{"id":"https://openalex.org/W3134300625","doi":"https://doi.org/10.1186/s12859-021-04039-1","title":"vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration","display_name":"vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration","publication_year":2021,"publication_date":"2021-03-02","ids":{"openalex":"https://openalex.org/W3134300625","doi":"https://doi.org/10.1186/s12859-021-04039-1","mag":"3134300625","pmid":"https://pubmed.ncbi.nlm.nih.gov/33653260"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-021-04039-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04039-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04039-1","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04039-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5050505202","display_name":"Robert H. Dolin","orcid":"https://orcid.org/0000-0002-6235-6964"},"institutions":[{"id":"https://openalex.org/I4210097878","display_name":"Electronics for Imaging (United States)","ror":"https://ror.org/00zymfp03","country_code":"US","type":"company","lineage":["https://openalex.org/I4210097878"]},{"id":"https://openalex.org/I4210149001","display_name":"ElSohly Laboratories (United States)","ror":"https://ror.org/04c1def54","country_code":"US","type":"company","lineage":["https://openalex.org/I4210149001"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Robert H. Dolin","raw_affiliation_strings":["Elimu Informatics, 1160 Brickyard Cove Rd Ste 200, Richmond, CA, 94801-4173, USA. bdolin@elimu.io","Elimu Informatics, 1160 Brickyard Cove Rd Ste 200, Richmond, CA, 94801-4173, USA"],"raw_orcid":"https://orcid.org/0000-0002-6235-6964","affiliations":[{"raw_affiliation_string":"Elimu Informatics, 1160 Brickyard Cove Rd Ste 200, Richmond, CA, 94801-4173, USA. bdolin@elimu.io","institution_ids":["https://openalex.org/I4210149001"]},{"raw_affiliation_string":"Elimu Informatics, 1160 Brickyard Cove Rd Ste 200, Richmond, CA, 94801-4173, USA","institution_ids":["https://openalex.org/I4210097878"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082848436","display_name":"Shaileshbhai Revabhai Gothi","orcid":null},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shaileshbhai R. Gothi","raw_affiliation_strings":["Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021099456","display_name":"Aziz A. Boxwala","orcid":"https://orcid.org/0000-0002-5910-5523"},"institutions":[{"id":"https://openalex.org/I4210097878","display_name":"Electronics for Imaging (United States)","ror":"https://ror.org/00zymfp03","country_code":"US","type":"company","lineage":["https://openalex.org/I4210097878"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aziz Boxwala","raw_affiliation_strings":["Elimu Informatics, 1160 Brickyard Cove Rd Ste 200, Richmond, CA, 94801-4173, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Elimu Informatics, 1160 Brickyard Cove Rd Ste 200, Richmond, CA, 94801-4173, USA","institution_ids":["https://openalex.org/I4210097878"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083706469","display_name":"Bret S.E. Heale","orcid":"https://orcid.org/0000-0001-8190-9918"},"institutions":[{"id":"https://openalex.org/I108785884","display_name":"Intermountain Healthcare","ror":"https://ror.org/04mvr1r74","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I108785884"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bret S. E. Heale","raw_affiliation_strings":["Intermountain Healthcare, Salt Lake City, UT, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Intermountain Healthcare, Salt Lake City, UT, USA","institution_ids":["https://openalex.org/I108785884"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062975155","display_name":"Ammar Husami","orcid":"https://orcid.org/0000-0002-4287-2857"},"institutions":[{"id":"https://openalex.org/I1285204247","display_name":"Cincinnati Children's Hospital Medical Center","ror":"https://ror.org/01hcyya48","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1285204247"]},{"id":"https://openalex.org/I63135867","display_name":"University of Cincinnati","ror":"https://ror.org/01e3m7079","country_code":"US","type":"education","lineage":["https://openalex.org/I63135867"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ammar Husami","raw_affiliation_strings":["Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA","institution_ids":["https://openalex.org/I1285204247","https://openalex.org/I63135867"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103957052","display_name":"James Jones","orcid":null},"institutions":[{"id":"https://openalex.org/I1288882113","display_name":"Boston Children's Hospital","ror":"https://ror.org/00dvg7y05","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1288882113"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James Jones","raw_affiliation_strings":["Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA","institution_ids":["https://openalex.org/I1288882113"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066878574","display_name":"Himanshu