{"id":"https://openalex.org/W4368616878","doi":"https://doi.org/10.1186/s12911-023-02181-9","title":"Ontology-driven and weakly supervised rare disease identification from clinical notes","display_name":"Ontology-driven and weakly supervised rare disease identification from clinical notes","publication_year":2023,"publication_date":"2023-05-05","ids":{"openalex":"https://openalex.org/W4368616878","doi":"https://doi.org/10.1186/s12911-023-02181-9","pmid":"https://pubmed.ncbi.nlm.nih.gov/37147628"},"language":"en","primary_location":{"id":"doi:10.1186/s12911-023-02181-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12911-023-02181-9","pdf_url":"https://bmcmedinformdecismak.biomedcentral.com/counter/pdf/10.1186/s12911-023-02181-9","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/s12911-023-02181-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5035163413","display_name":"Hang Dong","orcid":"https://orcid.org/0000-0001-6828-6891"},"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"]},{"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/I4210146410","display_name":"Science Oxford","ror":"https://ror.org/04j8yhy50","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I4210146410"]},{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Hang Dong","raw_affiliation_strings":["Centre for Medical Informatics, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom. hang.dong@cs.ox.ac.uk","Department of Computer Science, University of Oxford, Oxford, United Kingdom. hang.dong@cs.ox.ac.uk","Health Data Research UK, London, United Kingdom. hang.dong@cs.ox.ac.uk","Centre for Medical Informatics, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Medical Informatics, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom. hang.dong@cs.ox.ac.uk","institution_ids":["https://openalex.org/I98677209"]},{"raw_affiliation_string":"Department of Computer Science, University of Oxford, Oxford, United Kingdom. hang.dong@cs.ox.ac.uk","institution_ids":["https://openalex.org/I40120149","https://openalex.org/I4210146410"]},{"raw_affiliation_string":"Health Data Research UK, London, United Kingdom. hang.dong@cs.ox.ac.uk","institution_ids":["https://openalex.org/I4210142469"]},{"raw_affiliation_string":"Centre for Medical Informatics, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065663251","display_name":"V\u00edctor Su\u00e1rez-Paniagua","orcid":"https://orcid.org/0000-0002-6036-5322"},"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/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"V\u00edctor Su\u00e1rez-Paniagua","raw_affiliation_strings":["Centre for Medical Informatics, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom","Health Data Research UK, London, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Medical Informatics, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom","institution_ids":["https://openalex.org/I98677209"]},{"raw_affiliation_string":"Health Data Research UK, London, United Kingdom","institution_ids":["https://openalex.org/I4210142469"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101408516","display_name":"Huayu Zhang","orcid":"https://orcid.org/0009-0004-0956-9073"},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Huayu Zhang","raw_affiliation_strings":["Advanced Care Research Centre, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Advanced Care Research Centre, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025000366","display_name":"Minhong Wang","orcid":"https://orcid.org/0000-0002-1084-6814"},"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":"Minhong Wang","raw_affiliation_strings":["Institute of Health Informatics, University College London, London, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Health Informatics, University College London, London, United Kingdom","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076964550","display_name":"Arlene Casey","orcid":"https://orcid.org/0000-0003-3256-0654"},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Arlene Casey","raw_affiliation_strings":["Advanced Care Research Centre, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Advanced Care Research Centre, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112781195","display_name":"Emma J. Davidson","orcid":null},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Emma Davidson","raw_affiliation_strings":["Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085691361","display_name":"Jiaoyan Chen","orcid":"https://orcid.org/0000-0003-4643-6750"},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jiaoyan Chen","raw_affiliation_strings":["Department of Computer Science, The University