{"id":"https://openalex.org/W7124316889","doi":"https://doi.org/10.1093/jamia/ocaf213","title":"Information extraction from clinical notes: are we ready to switch to large language models?","display_name":"Information extraction from clinical notes: are we ready to switch to large language models?","publication_year":2025,"publication_date":"2025-11-21","ids":{"openalex":"https://openalex.org/W7124316889","doi":"https://doi.org/10.1093/jamia/ocaf213","pmid":"https://pubmed.ncbi.nlm.nih.gov/41533750"},"language":"en","primary_location":{"id":"doi:10.1093/jamia/ocaf213","is_oa":false,"landing_page_url":"https://doi.org/10.1093/jamia/ocaf213","pdf_url":null,"source":{"id":"https://openalex.org/S129839026","display_name":"Journal of the American Medical Informatics Association","issn_l":"1067-5027","issn":["1067-5027","1527-974X"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of the American Medical Informatics Association","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102891584","display_name":"Yan Hu","orcid":"https://orcid.org/0000-0001-8723-9900"},"institutions":[{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yan Hu","raw_affiliation_strings":["McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston, TX 77030,"],"affiliations":[{"raw_affiliation_string":"McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston, TX 77030,","institution_ids":["https://openalex.org/I919571938"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123165575","display_name":"Xu Zuo","orcid":null},"institutions":[{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xu Zuo","raw_affiliation_strings":["McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston, TX 77030,"],"affiliations":[{"raw_affiliation_string":"McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston, TX 77030,","institution_ids":["https://openalex.org/I919571938"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101509576","display_name":"Yujia Zhou","orcid":"https://orcid.org/0000-0002-3716-7854"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yujia Zhou","raw_affiliation_strings":["Department of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University , New Haven, CT 06510,"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University , New Haven, CT 06510,","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101317327","display_name":"Xueqing Peng","orcid":null},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xueqing Peng","raw_affiliation_strings":["Department of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University , New Haven, CT 06510,"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University , New Haven, CT 06510,","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123165753","display_name":"Jimin Huang","orcid":null},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jimin Huang","raw_affiliation_strings":["Department of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University , New Haven, CT 06510,"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University , New Haven, CT 06510,","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123154218","display_name":"Vipina K Keloth","orcid":null},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vipina K Keloth","raw_affiliation_strings":["Department of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University , New Haven, CT 06510,"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University , New Haven, CT 06510,","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082141622","display_name":"Vincent Zhang","orcid":"https://orcid.org/0009-0002-3931-7374"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vincent J Zhang","raw_affiliation_strings":["Department of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University , New Haven, CT 06510,"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University , New Haven, CT 06510,","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123168633","display_name":"Ruey-Ling Weng","orcid":null},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ruey-Ling Weng","raw_affiliation_strings":["Department of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University , New Haven, CT 06510,"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University , New Haven, CT 06510,","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5119538409","display_name":"Cathy Shyr","orcid":null},"institutions":[{"id":"https://openalex.org/I901861585","display_name":"Vanderbilt University Medical Center","ror":"https://ror.org/05dq2gs74","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210162197","https://openalex.org/I901861585"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cathy Shyr","raw_affiliation_strings":["Department of Biomedical Informatics, Vanderbilt University Medical Center , Nashville, TN 37203,"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Vanderbilt University Medical Center , Nashville, TN 37203,","institution_ids":["https://openalex.org/I901861585"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123155118","display_name":"Qingyu Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qingyu Chen","raw_affiliation_strings":["Department of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University , New Haven, CT 06510,"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University , New Haven, CT 06510,","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123135386","display_name":"Xiaoqian Jiang","orcid":null},"institutions":[{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaoqian Jiang","raw_affiliation_strings":["McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston, TX 77030,"],"affiliations":[{"raw_affiliation_string":"McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston, TX 77030,","institution_ids":["https://openalex.org/I919571938"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123122250","display_name":"Kirk E Roberts","orcid":null},"institutions":[{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kirk E Roberts","raw_affiliation_strings":["McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston, TX 