{"id":"https://openalex.org/W4403174382","doi":"https://doi.org/10.1186/s12911-024-02698-7","title":"A hybrid framework with large language models for rare disease phenotyping","display_name":"A hybrid framework with large language models for rare disease phenotyping","publication_year":2024,"publication_date":"2024-10-08","ids":{"openalex":"https://openalex.org/W4403174382","doi":"https://doi.org/10.1186/s12911-024-02698-7","pmid":"https://pubmed.ncbi.nlm.nih.gov/39375687"},"language":"en","primary_location":{"id":"doi:10.1186/s12911-024-02698-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12911-024-02698-7","pdf_url":"https://bmcmedinformdecismak.biomedcentral.com/counter/pdf/10.1186/s12911-024-02698-7","source":{"id":"https://openalex.org/S107516304","display_name":"BMC Medical Informatics and Decision Making","issn_l":"1472-6947","issn":["1472-6947"],"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 Medical Informatics and Decision Making","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcmedinformdecismak.biomedcentral.com/counter/pdf/10.1186/s12911-024-02698-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111207139","display_name":"Jinge Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I4210134054","display_name":"UCB Pharma (United Kingdom)","ror":"https://ror.org/03428qp74","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210134054","https://openalex.org/I85722119"]},{"id":"https://openalex.org/I4210142469","display_name":"Health Data Research UK","ror":"https://ror.org/04rtjaj74","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I4210142469"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jinge Wu","raw_affiliation_strings":["Institute of Health Informatics, University College London, London, UK. jinge.wu.20@ucl.ac.uk","UCB Pharma UK, Slough, UK. jinge.wu.20@ucl.ac.uk","Institute of Health Informatics, University College London, London, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Health Informatics, University College London, London, UK. jinge.wu.20@ucl.ac.uk","institution_ids":["https://openalex.org/I4210142469","https://openalex.org/I45129253"]},{"raw_affiliation_string":"UCB Pharma UK, Slough, UK. jinge.wu.20@ucl.ac.uk","institution_ids":["https://openalex.org/I4210134054"]},{"raw_affiliation_string":"Institute of Health Informatics, University College London, London, UK","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035163413","display_name":"Hang Dong","orcid":"https://orcid.org/0000-0001-6828-6891"},"institutions":[{"id":"https://openalex.org/I23923803","display_name":"University of Exeter","ror":"https://ror.org/03yghzc09","country_code":"GB","type":"education","lineage":["https://openalex.org/I23923803"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Hang Dong","raw_affiliation_strings":["Department of Computer Science, University of Exeter, Exeter, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Exeter, Exeter, UK","institution_ids":["https://openalex.org/I23923803"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049546968","display_name":"Zexi Li","orcid":"https://orcid.org/0000-0002-4663-1356"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Zexi Li","raw_affiliation_strings":["The Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115695249","display_name":"Haowei Wang","orcid":"https://orcid.org/0009-0004-1186-4303"},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Haowei Wang","raw_affiliation_strings":["Division of Medicine, University College London, London, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Medicine, University College London, London, UK","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076189337","display_name":"R Li","orcid":null},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Runci Li","raw_affiliation_strings":["EGA- Institute for Women's Health, University College London, London, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"EGA- Institute for Women's Health, University College London, London, UK","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113051762","display_name":"Arijit Patra","orcid":null},"institutions":[{"id":"https://openalex.org/I4210134054","display_name":"UCB Pharma (United Kingdom)","ror":"https://ror.org/03428qp74","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210134054","https://openalex.org/I85722119"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Arijit Patra","raw_affiliation_strings":["UCB Pharma UK, Slough, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UCB Pharma