of Manchester, Manchester, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, The University of Manchester, Manchester, United Kingdom","institution_ids":["https://openalex.org/I28407311"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043179000","display_name":"Beatrice Alex","orcid":"https://orcid.org/0000-0002-7279-1476"},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Beatrice Alex","raw_affiliation_strings":["Edinburgh Futures Institute, University of Edinburgh, Edinburgh, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Edinburgh Futures Institute, University of Edinburgh, Edinburgh, United Kingdom","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058224218","display_name":"William Whiteley","orcid":"https://orcid.org/0000-0002-4816-8991"},"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/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"William Whiteley","raw_affiliation_strings":["Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom","Health Data Research UK, London, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom","institution_ids":["https://openalex.org/I98677209"]},{"raw_affiliation_string":"Health Data Research UK, London, United Kingdom","institution_ids":["https://openalex.org/I4210142469"]}]},{"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"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Honghan Wu","raw_affiliation_strings":["Health Data Research UK, London, United Kingdom. honghan.wu@ucl.ac.uk","Institute of Health Informatics, University College London, London, United Kingdom. honghan.wu@ucl.ac.uk","Institute of Health Informatics, University College London, London, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Health Data Research UK, London, United Kingdom. honghan.wu@ucl.ac.uk","institution_ids":["https://openalex.org/I4210142469"]},{"raw_affiliation_string":"Institute of Health Informatics, University College London, London, United Kingdom. honghan.wu@ucl.ac.uk","institution_ids":["https://openalex.org/I4210142469","https://openalex.org/I45129253"]},{"raw_affiliation_string":"Institute of Health Informatics, University College London, London, United Kingdom","institution_ids":["https://openalex.org/I45129253"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5035163413","https://openalex.org/A5043821806"],"corresponding_institution_ids":["https://openalex.org/I40120149","https://openalex.org/I4210142469","https://openalex.org/I4210146410","https://openalex.org/I45129253","https://openalex.org/I98677209"],"apc_list":{"value":1570,"currency":"GBP","value_usd":1925},"apc_paid":{"value":1570,"currency":"GBP","value_usd":1925},"fwci":5.4971,"has_fulltext":true,"cited_by_count":25,"citation_normalized_percentile":{"value":0.965485,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"23","issue":"1","first_page":"86","last_page":"86"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.5138999819755554,"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":0.5138999819755554,"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":0.14249999821186066,"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":0.14079999923706055,"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":0.9587502479553223},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7545729875564575},{"id":"https://openalex.org/keywords/snomed-ct","display_name":"SNOMED CT","score":0.7481228709220886},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.7004323601722717},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.605144739151001},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5985028743743896},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5801985263824463},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5619999766349792},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.5271834135055542},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5048988461494446},{"id":"https://openalex.org/keywords/open-biomedical-ontologies","display_name":"Open Biomedical Ontologies","score":0.4642781615257263},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.41679850220680237},{"id":"https://openalex.org/keywords/terminology","display_name":"Terminology","score":0.25416135787963867},{"id":"https://openalex.org/keywords/ontology-alignment","display_name":"Ontology alignment","score":0.24733689427375793},{"id":"https://openalex.org/keywords/domain-knowledge","display_name":"Domain knowledge","score":0.24096035957336426},{"id":"https://openalex.org/keywords/upper-ontology","display_name":"Upper