{"id":"https://openalex.org/W4389004882","doi":"https://doi.org/10.1093/bioinformatics/btad716","title":"Term-BLAST-like alignment tool for concept recognition in noisy clinical texts","display_name":"Term-BLAST-like alignment tool for concept recognition in noisy clinical texts","publication_year":2023,"publication_date":"2023-11-24","ids":{"openalex":"https://openalex.org/W4389004882","doi":"https://doi.org/10.1093/bioinformatics/btad716","pmid":"https://pubmed.ncbi.nlm.nih.gov/38001031"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad716","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad716","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad716/53792331/btad716.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad716/53792331/btad716.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011041769","display_name":"Tudor Groza","orcid":"https://orcid.org/0000-0003-2267-8333"},"institutions":[{"id":"https://openalex.org/I175234967","display_name":"The Kids Research Institute Australia","ror":"https://ror.org/01dbmzx78","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I175234967"]},{"id":"https://openalex.org/I2800419323","display_name":"Princess Margaret Hospital for Children","ror":"https://ror.org/04ec98z42","country_code":"AU","type":"healthcare","lineage":["https://openalex.org/I2799506148","https://openalex.org/I2800419323","https://openalex.org/I2800882159"]},{"id":"https://openalex.org/I4387155440","display_name":"Perth Children's Hospital","ror":"https://ror.org/015zx6n37","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I4387155440"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Tudor Groza","raw_affiliation_strings":["Genetics and Rare Diseases Program, Telethon Kids Institute , Nedlands, WA 6009, Australia","Rare Care Centre, Perth Children\u2019s Hospital , Nedlands, WA 6009, Australia"],"raw_orcid":"https://orcid.org/0000-0003-2267-8333","affiliations":[{"raw_affiliation_string":"Genetics and Rare Diseases Program, Telethon Kids Institute , Nedlands, WA 6009, Australia","institution_ids":["https://openalex.org/I175234967"]},{"raw_affiliation_string":"Rare Care Centre, Perth Children\u2019s Hospital , Nedlands, WA 6009, Australia","institution_ids":["https://openalex.org/I2800419323","https://openalex.org/I4387155440"]}]},{"author_position":"middle","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"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Honghan Wu","raw_affiliation_strings":["Institute of Health Informatics, University College London , London WC1E 6BT, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-0213-5668","affiliations":[{"raw_affiliation_string":"Institute of Health Informatics, University College London , London WC1E 6BT, United Kingdom","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049900685","display_name":"Marcel E. Dinger","orcid":"https://orcid.org/0000-0003-4423-934X"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]},{"id":"https://openalex.org/I1311436738","display_name":"New South Wales Department of Health","ror":"https://ror.org/03tb4gf50","country_code":"AU","type":"government","lineage":["https://openalex.org/I1311436738","https://openalex.org/I2801351115"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Marcel E Dinger","raw_affiliation_strings":["Pryzm Health , Sydney, NSW 2089, Australia","School of Life and Environmental Sciences, Faculty of Science, University of Sydney , NSW 2006, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pryzm Health , Sydney, NSW 2089, Australia","institution_ids":["https://openalex.org/I1311436738"]},{"raw_affiliation_string":"School of Life and Environmental Sciences, Faculty of Science, University of Sydney , NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041560815","display_name":"Daniel Dani\u0161","orcid":"https://orcid.org/0000-0003-0900-3411"},"institutions":[{"id":"https://openalex.org/I4210115256","display_name":"Jackson Laboratory","ror":"https://ror.org/021sy4w91","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel Danis","raw_affiliation_strings":["The Jackson Laboratory for Genomic Medicine , Farmington, CT 06032, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Jackson Laboratory for Genomic Medicine , Farmington, CT 06032, United States","institution_ids":["https://openalex.org/I4210115256"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063216470","display_name":"Coleman Hilton","orcid":"https://orcid.org/0000-0001-9070-7680"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Coleman Hilton","raw_affiliation_strings":["Shriners Children\u2019s Corporate Headquarters , Tampa, FL 33607, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shriners Children\u2019s Corporate Headquarters , Tampa, FL 33607, United States","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010851534","display_name":"Anita Bagley","orcid":"https://orcid.org/0000-0001-9118-8798"},"institutions":[{"id":"https://openalex.org/I4210103356","display_name":"Shriners Hospitals for Children - Northern California","ror":"https://ror.org/01dmyj570","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210103356","https://openalex.org/I4210144267"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anita Bagley","raw_affiliation_strings":["Shriners Children's Northern California , Sacramento, CA 95817, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shriners Children's Northern California , Sacramento, CA 95817, United States","institution_ids":["https://openalex.org/I4210103356"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000602263","display_name":"Jon R. Davids","orcid":"https://orcid.org/0000-0002-1639-6519"},"institutions":[{"id":"https://openalex.org/I4210103356","display_name":"Shriners Hospitals for Children - Northern California","ror":"https://ror.org/01dmyj570","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210103356","https://openalex.org/I4210144267"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jon