UK, Slough, UK","institution_ids":["https://openalex.org/I4210134054"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015055434","display_name":"Chengliang Dai","orcid":"https://orcid.org/0000-0002-9931-5437"},"institutions":[{"id":"https://openalex.org/I4210134054","display_name":"UCB Pharma (United Kingdom)","ror":"https://ror.org/03428qp74","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210134054","https://openalex.org/I85722119"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Chengliang Dai","raw_affiliation_strings":["UCB Pharma UK, Slough, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UCB Pharma UK, Slough, UK","institution_ids":["https://openalex.org/I4210134054"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079392897","display_name":"Waqar Ali","orcid":"https://orcid.org/0000-0002-6308-8682"},"institutions":[{"id":"https://openalex.org/I4210134054","display_name":"UCB Pharma (United Kingdom)","ror":"https://ror.org/03428qp74","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210134054","https://openalex.org/I85722119"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Waqar Ali","raw_affiliation_strings":["UCB Pharma UK, Slough, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UCB Pharma UK, Slough, UK","institution_ids":["https://openalex.org/I4210134054"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021103092","display_name":"Phil Scordis","orcid":"https://orcid.org/0000-0003-3477-9959"},"institutions":[{"id":"https://openalex.org/I4210134054","display_name":"UCB Pharma (United Kingdom)","ror":"https://ror.org/03428qp74","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210134054","https://openalex.org/I85722119"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Phil Scordis","raw_affiliation_strings":["UCB Pharma UK, Slough, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UCB Pharma UK, Slough, UK","institution_ids":["https://openalex.org/I4210134054"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043821806","display_name":"Honghan Wu","orcid":"https://orcid.org/0000-0002-0213-5668"},"institutions":[{"id":"https://openalex.org/I4210142469","display_name":"Health Data Research UK","ror":"https://ror.org/04rtjaj74","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I4210142469"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]},{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Honghan Wu","raw_affiliation_strings":["Institute of Health Informatics, University College London, London, UK. honghan.wu@ucl.ac.uk","School of Health and Wellbeing, University of Glasgow, Glasgow, UK. honghan.wu@ucl.ac.uk","School of Health and Wellbeing, University of Glasgow, Glasgow, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Health Informatics, University College London, London, UK. honghan.wu@ucl.ac.uk","institution_ids":["https://openalex.org/I4210142469","https://openalex.org/I45129253"]},{"raw_affiliation_string":"School of Health and Wellbeing, University of Glasgow, Glasgow, UK. honghan.wu@ucl.ac.uk","institution_ids":["https://openalex.org/I7882870"]},{"raw_affiliation_string":"School of Health and Wellbeing, University of Glasgow, Glasgow, UK","institution_ids":["https://openalex.org/I7882870"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5043821806"],"corresponding_institution_ids":["https://openalex.org/I4210142469","https://openalex.org/I45129253","https://openalex.org/I7882870"],"apc_list":{"value":1570,"currency":"GBP","value_usd":2690},"apc_paid":{"value":1570,"currency":"GBP","value_usd":2690},"fwci":10.6711,"has_fulltext":true,"cited_by_count":27,"citation_normalized_percentile":{"value":0.98806109,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"24","issue":"1","first_page":"289","last_page":"289"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.8532000184059143,"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":0.8532000184059143,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.10920000076293945,"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/T10028","display_name":"Topic Modeling","score":0.010700000450015068,"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/unified-medical-language-system","display_name":"Unified Medical Language System","score":0.7411388158798218},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7322568893432617},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5978500247001648},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.5557568669319153},{"id":"https://openalex.org/keywords/vocabulary","display_name":"Vocabulary","score":0.5456604957580566},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5345593690872192},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.4739425480365753},{"id":"https://openalex.org/keywords/rare-disease","display_name":"Rare