77030,"],"affiliations":[{"raw_affiliation_string":"McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston, TX 77030,","institution_ids":["https://openalex.org/I919571938"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5123159125","display_name":"Hua Xu","orcid":null},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hua Xu","raw_affiliation_strings":["Department of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University , New Haven, CT 06510,"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University , New Haven, CT 06510,","institution_ids":["https://openalex.org/I32971472"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":13,"corresponding_author_ids":["https://openalex.org/A5102891584"],"corresponding_institution_ids":["https://openalex.org/I919571938"],"apc_list":{"value":3967,"currency":"USD","value_usd":3967},"apc_paid":null,"fwci":4.9917,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.96040841,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"33","issue":"3","first_page":"553","last_page":"562"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.5770000219345093,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.5770000219345093,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.19449999928474426,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"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/T13702","display_name":"Machine Learning in Healthcare","score":0.06560000032186508,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.5857999920845032},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.40369999408721924},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.38359999656677246},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.35670000314712524},{"id":"https://openalex.org/keywords/extraction","display_name":"Extraction (chemistry)","score":0.33629998564720154},{"id":"https://openalex.org/keywords/information-model","display_name":"Information model","score":0.32829999923706055}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8083000183105469},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.5857999920845032},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.4862000048160553},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.45899999141693115},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.40369999408721924},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.38359999656677246},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3637999892234802},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.35670000314712524},{"id":"https://openalex.org/C4725764","wikidata":"https://www.wikidata.org/wiki/Q844704","display_name":"Extraction (chemistry)","level":2,"score":0.33629998564720154},{"id":"https://openalex.org/C21338462","wikidata":"https://www.wikidata.org/wiki/Q1662581","display_name":"Information model","level":2,"score":0.32829999923706055},{"id":"https://openalex.org/C2777466982","wikidata":"https://www.wikidata.org/wiki/Q5227287","display_name":"Data extraction","level":3,"score":0.3066999912261963},{"id":"https://openalex.org/C35639132","wikidata":"https://www.wikidata.org/wiki/Q7452468","display_name":"Sequence labeling","level":3,"score":0.2720000147819519},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.26409998536109924},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.26269999146461487}],"mesh":[{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","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":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/jamia/ocaf213","is_oa":false,"landing_page_url":"https://doi.org/10.1093/jamia/ocaf213","pdf_url":null,"source":{"id":"https://openalex.org/S129839026","display_name":"Journal of the American Medical Informatics Association","issn_l":"1067-5027","issn":["1067-5027","1527-974X"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of the American Medical Informatics Association","raw_type":"journal-article"},{"id":"pmid:41533750","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41533750","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":"Journal of the American Medical Informatics Association : JAMIA","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6258333921432495,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W1672757658","https://openalex.org/W1995522051","https://openalex.org/W2109206523","https://openalex.org/W2114039834","https://openalex.org/W2132724073","https://openalex.org/W2137407193","https://openalex.org/W2150344954","https://openalex.org/W2168041406","https://openalex.org/W2396881363","https://openalex.org/W2735580341","https://openalex.org/W2768488789","https://openalex.org/W2770096843","https://openalex.org/W2904133818","https://openalex.org/W2955483668","https://openalex.org/W2966351171","https://openalex.org/W2979250794","https://openalex.org/W2988383538","https://openalex.org/W3011594683","https://openalex.org/W3046375318","https://openalex.org/W3094834348","https://openalex.org/W3131198033","https://openalex.org/W3196385594","https://openalex.org/W3198980621","https://openalex.org/W4385988359","https://openalex.org/W4389043118","https://openalex.org/W4391292768","https://openalex.org/W4391836235","https://openalex.org/W4392240262","https://openalex.org/W4393094733","https://openalex.org/W4407191181","https://openalex.org/W4408345962","https://openalex.org/W4408886719"],"related_works":[],"abstract_inverted_index":{"Instruction-tuned":[0],"LLaMA":[1,37],"models":[2,40],"show":[3],"promise":[4],"for":[5],"clinical":[6,42],"NER":[7],"and":[8,17,38],"RE":[9],"tasks.":[10],"However,":[11],"the":[12,33],"tradeoff":[13],"between":[14],"improved":[15],"performance":[16],"increased":[18],"computational":[19],"cost":[20],"must":[21],"be":[22],"carefully":[23],"evaluated.":[24],"We":[25],"release":[26],"our":[27],"Kiwi":[28],"package":[29],"(https://kiwi.clinicalnlp.org/)":[30],"to":[31],"facilitate":[32],"application":[34],"of":[35],"both":[36],"BERT":[39],"in":[41],"IE":[43],"applications.":[44]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-03-28T08:17:26.163206","created_date":"2026-01-16T00:00:00"}
