{"id":"https://openalex.org/W4413050975","doi":"https://doi.org/10.3233/shti250944","title":"Comparative Analysis of NLP Models for Automatic LOINC Document Ontology Named Entity Recognition in Clinical Note Titles","display_name":"Comparative Analysis of NLP Models for Automatic LOINC Document Ontology Named Entity Recognition in Clinical Note Titles","publication_year":2025,"publication_date":"2025-08-07","ids":{"openalex":"https://openalex.org/W4413050975","doi":"https://doi.org/10.3233/shti250944","pmid":"https://pubmed.ncbi.nlm.nih.gov/40775962"},"language":"en","primary_location":{"id":"doi:10.3233/shti250944","is_oa":true,"landing_page_url":"https://doi.org/10.3233/shti250944","pdf_url":null,"source":{"id":"https://openalex.org/S4210179765","display_name":"Studies in health technology and informatics","issn_l":"0926-9630","issn":["0926-9630","1879-8365"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"book series"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Studies in Health Technology and Informatics","raw_type":"book-chapter"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.3233/shti250944","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5104116748","display_name":"Annie E. Bowles","orcid":null},"institutions":[{"id":"https://openalex.org/I4210089864","display_name":"VA Salt Lake City Healthcare System","ror":"https://ror.org/007fyq698","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1322918889","https://openalex.org/I2799886695","https://openalex.org/I4210089864","https://openalex.org/I4210113540"]},{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Annie E. Bowles","raw_affiliation_strings":["Department of Internal Medicine, University of Utah Medical School, Salt Lake City, UT, USA","VA Salt Lake City Health Care System"],"affiliations":[{"raw_affiliation_string":"Department of Internal Medicine, University of Utah Medical School, Salt Lake City, UT, USA","institution_ids":["https://openalex.org/I223532165"]},{"raw_affiliation_string":"VA Salt Lake City Health Care System","institution_ids":["https://openalex.org/I4210089864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061308443","display_name":"Qiwei Gan","orcid":"https://orcid.org/0000-0002-6830-9544"},"institutions":[{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]},{"id":"https://openalex.org/I4210089864","display_name":"VA Salt Lake City Healthcare System","ror":"https://ror.org/007fyq698","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1322918889","https://openalex.org/I2799886695","https://openalex.org/I4210089864","https://openalex.org/I4210113540"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qiwei Gan","raw_affiliation_strings":["Department of Internal Medicine, University of Utah Medical School, Salt Lake City, UT, USA","VA Salt Lake City Health Care System"],"affiliations":[{"raw_affiliation_string":"Department of Internal Medicine, University of Utah Medical School, Salt Lake City, UT, USA","institution_ids":["https://openalex.org/I223532165"]},{"raw_affiliation_string":"VA Salt Lake City Health Care System","institution_ids":["https://openalex.org/I4210089864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036033113","display_name":"Elizabeth Hanchrow","orcid":null},"institutions":[{"id":"https://openalex.org/I4210089864","display_name":"VA Salt Lake City Healthcare System","ror":"https://ror.org/007fyq698","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1322918889","https://openalex.org/I2799886695","https://openalex.org/I4210089864","https://openalex.org/I4210113540"]},{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Elizabeth Hanchrow","raw_affiliation_strings":["Department of Internal Medicine, University of Utah Medical School, Salt Lake City, UT, USA","VA Salt Lake City Health Care System"],"affiliations":[{"raw_affiliation_string":"Department of Internal Medicine, University of Utah Medical School, Salt Lake City, UT, USA","institution_ids":["https://openalex.org/I223532165"]},{"raw_affiliation_string":"VA Salt Lake City Health Care System","institution_ids":["https://openalex.org/I4210089864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037435182","display_name":"Scott L. DuVall","orcid":"https://orcid.org/0000-0002-4898-3865"},"institutions":[{"id":"https://openalex.org/I4210089864","display_name":"VA Salt Lake City Healthcare System","ror":"https://ror.org/007fyq698","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1322918889","https://openalex.org/I2799886695","https://openalex.org/I4210089864","https://openalex.org/I4210113540"]},{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Scott