformatics, vol. 41, no. 10. https://doi.org/10.1093/bioinformatics/btaf503","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:europepmc.org:11305775","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12496131","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12496131","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12496131/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf503","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf503","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf503/64237226/btaf503.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4620450428","display_name":"Protein Structure, Molecular Mechanisms and Human Genetic Disease: Beyond the Loss-of-function Paradigm","funder_award_id":"101001169","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4956428346","display_name":null,"funder_award_id":"Horizon 2020 research and innovatio","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5566807808","display_name":null,"funder_award_id":"MC_UU_","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G7564801717","display_name":"Protein Variant Interpretation","funder_award_id":"MC_UU_00035/9","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G8318064016","display_name":null,"funder_award_id":"Horizon","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320338335","display_name":"H2020 European Research Council","ror":"https://ror.org/0472cxd90"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4414111067.pdf","grobid_xml":"https://content.openalex.org/works/W4414111067.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W1489950266","https://openalex.org/W1701211704","https://openalex.org/W2017818880","https://openalex.org/W2021396690","https://openalex.org/W2051978340","https://openalex.org/W2127184121","https://openalex.org/W2129905273","https://openalex.org/W2165715420","https://openalex.org/W2781534540","https://openalex.org/W2868860358","https://openalex.org/W2885278423","https://openalex.org/W2889874867","https://openalex.org/W2967605415","https://openalex.org/W2990435446","https://openalex.org/W3005785247","https://openalex.org/W3111162271","https://openalex.org/W3115988811","https://openalex.org/W3173285777","https://openalex.org/W4283700603","https://openalex.org/W4284881539","https://openalex.org/W4309643822","https://openalex.org/W4368372867","https://openalex.org/W4382893389","https://openalex.org/W4385637034","https://openalex.org/W4386841760","https://openalex.org/W4386861232","https://openalex.org/W4387931371","https://openalex.org/W4389367121","https://openalex.org/W4391956897","https://openalex.org/W4400863624","https://openalex.org/W4401542241","https://openalex.org/W4401763802","https://openalex.org/W4404466258","https://openalex.org/W4405067042","https://openalex.org/W4406674953","https://openalex.org/W4408278568","https://openalex.org/W4409669254"],"related_works":["https://openalex.org/W4362597605","https://openalex.org/W1574414179","https://openalex.org/W4297676672","https://openalex.org/W3009056573","https://openalex.org/W2922073769","https://openalex.org/W4281702477","https://openalex.org/W4410497501","https://openalex.org/W2989932438","https://openalex.org/W4387297750","https://openalex.org/W2186333919"],"abstract_inverted_index":{"The":[0],"R":[1],"package":[2],"and":[3],"Colab":[4],"notebook":[5],"are":[6],"available":[7],"at":[8],"https://github.com/badonyi/acmgscaler.":[9]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3}],"updated_date":"2026-04-13T07:58:08.660418","created_date":"2025-09-11T00:00:00"}