ontology","score":0.13676783442497253},{"id":"https://openalex.org/keywords/linguistics","display_name":"Linguistics","score":0.12979212403297424},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.11236560344696045}],"concepts":[{"id":"https://openalex.org/C69505689","wikidata":"https://www.wikidata.org/wiki/Q455338","display_name":"Unified Medical Language System","level":2,"score":0.9587502479553223},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7545729875564575},{"id":"https://openalex.org/C206497026","wikidata":"https://www.wikidata.org/wiki/Q1753883","display_name":"SNOMED CT","level":3,"score":0.7481228709220886},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.7004323601722717},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.605144739151001},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5985028743743896},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5801985263824463},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5619999766349792},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.5271834135055542},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5048988461494446},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.4642781615257263},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.41679850220680237},{"id":"https://openalex.org/C547195049","wikidata":"https://www.wikidata.org/wiki/Q1725664","display_name":"Terminology","level":2,"score":0.25416135787963867},{"id":"https://openalex.org/C98893333","wikidata":"https://www.wikidata.org/wiki/Q4339878","display_name":"Ontology alignment","level":4,"score":0.24733689427375793},{"id":"https://openalex.org/C207685749","wikidata":"https://www.wikidata.org/wiki/Q2088941","display_name":"Domain knowledge","level":2,"score":0.24096035957336426},{"id":"https://openalex.org/C78726541","wikidata":"https://www.wikidata.org/wiki/Q3882785","display_name":"Upper ontology","level":3,"score":0.13676783442497253},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.12979212403297424},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.11236560344696045},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"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},{"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/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","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}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":"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":"D017432","descriptor_name":"Unified Medical Language System","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":false},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","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":false},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D038801","descriptor_name":"International Classification of Diseases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D038801","descriptor_name":"International Classification of Diseases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D038801","descriptor_name":"International Classification of Diseases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D038801","descriptor_name":"International Classification of Diseases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D038801","descriptor_name":"International Classification of Diseases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1186/s12911-023-02181-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12911-023-02181-9","pdf_url":"https://bmcmedinformdecismak.biomedcentral.com/counter/pdf/10.1186/s12911-023-02181-9","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:37147628","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37147628","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:326954","is_oa":true,"landing_page_url":"https://eprints.gla.ac.uk/view/author/77060.html>","pdf_url":"https://eprints.gla.ac.uk/326954/1/326954.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:10162001","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10162001","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10162001/pdf/12911_2023_Article_2181.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:ddad622df8154c81a37d192f7e613ad8","is_oa":true,"landing_page_url":"https://doaj.org/article/ddad622df8154c81a37d192f7e613ad8","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 Medical Informatics and Decision Making, Vol 23, Iss 1, Pp 1-17 (2023)","raw_type":"article"},{"id":"pmh:oai:pure.ed.ac.uk:openaire/9a1423d2-9755-4c95-9bb3-1b21006a5707","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/files/346210366/s12911_023_02181_9.