Khangar","orcid":null},"institutions":[{"id":"https://openalex.org/I4210097878","display_name":"Electronics for Imaging (United States)","ror":"https://ror.org/00zymfp03","country_code":"US","type":"company","lineage":["https://openalex.org/I4210097878"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Himanshu Khangar","raw_affiliation_strings":["Elimu Informatics, 1160 Brickyard Cove Rd Ste 200, Richmond, CA, 94801-4173, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Elimu Informatics, 1160 Brickyard Cove Rd Ste 200, Richmond, CA, 94801-4173, USA","institution_ids":["https://openalex.org/I4210097878"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058752316","display_name":"Shubham Londhe","orcid":null},"institutions":[{"id":"https://openalex.org/I4210097878","display_name":"Electronics for Imaging (United States)","ror":"https://ror.org/00zymfp03","country_code":"US","type":"company","lineage":["https://openalex.org/I4210097878"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shubham Londhe","raw_affiliation_strings":["Elimu Informatics, 1160 Brickyard Cove Rd Ste 200, Richmond, CA, 94801-4173, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Elimu Informatics, 1160 Brickyard Cove Rd Ste 200, Richmond, CA, 94801-4173, USA","institution_ids":["https://openalex.org/I4210097878"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065534143","display_name":"Frank Naeymi-Rad","orcid":null},"institutions":[{"id":"https://openalex.org/I4210096445","display_name":"Leap of Faith Technologies (United States)","ror":"https://ror.org/00q2yft10","country_code":"US","type":"company","lineage":["https://openalex.org/I4210096445"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Frank Naeymi-Rad","raw_affiliation_strings":["Leap of Faith, Libertyville, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Leap of Faith, Libertyville, IL, USA","institution_ids":["https://openalex.org/I4210096445"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066208451","display_name":"Soujanya Rao","orcid":null},"institutions":[{"id":"https://openalex.org/I4210097878","display_name":"Electronics for Imaging (United States)","ror":"https://ror.org/00zymfp03","country_code":"US","type":"company","lineage":["https://openalex.org/I4210097878"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Soujanya Rao","raw_affiliation_strings":["Elimu Informatics, 1160 Brickyard Cove Rd Ste 200, Richmond, CA, 94801-4173, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Elimu Informatics, 1160 Brickyard Cove Rd Ste 200, Richmond, CA, 94801-4173, USA","institution_ids":["https://openalex.org/I4210097878"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016349610","display_name":"Barbara Rapchak","orcid":"https://orcid.org/0000-0001-9234-780X"},"institutions":[{"id":"https://openalex.org/I4210097878","display_name":"Electronics for Imaging (United States)","ror":"https://ror.org/00zymfp03","country_code":"US","type":"company","lineage":["https://openalex.org/I4210097878"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Barbara Rapchak","raw_affiliation_strings":["Elimu Informatics, 1160 Brickyard Cove Rd Ste 200, Richmond, CA, 94801-4173, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Elimu Informatics, 1160 Brickyard Cove Rd Ste 200, Richmond, CA, 94801-4173, USA","institution_ids":["https://openalex.org/I4210097878"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088083912","display_name":"James Shalaby","orcid":null},"institutions":[{"id":"https://openalex.org/I4210097878","display_name":"Electronics for Imaging (United States)","ror":"https://ror.org/00zymfp03","country_code":"US","type":"company","lineage":["https://openalex.org/I4210097878"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James Shalaby","raw_affiliation_strings":["Elimu Informatics, 1160 Brickyard Cove Rd Ste 200, Richmond, CA, 94801-4173, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Elimu Informatics, 1160 Brickyard Cove Rd Ste 200, Richmond, CA, 94801-4173, USA","institution_ids":["https://openalex.org/I4210097878"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025281225","display_name":"Varun Suraj","orcid":"https://orcid.org/0000-0002-9090-0859"},"institutions":[{"id":"https://openalex.org/I4210143528","display_name":"Lexington City Schools","ror":"https://ror.org/043f52r95","country_code":"US","type":"education","lineage":["https://openalex.org/I4210143528"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Varun Suraj","raw_affiliation_strings":["Lexington High School, Lexington, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lexington High School, Lexington, MA, USA","institution_ids":["https://openalex.org/I4210143528"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109483970","display_name":"Ning