Duvall","raw_affiliation_strings":["Department of Internal Medicine, University of Utah Medical School, Salt Lake City, UT, USA","VA Salt Lake City Health Care System"],"affiliations":[{"raw_affiliation_string":"Department of Internal Medicine, University of Utah Medical School, Salt Lake City, UT, USA","institution_ids":["https://openalex.org/I223532165"]},{"raw_affiliation_string":"VA Salt Lake City Health Care System","institution_ids":["https://openalex.org/I4210089864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080489523","display_name":"Patrick R. Alba","orcid":"https://orcid.org/0000-0002-5176-5447"},"institutions":[{"id":"https://openalex.org/I4210089864","display_name":"VA Salt Lake City Healthcare System","ror":"https://ror.org/007fyq698","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1322918889","https://openalex.org/I2799886695","https://openalex.org/I4210089864","https://openalex.org/I4210113540"]},{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Patrick R. Alba","raw_affiliation_strings":["Department of Internal Medicine, University of Utah Medical School, Salt Lake City, UT, USA","VA Salt Lake City Health Care System"],"affiliations":[{"raw_affiliation_string":"Department of Internal Medicine, University of Utah Medical School, Salt Lake City, UT, USA","institution_ids":["https://openalex.org/I223532165"]},{"raw_affiliation_string":"VA Salt Lake City Health Care System","institution_ids":["https://openalex.org/I4210089864"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101778639","display_name":"Jianlin Shi","orcid":"https://orcid.org/0000-0003-2950-8038"},"institutions":[{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]},{"id":"https://openalex.org/I4210089864","display_name":"VA Salt Lake City Healthcare System","ror":"https://ror.org/007fyq698","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1322918889","https://openalex.org/I2799886695","https://openalex.org/I4210089864","https://openalex.org/I4210113540"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jianlin Shi","raw_affiliation_strings":["Department of Internal Medicine, University of Utah Medical School, Salt Lake City, UT, USA","VA Salt Lake City Health Care System"],"affiliations":[{"raw_affiliation_string":"Department of Internal Medicine, University of Utah Medical School, Salt Lake City, UT, USA","institution_ids":["https://openalex.org/I223532165"]},{"raw_affiliation_string":"VA Salt Lake City Health Care System","institution_ids":["https://openalex.org/I4210089864"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5104116748"],"corresponding_institution_ids":["https://openalex.org/I223532165","https://openalex.org/I4210089864"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.38059352,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"329","issue":null,"first_page":"769","last_page":"773"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9965000152587891,"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":0.9965000152587891,"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":0.9909999966621399,"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/T10181","display_name":"Natural Language Processing Techniques","score":0.9391000270843506,"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/computer-science","display_name":"Computer science","score":0.8112618327140808},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.7194515466690063},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.718608021736145},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.646762490272522},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5945197343826294},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5403301119804382},{"id":"https://openalex.org/keywords/open-biomedical-ontologies","display_name":"Open Biomedical Ontologies","score":0.4894522726535797},{"id":"https://openalex.org/keywords/named-entity","display_name":"Named entity","score":0.4463910162448883},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4367297291755676},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.4332265853881836},{"id":"https://openalex.org/keywords/upper-ontology","display_name":"Upper ontology","score":0.36031603813171387},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.22602349519729614},{"id":"https://openalex.org/keywords/suggested-upper-merged-ontology","display_name":"Suggested Upper Merged