disease","score":0.44702789187431335},{"id":"https://openalex.org/keywords/unstructured-data","display_name":"Unstructured data","score":0.4281002879142761},{"id":"https://openalex.org/keywords/health-informatics","display_name":"Health informatics","score":0.4235348701477051},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.42231595516204834},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.4100561738014221},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3577476143836975},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.2998426556587219},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.1719365119934082},{"id":"https://openalex.org/keywords/pathology","display_name":"Pathology","score":0.14671576023101807},{"id":"https://openalex.org/keywords/public-health","display_name":"Public health","score":0.14363184571266174},{"id":"https://openalex.org/keywords/big-data","display_name":"Big data","score":0.1359902024269104},{"id":"https://openalex.org/keywords/linguistics","display_name":"Linguistics","score":0.1194174587726593}],"concepts":[{"id":"https://openalex.org/C69505689","wikidata":"https://www.wikidata.org/wiki/Q455338","display_name":"Unified Medical Language System","level":2,"score":0.7411388158798218},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7322568893432617},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5978500247001648},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5557568669319153},{"id":"https://openalex.org/C2777601683","wikidata":"https://www.wikidata.org/wiki/Q6499736","display_name":"Vocabulary","level":2,"score":0.5456604957580566},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5345593690872192},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.4739425480365753},{"id":"https://openalex.org/C2779701055","wikidata":"https://www.wikidata.org/wiki/Q929833","display_name":"Rare disease","level":3,"score":0.44702789187431335},{"id":"https://openalex.org/C2781252014","wikidata":"https://www.wikidata.org/wiki/Q1141900","display_name":"Unstructured data","level":3,"score":0.4281002879142761},{"id":"https://openalex.org/C145642194","wikidata":"https://www.wikidata.org/wiki/Q870895","display_name":"Health informatics","level":3,"score":0.4235348701477051},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.42231595516204834},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.4100561738014221},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3577476143836975},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.2998426556587219},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.1719365119934082},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.14671576023101807},{"id":"https://openalex.org/C138816342","wikidata":"https://www.wikidata.org/wiki/Q189603","display_name":"Public health","level":2,"score":0.14363184571266174},{"id":"https://openalex.org/C75684735","wikidata":"https://www.wikidata.org/wiki/Q858810","display_name":"Big data","level":2,"score":0.1359902024269104},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.1194174587726593},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"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":"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":"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":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035583","descriptor_name":"Rare Diseases","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D035583","descriptor_name":"Rare Diseases","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D035583","descriptor_name":"Rare Diseases","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D035583","descriptor_name":"Rare Diseases","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D035583","descriptor_name":"Rare Diseases","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"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},{"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":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12911-024-02698-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12911-024-02698-7","pdf_url":"https://bmcmedinformdecismak.biomedcentral.com/counter/pdf/10.1186/s12911-024-02698-7","source":{"id":"https://openalex.org/S107516304","display_name":"BMC Medical Informatics and Decision