R Davids","raw_affiliation_strings":["Shriners Children's Northern California , Sacramento, CA 95817, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shriners Children's Northern California , Sacramento, CA 95817, United States","institution_ids":["https://openalex.org/I4210103356"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100619435","display_name":"Ling Luo","orcid":"https://orcid.org/0000-0002-5141-0259"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ling Luo","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health , Bethesda, MD 20894, United States"],"raw_orcid":"https://orcid.org/0000-0002-5141-0259","affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health , Bethesda, MD 20894, United States","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083081872","display_name":"Zhiyong Lu","orcid":"https://orcid.org/0000-0001-9998-916X"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhiyong Lu","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health , Bethesda, MD 20894, United States"],"raw_orcid":"https://orcid.org/0000-0001-9998-916X","affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health , Bethesda, MD 20894, United States","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033225381","display_name":"Peter N. Robinson","orcid":"https://orcid.org/0000-0002-0736-9199"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]},{"id":"https://openalex.org/I4210115256","display_name":"Jackson Laboratory","ror":"https://ror.org/021sy4w91","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Peter N Robinson","raw_affiliation_strings":["Institute for Systems Genomics, University of Connecticut , Farmington, CT 06032, United States","The Jackson Laboratory for Genomic Medicine , Farmington, CT 06032, United States"],"raw_orcid":"https://orcid.org/0000-0002-0736-9199","affiliations":[{"raw_affiliation_string":"Institute for Systems Genomics, University of Connecticut , Farmington, CT 06032, United States","institution_ids":["https://openalex.org/I140172145"]},{"raw_affiliation_string":"The Jackson Laboratory for Genomic Medicine , Farmington, CT 06032, United States","institution_ids":["https://openalex.org/I4210115256"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5033225381"],"corresponding_institution_ids":["https://openalex.org/I140172145","https://openalex.org/I4210115256"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.4238,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.6729257,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":96},"biblio":{"volume":"39","issue":"12","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.8240000009536743,"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"}},"topics":[{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.8240000009536743,"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":0.14470000565052032,"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/T10181","display_name":"Natural Language Processing Techniques","score":0.0052999998442828655,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8039371967315674},{"id":"https://openalex.org/keywords/spelling","display_name":"Spelling","score":0.7515561580657959},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.5960432887077332},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5655178427696228},{"id":"https://openalex.org/keywords/complement","display_name":"Complement (music)","score":0.5479089021682739},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5291628837585449},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.48380011320114136},{"id":"https://openalex.org/keywords/precision-and-recall","display_name":"Precision and recall","score":0.4582078456878662},{"id":"https://openalex.org/keywords/recall","display_name":"Recall","score":0.42165765166282654}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8039371967315674},{"id":"https://openalex.org/C2777801307","wikidata":"https://www.wikidata.org/wiki/Q2088390","display_name":"Spelling","level":2,"score":0.7515561580657959},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5960432887077332},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5655178427696228},{"id":"https://openalex.org/C112313634","wikidata":"https://www.wikidata.org/wiki/Q7886648","display_name":"Complement (music)","level":5,"score":0.5479089021682739},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5291628837585449},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.48380011320114136},{"id":"https://openalex.org/C81669768","wikidata":"https://www.wikidata.org/wiki/Q2359161","display_name":"Precision and recall","level":2,"score":0.4582078456878662},{"id":"https://openalex.org/C100660578","wikidata":"https://www.wikidata.org/wiki/Q18733","display_name":"Recall","level":2,"score":0.42165765166282654},{"id":"https://openalex.org/C188082640","wikidata":"https://www.wikidata.org/wiki/Q1780899","display_name":"Complementation","level":4,"score":0.0},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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":"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}],"locations_count":7,"locations":[{"id":"doi:10.1093/bioinformatics/btad716","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad716","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad716/53792331/btad716.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38001031","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38001031","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:eprints.gla.ac.uk:326948","is_oa":true,"landing_page_url":null,"pdf_url":"https://eprints.gla.ac.uk/326948/1/326948.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":"","raw_type":"Articles"},{"id":"pmh:oai:eprints.ucl.ac.uk.OAI2:10182387","is_oa":true,"landing_page_url":"https://discovery.ucl.ac.uk/id/eprint/10182387/","pdf_url":"https://discovery.ucl.ac.uk/10182387/1/btad716.