Xie","orcid":null},"institutions":[{"id":"https://openalex.org/I1283280774","display_name":"Brigham and Women's Hospital","ror":"https://ror.org/04b6nzv94","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1283280774","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ning Xie","raw_affiliation_strings":["Biomedical Cybernetics Laboratory, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Cybernetics Laboratory, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA","institution_ids":["https://openalex.org/I1283280774"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043041208","display_name":"Srikar Chamala","orcid":"https://orcid.org/0000-0001-6367-7615"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Srikar Chamala","raw_affiliation_strings":["Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076921758","display_name":"Gil Alterovitz","orcid":"https://orcid.org/0000-0002-0495-7059"},"institutions":[{"id":"https://openalex.org/I1283280774","display_name":"Brigham and Women's Hospital","ror":"https://ror.org/04b6nzv94","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1283280774","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210092658","display_name":"Harvard\u2013MIT Division of Health Sciences and Technology","ror":"https://ror.org/00jjeh629","country_code":"US","type":"education","lineage":["https://openalex.org/I4210092658"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gil Alterovitz","raw_affiliation_strings":["Brigham and Women's Hospital, Boston, MA, USA","Harvard/MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Brigham and Women's Hospital, Boston, MA, USA","institution_ids":["https://openalex.org/I1283280774"]},{"raw_affiliation_string":"Harvard/MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, USA","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I4210092658"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":12,"corresponding_author_ids":["https://openalex.org/A5050505202"],"corresponding_institution_ids":["https://openalex.org/I4210097878","https://openalex.org/I4210149001"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2790},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2790},"fwci":2.2717,"has_fulltext":true,"cited_by_count":22,"citation_normalized_percentile":{"value":0.88723258,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"22","issue":"1","first_page":"104","last_page":"104"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.8641999959945679,"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":0.8641999959945679,"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/T10769","display_name":"BRCA gene mutations in cancer","score":0.038100000470876694,"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":0.013299999758601189,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.6079937219619751},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5501053929328918},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37755030393600464},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.34413084387779236},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2433769702911377},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22788304090499878},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16352760791778564}],"concepts":[{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.6079937219619751},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5501053929328918},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37755030393600464},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.34413084387779236},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2433769702911377},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22788304090499878},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16352760791778564}],"mesh":[{"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":"D009857","descriptor_name":"Oncogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009857","descriptor_name":"Oncogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009857","descriptor_name":"Oncogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020000","descriptor_name":"Decision Support Systems, Clinical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020000","descriptor_name":"Decision Support Systems, Clinical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020000","descriptor_name":"Decision Support Systems, Clinical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-021-04039-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04039-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04039-1","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33653260","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33653260","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:99d9ca08a72249798090ee08fc5ab9d3","is_oa":true,"landing_page_url":"https://doaj.org/article/99d9ca08a72249798090ee08fc5ab9d3","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 22, Iss 1, Pp 1-11 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7923512","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7923512","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-021-04039-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04039-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04039-1","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3134300625.pdf","grobid_xml":"https://content.openalex.org/works/W3134300625.