Making","issn_l":"1472-6947","issn":["1472-6947"],"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 Medical Informatics and Decision Making","raw_type":"journal-article"},{"id":"pmid:39375687","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39375687","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 medical informatics and decision making","raw_type":null},{"id":"pmh:oai:eprints.gla.ac.uk:338021","is_oa":true,"landing_page_url":"http://eprints.gla.ac.uk/view/author/77060.html>","pdf_url":"https://eprints.gla.ac.uk/338021/2/338021.pdf","source":{"id":"https://openalex.org/S4210235606","display_name":"ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam)","issn_l":"2622-8912","issn":["2622-8912","2622-8920"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Articles"},{"id":"pmh:oai:pubmedcentral.nih.gov:11460004","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11460004","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11460004/pdf/12911_2024_Article_2698.pdf","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 Med Inform Decis Mak","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:7f3521330ad64b7c9b1c79de381d496e","is_oa":false,"landing_page_url":"https://doaj.org/article/7f3521330ad64b7c9b1c79de381d496e","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Medical Informatics and Decision Making, Vol 24, Iss 1, Pp 1-19 (2024)","raw_type":"article"},{"id":"pmh:oai:ora.ox.ac.uk:uuid:8828777d-00dd-4cc8-b00c-db647a92db65","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402636","display_name":"Oxford University Research Archive (ORA) (University of Oxford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40120149","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/I40120149"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Jisc Publications Router","raw_type":"Journal article"}],"best_oa_location":{"id":"doi:10.1186/s12911-024-02698-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12911-024-02698-7","pdf_url":"https://bmcmedinformdecismak.biomedcentral.com/counter/pdf/10.1186/s12911-024-02698-7","source":{"id":"https://openalex.org/S107516304","display_name":"BMC Medical Informatics and Decision Making","issn_l":"1472-6947","issn":["1472-6947"],"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 Medical Informatics and Decision Making","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Quality Education","score":0.7599999904632568,"id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G521842188","display_name":null,"funder_award_id":"MR/X030075/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G5436805323","display_name":"Artificial Intelligence and Multimorbidity: Clustering in Individuals, Space and Clinical Context (AIM-CISC)","funder_award_id":"NIHR202639","funder_id":"https://openalex.org/F4320319990","funder_display_name":"National Institute for Health and Care Research"},{"id":"https://openalex.org/G5747038093","display_name":"QMIA: Quantifying and Mitigating Bias affecting and induced by AI in Medicine","funder_award_id":"MR/X030075/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G7306783740","display_name":null,"funder_award_id":"MR/S004149/2","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G7475414022","display_name":"Deriving an actionable patient phenome from healthcare data","funder_award_id":"MR/S004149/2","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G956835308","display_name":null,"funder_award_id":"MR/S004149/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320319990","display_name":"National Institute for Health and Care Research","ror":"https://ror.org/0187kwz08"},{"id":"https://openalex.org/F4320319994","display_name":"Department of Health and Social Care","ror":"https://ror.org/03sbpja79"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4403174382.pdf","grobid_xml":"https://content.openalex.org/works/W4403174382.