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306400321","display_name":"Edinburgh Research Explorer (University of Edinburgh)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98677209","host_organization_name":"University of Edinburgh","host_organization_lineage":["https://openalex.org/I98677209"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Dong, H, Su\u00e1rez-Paniagua, V, Zhang, H, Wang, M, Casey, A, Davidson, E, Chen, J, Alex, B, Whiteley, W & Wu, H 2023, 'Ontology-driven and weakly supervised rare disease identification from clinical notes', Bmc medical informatics and decision making, vol. 23, no. 1. https://doi.org/10.1186/s12911-023-02181-9","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:pure.ed.ac.uk:publications/9a1423d2-9755-4c95-9bb3-1b21006a5707","is_oa":true,"landing_page_url":"https://hdl.handle.net/20.500.11820/9a1423d2-9755-4c95-9bb3-1b21006a5707","pdf_url":null,"source":{"id":"https://openalex.org/S4406922455","display_name":"Edinburgh Research Explorer","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},{"id":"pmh:oai:pure.ed.ac.uk:publications/9a1423d2-9755-4c95-9bb3-1b21006a5707","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/en/publications/9a1423d2-9755-4c95-9bb3-1b21006a5707","pdf_url":null,"source":{"id":"https://openalex.org/S4306400321","display_name":"Edinburgh Research Explorer (University of Edinburgh)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98677209","host_organization_name":"University of Edinburgh","host_organization_lineage":["https://openalex.org/I98677209"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Dong, H, Su\u00e1rez-Paniagua, V, Zhang, H, Wang, M, Casey, A, Davidson, E, Chen, J, Alex, B, Whiteley, W & Wu, H 2023, 'Ontology-driven and weakly supervised rare disease identification from clinical notes', Bmc medical informatics and decision making, vol. 23, no. 1. https://doi.org/10.1186/s12911-023-02181-9","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":{"id":"doi:10.1186/s12911-023-02181-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12911-023-02181-9","pdf_url":"https://bmcmedinformdecismak.biomedcentral.com/counter/pdf/10.1186/s12911-023-02181-9","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":0.7300000190734863,"id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G2491762334","display_name":null,"funder_award_id":"PIII009, PIII029, PIII032, PIII054","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G2737221419","display_name":null,"funder_award_id":"PIII029","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G3253514882","display_name":"ConCur: Knowledge Base Construction and Curation","funder_award_id":"EP/V050869/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G3661244400","display_name":null,"funder_award_id":"PIII054","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G5427307698","display_name":null,"funder_award_id":"PIII032","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G5790283667","display_name":null,"funder_award_id":"PIII009","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G6426385615","display_name":"Deriving an actionable patient phenome from healthcare data","funder_award_id":"MR/S004149/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G7513764588","display_name":null,"funder_award_id":"EP/V050869/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences 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/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"},{"id":"https://openalex.org/F7757660664","display_name":"Health Data Research UK","ror":"https://ror.org/04rtjaj74"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4368616878.pdf"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W112052496","https://openalex.org/W152321165","https://openalex.org/W1505770165","https://openalex.org/W1964189668","https://openalex.org/W1964625659","https://openalex.org/W2029517229","https://openalex.org/W2101086247","https://openalex.org/W2151068025","https://openalex.org/W2283041611","https://openalex.org/W2396881363","https://openalex.org/W2778088240","https://openalex.org/W2789877489","https://openalex.org/W2887535136","https://openalex.org/W2927032858","https://openalex.org/W2959716049","https://openalex.org/W2963341956","https://openalex.org/W2971258845","https://openalex.org/W2973267506","https://openalex.org/W2981443541","https://openalex.org/W3034238904","https://openalex.org/W3037562983","https://openalex.org/W3044693911","https://openalex.org/W3046375318","https://openalex.org/W3047309846","https://openalex.org/W3103842844","https://openalex.org/W3126592082","https://openalex.org/W3134691471","https://openalex.org/W3145725122","https://openalex.org/W3153866062","https://openalex.org/W3156071020","https://openalex.org/W3158665049","https://openalex.org/W3159907