Ontology","score":0.22529760003089905},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.12419503927230835},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.07526010274887085}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8112618327140808},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.7194515466690063},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.718608021736145},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.646762490272522},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5945197343826294},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5403301119804382},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.4894522726535797},{"id":"https://openalex.org/C2777889803","wikidata":"https://www.wikidata.org/wiki/Q25047676","display_name":"Named entity","level":2,"score":0.4463910162448883},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4367297291755676},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.4332265853881836},{"id":"https://openalex.org/C78726541","wikidata":"https://www.wikidata.org/wiki/Q3882785","display_name":"Upper ontology","level":3,"score":0.36031603813171387},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.22602349519729614},{"id":"https://openalex.org/C50971890","wikidata":"https://www.wikidata.org/wiki/Q7635093","display_name":"Suggested Upper Merged Ontology","level":4,"score":0.22529760003089905},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.12419503927230835},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.07526010274887085},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"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":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D039703","descriptor_name":"Logical Observation Identifiers Names and Codes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D039703","descriptor_name":"Logical Observation Identifiers Names and Codes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.3233/shti250944","is_oa":true,"landing_page_url":"https://doi.org/10.3233/shti250944","pdf_url":null,"source":{"id":"https://openalex.org/S4210179765","display_name":"Studies in health technology and informatics","issn_l":"0926-9630","issn":["0926-9630","1879-8365"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"book series"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Studies in Health Technology and Informatics","raw_type":"book-chapter"},{"id":"pmid:40775962","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40775962","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":"Studies in health technology and informatics","raw_type":null}],"best_oa_location":{"id":"doi:10.3233/shti250944","is_oa":true,"landing_page_url":"https://doi.org/10.3233/shti250944","pdf_url":null,"source":{"id":"https://openalex.org/S4210179765","display_name":"Studies in health technology and informatics","issn_l":"0926-9630","issn":["0926-9630","1879-8365"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"book series"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Studies in Health Technology and Informatics","raw_type":"book-chapter"},"sustainable_development_goals":[{"score":0.4399999976158142,"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":0,"referenced_works":[],"related_works":["https://openalex.org/W2032007337","https://openalex.org/W2186562580","https://openalex.org/W1884363728","https://openalex.org/W2155874911","https://openalex.org/W2916255597","https://openalex.org/W4386977977","https://openalex.org/W4253099099","https://openalex.org/W4200491110","https://openalex.org/W2593907245","https://openalex.org/W4255258373"],"abstract_inverted_index":{"In":[0],"order":[1],"to":[2,12,19,40,74,94],"utilize":[3],"clinical":[4],"notes":[5],"for":[6],"research":[7],"studies,":[8],"it":[9],"is":[10],"necessary":[11],"identify":[13,42],"the":[14,20,30,57],"most":[15],"relevant":[16],"notes.":[17],"Mapping":[18],"LOINC":[21,43,96],"Document":[22],"Ontology":[23],"makes":[24],"this":[25],"process":[26],"easier":[27],"by":[28,78],"reducing":[29],"variability":[31],"of":[32,68],"note":[33,48,76,81],"types.":[34],"We":[35],"experimented":[36],"with":[37,86],"three":[38],"models":[39,61],"automatically":[41],"DO":[44],"entities":[45],"in":[46],"VA":[47],"titles.":[49],"The":[50],"supervised":[51],"BERT":[52],"model":[53],"performed":[54,63],"best,":[55],"but":[56],"open-source":[58],"large":[59],"language":[60],"(LLMs)":[62],"well":[64],"despite":[65],"a":[66],"lack":[67],"fine-tuning.":[69],"Future":[70],"work":[71],"will":[72],"aim":[73],"improve":[75],"classification":[77],"including":[79],"additional":[80],"metadata":[82],"and":[83,92],"contents,":[84],"hybridizing":[85],"rule-based":[87],"approaches,":[88],"testing":[89],"fine-tuned":[90],"LLMs,":[91],"mapping":[93],"exact":[95],"codes.":[97]},"counts_by_year":[],"updated_date":"2025-12-28T23:10:05.387466","created_date":"2025-10-10T00:00:00"}