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"   Bioinformatics , 39  (12)    , Article btad716. (2023)      ","raw_type":"Article"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt7q85z32j","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/7q85z32j","pdf_url":"https://escholarship.org/content/qt7q85z32j/qt7q85z32j.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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":"Bioinformatics, vol 39, iss 12","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10710372","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10710372","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10710372/pdf/btad716.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":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:mouseion.jax.org:stfb2023-1310","is_oa":true,"landing_page_url":"https://mouseion.jax.org/stfb2023/304","pdf_url":null,"source":{"id":"https://openalex.org/S4377196421","display_name":"The Mouseion at the JAXlibrary (Jackson Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210115256","host_organization_name":"Jackson Laboratory","host_organization_lineage":["https://openalex.org/I4210115256"],"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":"Faculty Research 2023","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad716","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad716","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad716/53792331/btad716.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.550000011920929}],"awards":[],"funders":[{"id":"https://openalex.org/F4320313288","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337349","display_name":"NIH Office of the Director","ror":"https://ror.org/00fj8a872"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4389004882.pdf"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W102787101","https://openalex.org/W2012361142","https://openalex.org/W2029195137","https://openalex.org/W2050006154","https://openalex.org/W2055043387","https://openalex.org/W2119613819","https://openalex.org/W2130222341","https://openalex.org/W2136410628","https://openalex.org/W2137724373","https://openalex.org/W2137854030","https://openalex.org/W2158714788","https://openalex.org/W2278812662","https://openalex.org/W2510298658","https://openalex.org/W2558643140","https://openalex.org/W2767470330","https://openalex.org/W2805193585","https://openalex.org/W2809721358","https://openalex.org/W2911489562","https://openalex.org/W2928818852","https://openalex.org/W2946102094","https://openalex.org/W2951146425","https://openalex.org/W3087028093","https://openalex.org/W3212464243","https://openalex.org/W4212919921","https://openalex.org/W4226322299","https://openalex.org/W4229444535","https://openalex.org/W4282918066","https://openalex.org/W4381594492","https://openalex.org/W4395677977","https://openalex.org/W6604181502","https://openalex.org/W6809835526","https://openalex.org/W6865393773"],"related_works":["https://openalex.org/W2161008081","https://openalex.org/W2100947578","https://openalex.org/W4298186509","https://openalex.org/W2556702969","https://openalex.org/W217221262","https://openalex.org/W611030372","https://openalex.org/W2358294942","https://openalex.org/W2794206341","https://openalex.org/W4367460280","https://openalex.org/W4328049145"],"abstract_inverted_index":{"MOTIVATION:":[0],"Methods":[1],"for":[2,52,58,98,107,185],"concept":[3],"recognition":[4],"(CR)":[5],"in":[6,131,139],"clinical":[7,39,84],"texts":[8,22,57],"have":[9],"largely":[10],"been":[11],"tested":[12],"on":[13,61,72,133,141],"abstracts":[14],"or":[15,167],"articles":[16],"from":[17,23,81],"the":[18,49,62,88,147,157,199],"medical":[19],"literature.":[20],"However,":[21],"electronic":[24],"health":[25],"records":[26,143],"(EHRs)":[27],"frequently":[28],"contain":[29],"spelling":[30,78],"errors,":[31],"abbreviations,":[32],"and":[33,68,136,193],"other":[34],"nonstandard":[35],"ways":[36],"of":[37,64,77,117,129,156,188],"representing":[38],"concepts.":[40],"RESULTS:":[41],"Here,":[42],"we":[43],"present":[44,112],"a":[45,94,103,113,153,169,179],"method":[46,106,162],"inspired":[47],"by":[48],"BLAST":[50],"algorithm":[51],"biosequence":[53],"alignment":[54,90],"that":[55,182],"screens":[56],"potential":[59],"matches":[60],"basis":[63],"matching":[65],"k-mer":[66],"counts":[67],"scores":[69],"candidates":[70],"based":[71],"conformance":[73],"to":[74,101,171],"typical":[75],"patterns":[76],"errors":[79,100],"derived":[80],"2.9":[82],"million":[83],"notes.":[85],"Our":[86],"method,":[87],"Term-BLAST-like":[89],"tool":[91],"(TBLAT)":[92],"leverages":[93],"gold":[95],"standard":[96],"corpus":[97],"typographical":[99],"implement":[102],"sequence":[104],"alignment-inspired":[105],"efficient":[108],"entity":[109,158],"linkage.":[110],"We":[111],"comprehensive":[114],"experimental":[115],"comparison":[116],"TBLAT":[118,184],"with":[119],"five":[120],"widely":[121],"used":[122,165],"tools.":[123],"Experimental":[124],"results":[125],"show":[126],"an":[127],"increase":[128,138],"10%":[130],"recall":[132,140],"scientific":[134],"publications":[135],"20%":[137],"EHR":[142],"(when":[144],"compared":[145],"against":[146],"next":[148],"best":[149],"method),":[150],"hence":[151],"supporting":[152],"significant":[154],"enhancement":[155],"linking":[159],"task.":[160],"The":[161],"can":[163],"be":[164],"stand-alone":[166],"as":[168],"complement":[170],"existing":[172],"approaches.":[173],"AVAILABILITY":[174],"AND":[175],"IMPLEMENTATION:":[176],"Fenominal":[177],"is":[178,194],"Java":[180],"library":[181],"implements":[183],"named":[186],"CR":[187],"Human":[189],"Phenotype":[190],"Ontology":[191],"terms":[192],"available":[195],"at":[196],"https://github.com/monarch-initiative/fenominal":[197],"under":[198],"GNU":[200],"General":[201],"Public":[202],"License":[203],"v3.0.":[204]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2}],"updated_date":"2026-06-22T08:00:12.763002","created_date":"2025-10-10T00:00:00"}