162","https://openalex.org/W3164540570","https://openalex.org/W3165661673","https://openalex.org/W3175234986","https://openalex.org/W3176553463","https://openalex.org/W3217764413","https://openalex.org/W4205619992","https://openalex.org/W4223429546","https://openalex.org/W4235216760","https://openalex.org/W4250160324","https://openalex.org/W4250526791","https://openalex.org/W4284698419","https://openalex.org/W6601548533","https://openalex.org/W6675354045","https://openalex.org/W6739901393"],"related_works":["https://openalex.org/W2044298438","https://openalex.org/W2240723216","https://openalex.org/W2186444170","https://openalex.org/W2181479088","https://openalex.org/W2795453480","https://openalex.org/W2037829818","https://openalex.org/W31701444","https://openalex.org/W2396508331","https://openalex.org/W4206342372","https://openalex.org/W4388685083"],"abstract_inverted_index":{"BACKGROUND:":[0],"Computational":[1],"text":[2],"phenotyping":[3],"is":[4,122],"the":[5,34,142,164,167,175,197,214,244,304,309],"practice":[6],"of":[7,193,308],"identifying":[8],"patients":[9],"with":[10,52,84,97,169,189,213],"certain":[11],"disorders":[12],"and":[13,33,49,89,94,100,154,166,208,270,277,306,313],"traits":[14],"from":[15,39,57,137,160,206],"clinical":[16,146,221,254,300],"notes.":[17,255,301],"Rare":[18,114],"diseases":[19,111,298],"are":[20],"challenging":[21],"to":[22,26,76,109,124,130,182,196,294],"be":[23],"identified":[24],"due":[25],"few":[27],"cases":[28],"available":[29],"for":[30,36,186,243,268,316],"machine":[31],"learning":[32,261],"need":[35],"data":[37,136,232],"annotation":[38,266],"domain":[40,138],"experts.":[41,139],"METHODS:":[42],"We":[43,140,302],"propose":[44,314],"a":[45,85,126,248],"method":[46],"using":[47],"ontologies":[48],"weak":[50,95,258,310],"supervision,":[51],"recent":[53],"pre-trained":[54],"contextual":[55,101,278],"representations":[56],"Bi-directional":[58],"Transformers":[59],"(e.g.":[60],"BERT).":[61],"The":[62,118,172,217,238,256,280],"ontology-driven":[63],"framework":[64],"includes":[65],"two":[66,161],"steps:":[67],"(i)":[68],"Text-to-UMLS,":[69],"extracting":[70],"phenotypes":[71],"by":[72,246,272],"contextually":[73],"linking":[74],"mentions":[75],"concepts":[77,108],"in":[78,112,163,174,230,299],"Unified":[79],"Medical":[80],"Language":[81,286],"System":[82],"(UMLS),":[83],"Named":[86],"Entity":[87],"Recognition":[88],"Linking":[90],"(NER+L)":[91],"tool,":[92,200],"SemEHR,":[93],"supervision":[96,311],"customised":[98],"rules":[99],"mention":[102],"representation;":[103],"(ii)":[104],"UMLS-to-ORDO,":[105],"matching":[106],"UMLS":[107],"rare":[110,225,297],"Orphanet":[113],"Disease":[115],"Ontology":[116],"(ORDO).":[117],"weakly":[119,249],"supervised":[120,250,259],"approach":[121,143,262,312],"proposed":[123,257],"learn":[125],"phenotype":[127],"confirmation":[128],"model":[129],"improve":[131],"Text-to-UMLS":[132,187],"linking,":[133],"without":[134],"annotated":[135],"evaluated":[141],"on":[144,203,253],"three":[145],"datasets,":[147],"MIMIC-III":[148,151,207],"discharge":[149,215],"summaries,":[150],"radiology":[152,204],"reports,":[153],"NHS":[155,209],"Tayside":[156,210],"brain":[157],"imaging":[158],"reports":[159,205],"institutions":[162],"US":[165],"UK,":[168],"annotations.":[170],"RESULTS:":[171],"improvements":[173],"precision":[176],"were":[177,211],"pronounced":[178],"(by":[179],"over":[180],"30%":[181],"50%":[183],"absolute":[184],"score":[185],"linking),":[188],"almost":[190],"no":[191,264],"loss":[192],"recall":[194],"compared":[195],"existing":[198],"NER+L":[199,275],"SemEHR.":[201],"Results":[202],"consistent":[212],"summaries.":[216],"overall":[218],"pipeline":[219,252],"processing":[220],"notes":[222],"can":[223,289],"extract":[224],"disease":[226],"cases,":[227],"mostly":[228],"uncaptured":[229],"structured":[231],"(manually":[233],"assigned":[234],"ICD":[235],"codes).":[236],"CONCLUSION:":[237],"study":[239,281],"provides":[240],"empirical":[241],"evidence":[242],"task":[245],"applying":[247],"NLP":[251],"deep":[260],"requires":[263],"human":[265],"except":[267],"validation":[269],"testing,":[271],"leveraging":[273],"ontologies,":[274],"tools,":[276],"representations.":[279],"also":[282],"demonstrates":[283],"that":[284],"Natural":[285],"Processing":[287],"(NLP)":[288],"complement":[290],"traditional":[291],"ICD-based":[292],"approaches":[293],"better":[295],"estimate":[296],"discuss":[303],"usefulness":[305],"limitations":[307],"directions":[315],"future":[317],"studies.":[318]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":8}],"updated_date":"2026-07-16T13:24:37.021932","created_date":"2025-10-10T00:00:00"}