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W1902503727","https://openalex.org/W2063073636","https://openalex.org/W2104549677","https://openalex.org/W2146297638","https://openalex.org/W2174602966","https://openalex.org/W2179435758","https://openalex.org/W2332528840","https://openalex.org/W2567598959","https://openalex.org/W2801182702","https://openalex.org/W2805834252","https://openalex.org/W2910316323","https://openalex.org/W2969270537","https://openalex.org/W2982632577","https://openalex.org/W3012096713"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2053972265"],"abstract_inverted_index":{"BACKGROUND:":[0],"VCF":[1,46,55,66,101,152],"formatted":[2],"files":[3],"are":[4,33,79,166],"the":[5,74,116,129,142,158,169,182,199,260,268,289,313,335],"lingua":[6],"franca":[7],"of":[8,28,151,157,181,188,252,292,303,315,331],"next-generation":[9],"sequencing,":[10],"whereas":[11],"HL7":[12,49],"FHIR":[13,50,59,171,321],"is":[14,211],"emerging":[15],"as":[16],"a":[17,58,69,111,120,132,149,212,236,285,301],"standard":[18],"language":[19],"for":[20,42,91],"electronic":[21],"health":[22],"record":[23],"interoperability.":[24],"A":[25],"growing":[26],"number":[27],"FHIR-based":[29],"clinical":[30,217,239,290],"genomics":[31,332],"applications":[32],"emerging.":[34],"Here,":[35],"we":[36,311],"describe":[37],"an":[38],"open":[39],"source":[40],"utility":[41,201,270,317],"converting":[43],"variants":[44,56,81],"from":[45],"format":[47],"into":[48,57,68,275,334],"format.":[51],"RESULTS:":[52],"vcf2fhir":[53,200,269],"converts":[54],"Genomics":[60,232,322],"Diagnostic":[61],"Report.":[62],"Conversion":[63,144],"translates":[64],"each":[65],"row":[67],"corresponding":[70],"FHIR-formatted":[71,238],"variant":[72],"in":[73,246,300],"generated":[75],"report.":[76],"In":[77],"scope":[78],"simple":[80],"(SNVs,":[82],"MNVs,":[83],"Indels),":[84],"along":[85],"with":[86,243,328],"zygosity":[87],"and":[88,95,103,109,131,163,187,240,257,324],"phase":[89],"relationships,":[90],"autosomes,":[92],"sex":[93],"chromosomes,":[94],"mitochondrial":[96],"DNA.":[97],"Input":[98],"parameters":[99],"include":[100,174],"file":[102],"genome":[104],"build":[105],"('GRCh37'":[106],"or":[107],"'GRCh38');":[108],"optionally":[110],"conversion":[112,159,183],"region":[113,122,134,184],"that":[114,123,135,177,215,267],"indicates":[115],"region(s)":[117],"to":[118,148,225,248,259,264,297,319,325],"convert,":[119],"studied":[121,127,137,162,190],"lists":[124,136],"genomic":[125,155,241,255],"regions":[126,138,165],"by":[128,141,153,220],"lab,":[130],"non-callable":[133,164],"deemed":[139,195],"uncallable":[140],"lab.":[143],"can":[145,271],"be":[146,272,284,298],"limited":[147],"subset":[150],"supplying":[154],"coordinates":[156],"region(s).":[160],"If":[161],"also":[167],"supplied,":[168],"output":[170],"report":[172],"will":[173,283],"'region-studied'":[175],"observations":[176],"detail":[178],"which":[179,192],"portions":[180,193],"were":[185,194],"studied,":[186],"those":[189],"regions,":[191],"uncallable.":[196],"We":[197],"illustrate":[198],"via":[202],"two":[203],"case":[204],"studies.":[205],"The":[206,229],"first,":[207],"'SMART":[208],"Cancer":[209],"Navigator',":[210],"web":[213],"application":[214],"offers":[216],"decision":[218],"support":[219],"linking":[221],"patient":[222],"EHR":[223],"information":[224],"cancerous":[226],"gene":[227],"variants.":[228],"second,":[230],"'Precision":[231],"Integration":[233],"Platform',":[234],"intersects":[235],"patient's":[237],"data":[242,306,333],"knowledge":[244],"bases":[245],"order":[247],"provide":[249],"on-demand":[250],"delivery":[251],"contextually":[253],"relevant":[254],"findings":[256],"recommendations":[258],"EHR.":[261,336],"CONCLUSIONS:":[262],"Experience":[263],"date":[265],"shows":[266],"effectively":[273],"woven":[274],"clinically":[276],"useful":[277],"genomic-EHR":[278],"integration":[279,330],"pipelines.":[280],"Additional":[281],"testing":[282],"critical":[286],"step":[287],"towards":[288],"validation":[291],"this":[293,316],"utility,":[294],"enabling":[295],"it":[296],"integrated":[299],"variety":[302],"real":[304],"world":[305],"flow":[307],"scenarios.":[308],"For":[309],"now,":[310],"propose":[312],"use":[314],"primarily":[318],"accelerate":[320],"understanding":[323],"facilitate":[326],"experimentation":[327],"further":[329]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":3}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}