{"id":"https://openalex.org/W3159907162","doi":"https://doi.org/10.1109/embc46164.2021.9630043","title":"Rare Disease Identification from Clinical Notes with Ontologies and Weak Supervision","display_name":"Rare Disease Identification from Clinical Notes with Ontologies and Weak Supervision","publication_year":2021,"publication_date":"2021-11-01","ids":{"openalex":"https://openalex.org/W3159907162","doi":"https://doi.org/10.1109/embc46164.2021.9630043","mag":"3159907162","pmid":"https://pubmed.ncbi.nlm.nih.gov/34891745"},"language":"en","primary_location":{"id":"doi:10.1109/embc46164.2021.9630043","is_oa":false,"landing_page_url":"https://doi.org/10.1109/embc46164.2021.9630043","pdf_url":null,"source":{"id":"https://openalex.org/S4363607750","display_name":"2021 43rd Annual International Conference of the IEEE Engineering in Medicine &amp; Biology Society (EMBC)","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":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 43rd Annual International Conference of the IEEE Engineering in Medicine &amp; Biology Society (EMBC)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":null,"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/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":true,"raw_author_name":"Hang Dong","raw_affiliation_strings":["Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK","Health Data Research UK, London, UK"],"affiliations":[{"raw_affiliation_string":"Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK","institution_ids":["https://openalex.org/I98677209"]},{"raw_affiliation_string":"Health Data Research UK, London, UK","institution_ids":["https://openalex.org/I4210142469"]}]},{"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":"Victor Suarez-Paniagua","raw_affiliation_strings":["Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK","Health Data Research UK, London, UK"],"affiliations":[{"raw_affiliation_string":"Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK","institution_ids":["https://openalex.org/I98677209"]},{"raw_affiliation_string":"Health Data Research UK, London, UK","institution_ids":["https://openalex.org/I4210142469"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101408515","display_name":"Huayu Zhang","orcid":"https://orcid.org/0000-0003-1625-4067"},"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, UK"],"affiliations":[{"raw_affiliation_string":"Advanced Care Research Centre, Usher Institute, University of Edinburgh, Edinburgh, UK","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013586174","display_name":"Minhong Wang","orcid":"https://orcid.org/0000-0001-7041-7045"},"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":"Minhong Wang","raw_affiliation_strings":["Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK"],"affiliations":[{"raw_affiliation_string":"Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040595677","display_name":"Emma Whitfield","orcid":"https://orcid.org/0000-0001-5427-7150"},"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"]},{"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"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Emma Whitfield","raw_affiliation_strings":["Health Data Research UK, London, UK","Institute of Health Informatics, University College London, London, UK"],"affiliations":[{"raw_affiliation_string":"Health Data Research UK, London, UK","institution_ids":["https://openalex.org/I4210142469"]},{"raw_affiliation_string":"Institute of Health Informatics, University College London, London, UK","institution_ids":["https://openalex.org/I45129253"]}]},{"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/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/I4210142469","display_name":"Health Data Research UK","ror":"https://ror.org/04rtjaj74","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I4210142469"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Honghan Wu","raw_affiliation_strings":["Health Data Research UK, London, UK","Institute of Health Informatics, University College London, London, UK"],"affiliations":[{"raw_affiliation_string":"Health Data Research UK, London, UK","institution_ids":["https://openalex.org/I4210142469"]},{"raw_affiliation_string":"Institute of Health Informatics, University College London, London, UK","institution_ids":["https://openalex.org/I45129253"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5035163413"],"corresponding_institution_ids":["https://openalex.org/I4210142469","https://openalex.org/I98677209"],"apc_list":null,"apc_paid":null,"fwci":1.1417,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.81161028,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"2021","issue":null,"first_page":"2294","last_page":"2298"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9987000226974487,"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":0.9976999759674072,"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":0.9581608772277832},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7984097003936768},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.6902182102203369},{"id":"https://openalex.org/keywords/snomed-ct","display_name":"SNOMED