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1964189668","https://openalex.org/W1983965561","https://openalex.org/W1994127362","https://openalex.org/W2094791001","https://openalex.org/W2132265655","https://openalex.org/W2136410628","https://openalex.org/W2146089916","https://openalex.org/W2159583324","https://openalex.org/W2283041611","https://openalex.org/W2317648909","https://openalex.org/W2405275595","https://openalex.org/W2765693998","https://openalex.org/W2778088240","https://openalex.org/W2783464703","https://openalex.org/W2789244308","https://openalex.org/W2911489562","https://openalex.org/W2921415194","https://openalex.org/W2928818852","https://openalex.org/W2964696298","https://openalex.org/W3017637887","https://openalex.org/W3160137267","https://openalex.org/W3170139103","https://openalex.org/W4224997359","https://openalex.org/W4226287018","https://openalex.org/W4283077570","https://openalex.org/W4285044905","https://openalex.org/W4313439128","https://openalex.org/W4323311324","https://openalex.org/W4368616878","https://openalex.org/W4385848332","https://openalex.org/W4387609936","https://openalex.org/W4390403247","https://openalex.org/W4390607929","https://openalex.org/W4399280731"],"related_works":["https://openalex.org/W79619734","https://openalex.org/W2010487328","https://openalex.org/W2340589664","https://openalex.org/W4281750475","https://openalex.org/W3087321790","https://openalex.org/W186091728","https://openalex.org/W2939811865","https://openalex.org/W2005677940","https://openalex.org/W2765673425","https://openalex.org/W4390701126"],"abstract_inverted_index":{"PURPOSE:":[0],"Rare":[1,78],"diseases":[2],"pose":[3],"significant":[4,197],"challenges":[5],"in":[6,173,206],"diagnosis":[7,286],"and":[8,15,34,82,115,125,130,139,162,166,252,272,276,287],"treatment":[9],"due":[10],"to":[11,36,41,58,89,103,144,158,213,255,265,269,277],"their":[12],"low":[13],"prevalence":[14],"heterogeneous":[16],"clinical":[17,20,65,109,238,282],"presentations.":[18],"Unstructured":[19],"notes":[21],"contain":[22],"valuable":[23],"information":[24],"for":[25,231,284],"identifying":[26],"rare":[27,60,93,105,174,201,233,258],"diseases,":[28],"but":[29],"manual":[30],"curation":[31],"is":[32,101,263],"time-consuming":[33],"prone":[35],"subjectivity.":[37],"This":[38],"study":[39],"aims":[40],"develop":[42],"a":[43,70,91,97,196],"hybrid":[44,72,152,220],"approach":[45,153,194,221,280],"combining":[46,222],"dictionary-based":[47,98,223],"natural":[48],"language":[49,55],"processing":[50],"(NLP)":[51],"tools":[52,225],"with":[53,179,226],"large":[54],"models":[56,127],"(LLMs)":[57],"improve":[59,116],"disease":[61,94,106,175,202,234,259],"identification":[62,235],"from":[63,108,236],"unstructured":[64,237],"reports.":[66,239],"METHODS:":[67],"We":[68],"propose":[69],"novel":[71],"framework":[73],"that":[74],"integrates":[75],"the":[76,83,113,146,169,183,193,242,247,253,279],"Orphanet":[77],"Disease":[79],"Ontology":[80],"(ORDO)":[81],"Unified":[84],"Medical":[85],"Language":[86],"System":[87],"(UMLS)":[88],"create":[90],"comprehensive":[92],"vocabulary.":[95],"SemEHR,":[96],"NLP":[99,160,224],"tool,":[100],"employed":[102],"extract":[104],"mentions":[107],"notes.":[110],"To":[111],"refine":[112],"results":[114],"accuracy,":[117],"we":[118],"leverage":[119],"various":[120],"LLMs,":[121],"including":[122],"LLaMA3,":[123],"Phi3-mini,":[124],"domain-specific":[126],"like":[128],"OpenBioLLM":[129],"BioMistral.":[131],"Different":[132],"prompting":[133,178],"strategies,":[134],"such":[135],"as":[136],"zero-shot,":[137],"few-shot,":[138],"knowledge-augmented":[140,187],"generation,":[141],"are":[142],"explored":[143],"optimize":[145],"LLMs'":[147],"performance.":[148],"RESULTS:":[149],"The":[150,219],"proposed":[151],"demonstrates":[154,249],"superior":[155,250],"performance":[156,251],"compared":[157],"traditional":[159],"systems":[161],"standalone":[163],"LLMs.":[164],"LLaMA3":[165],"Phi3-mini":[167],"achieve":[168],"highest":[170],"F1":[171],"scores":[172],"identification.":[176],"Few-shot":[177],"1-3":[180],"examples":[181],"yields":[182],"best":[184],"results,":[185],"while":[186],"generation":[188],"shows":[189,228],"limited":[190],"improvement.":[191],"Notably,":[192],"uncovers":[195],"number":[198],"of":[199,244],"potential":[200,254],"cases":[203],"not":[204],"documented":[205],"structured":[207],"diagnostic":[208],"records,":[209],"highlighting":[210],"its":[211],"ability":[212],"identify":[214],"previously":[215],"unrecognized":[216],"patients.":[217],"CONCLUSION:":[218],"LLMs":[227],"great":[229],"promise":[230],"improving":[232],"By":[240],"leveraging":[241],"strengths":[243],"both":[245],"techniques,":[246],"method":[248],"uncover":[256],"hidden":[257],"cases.":[260],"Further":[261],"research":[262],"needed":[264],"address":[266],"limitations":[267],"related":[268],"ontology":[270],"mapping":[271],"overlapping":[273],"case":[274],"identification,":[275],"integrate":[278],"into":[281],"practice":[283],"early":[285],"improved":[288],"patient":[289],"outcomes.":[290]},"counts_by_year":[{"year":2026,"cited_by_count":12},{"year":2025,"cited_by_count":15}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}