CT","score":0.63116455078125},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.57460618019104},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5673105120658875},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5301238894462585},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.508363664150238},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4838058352470398},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.46329841017723083},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.44718044996261597},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.4381251633167267},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.4310714602470398},{"id":"https://openalex.org/keywords/terminology","display_name":"Terminology","score":0.25546500086784363},{"id":"https://openalex.org/keywords/linguistics","display_name":"Linguistics","score":0.19857603311538696},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.14387983083724976}],"concepts":[{"id":"https://openalex.org/C69505689","wikidata":"https://www.wikidata.org/wiki/Q455338","display_name":"Unified Medical Language System","level":2,"score":0.9581608772277832},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7984097003936768},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.6902182102203369},{"id":"https://openalex.org/C206497026","wikidata":"https://www.wikidata.org/wiki/Q1753883","display_name":"SNOMED CT","level":3,"score":0.63116455078125},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.57460618019104},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5673105120658875},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5301238894462585},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.508363664150238},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4838058352470398},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.46329841017723083},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.44718044996261597},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.4381251633167267},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.4310714602470398},{"id":"https://openalex.org/C547195049","wikidata":"https://www.wikidata.org/wiki/Q1725664","display_name":"Terminology","level":2,"score":0.25546500086784363},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.19857603311538696},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.14387983083724976},{"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/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},{"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/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","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/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","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":"D008499","descriptor_name":"Medical Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008499","descriptor_name":"Medical Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008499","descriptor_name":"Medical Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008499","descriptor_name":"Medical Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008499","descriptor_name":"Medical Records","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":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","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":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","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":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}],"locations_count":7,"locations":[{"id":"doi:10.1109/embc46164.2021.9630043","is_oa":false,"landing_page_url":"https://doi.org/10.1109/embc46164.2021.9630043","pdf_url":null,"source":{"id":"https://openalex.org/S4363607750","display_name":"2021 43rd Annual International Conference of the IEEE Engineering in Medicine &amp; Biology Society (EMBC)","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":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 43rd Annual International Conference of the IEEE Engineering in Medicine &amp; Biology Society (EMBC)","raw_type":"proceedings-article"},{"id":"pmid:34891745","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34891745","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":"Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference","raw_type":null},{"id":"pmh:oai:eprints.gla.ac.uk:326985","is_oa":true,"landing_page_url":null,"pdf_url":null,"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":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Conference Proceedings"},{"id":"pmh:oai:eprints.ucl.ac.uk.OAI2:10147558","is_oa":false,"landing_page_url":"https://discovery.ucl.ac.uk/id/eprint/10147558/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400024","display_name":"UCL Discovery (University College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45129253","host_organization_name":"University College London","host_organization_lineage":["https://openalex.org/I45129253"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"     In:  2021 43rd Annual International Conference of the IEEE Engineering in Medicine &amp; Biology Society (EMBC).  (pp. pp. 2294-2298).  IEEE: Mexico. (2021)     ","raw_type":"Proceedings paper"},{"id":"pmh:oai:ora.ox.ac.uk:uuid:37d22df2-f9c9-46d0-8bd5-c73f88433158","is_oa":false,"landing_page_url":"https://ora.ox.ac.uk/objects/uuid:37d22df2-f9c9-46d0-8bd5-c73f88433158","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":"Symplectic Elements","raw_type":"Conference item"},{"id":"pmh:oai:pure.ed.ac.uk:openaire/f7215887-d201-4987-823f-ae9e8f60735f","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/en/publications/f7215887-d201-4987-823f-ae9e8f60735f","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Dong, H, Su\u00e1rez-Paniagua, V, Zhang, H, Wang, M, Whitfield, E & Wu, H 2021, 'Rare Disease Identification from Clinical Notes with Ontologies and Weak Supervision', Paper presented at 2021 43rd Annual International Conference of the IEEE Engineering in Medicine , 1/11/21 - 5/11/21 pp. 2298-2302. https://doi.org/10.1109/EMBC46164.2021.9630043","raw_type":"conferenceObject"},{"id":"pmh:oai:pure.ed.ac.uk:publications/f7215887-d201-4987-823f-ae9e8f60735f","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11820/f7215887-d201-4987-823f-ae9e8f60735f","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-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""}],"best_oa_location":{"id":"pmh:oai:eprints.gla.ac.uk:326985","is_oa":true,"landing_page_url":null,"pdf_url":null,"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":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Conference Proceedings"},"sustainable_development_goals":[{"score":0.7900000214576721,"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4"}],"awards":[{"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/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/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320338440","display_name":"HORIZON EUROPE Health","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W112052496","https://openalex.org/W2101234009","https://openalex.org/W2137171237","https://openalex.org/W2396881363","https://openalex.org/W2405275595","https://openalex.org/W2778088240","https://openalex.org/W2786253107","https://openalex.org/W2889577585","https://openalex.org/W2896457183","https://openalex.org/W2927032858","https://openalex.org/W2963341956","https://openalex.org/W2971258845","https://openalex.org/W3037562983","https://openalex.org/W3126592082","https://openalex.org/W3134691471","https://openalex.org/W4289293803","https://openalex.org/W6675354045","https://openalex.org/W6713841166","https://openalex.org/W6747880825","https://openalex.org/W6755207826","https://openalex.org/W6756416310"],"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/W2004600423","https://openalex.org/W4206342372"],"abstract_inverted_index":{"The":[0,42],"identification":[1],"of":[2,27,154],"rare":[3,92,143],"diseases":[4,93],"from":[5,30,79,128],"clinical":[6,31],"notes":[7],"with":[8,60,121],"Natural":[9],"Language":[10,57],"Processing":[11],"(NLP)":[12],"is":[13],"challenging":[14],"due":[15],"to":[16,52,91],"the":[17,25,114,135,155],"few":[18],"cases":[19],"available":[20],"for":[21],"machine":[22],"learning":[23],"and":[24,39,68,75,85],"need":[26],"data":[28,127],"annotation":[29],"experts.":[32,130],"We":[33],"propose":[34],"a":[35,61,108],"method":[36],"using":[37],"ontologies":[38],"weak":[40,69,122],"supervision.":[41],"approach":[43],"includes":[44],"two":[45],"steps:":[46],"(i)":[47],"Text-to-UMLS,":[48],"linking":[49,64],"text":[50],"mentions":[51],"concepts":[53,90],"in":[54,94,150],"Unified":[55],"Medical":[56],"System":[58],"(UMLS),":[59],"named":[62],"entity":[63],"tool":[65],"(e.g.":[66],"SemEHR)":[67],"supervision":[70],"based":[71,82],"on":[72],"customised":[73],"rules":[74],"Bidirectional":[76],"Encoder":[77],"Representations":[78],"Transformers":[80],"(BERT)":[81],"contextual":[83],"representations,":[84],"(ii)":[86],"UMLS-to-ORDO,":[87],"matching":[88],"UMLS":[89],"Orphanet":[95],"Rare":[96],"Disease":[97],"Ontology":[98],"(ORDO).":[99],"Using":[100],"MIMIC-III":[101],"US":[102],"intensive":[103],"care":[104],"discharge":[105,139],"summaries":[106,140],"as":[107],"case":[109],"study,":[110],"we":[111],"show":[112],"that":[113,134],"Text-to-UMLS":[115],"process":[116],"can":[117,141],"be":[118],"greatly":[119],"improved":[120],"supervision,":[123],"without":[124],"any":[125],"annotated":[126],"domain":[129],"Our":[131],"analysis":[132],"shows":[133],"overall":[136],"pipeline":[137],"processing":[138],"surface":[142],"disease":[144],"cases,":[145],"which":[146],"are":[147],"mostly":[148],"uncaptured":[149],"manual":[151],"ICD":[152],"codes":[153],"hospital":[156],"admissions.":[157]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
