{"id":"https://openalex.org/W3092040890","doi":"https://doi.org/10.1093/jamia/ocaa205","title":"The impact of learning Unified Medical Language System knowledge embeddings in relation extraction from biomedical texts","display_name":"The impact of learning Unified Medical Language System knowledge embeddings in relation extraction from biomedical texts","publication_year":2020,"publication_date":"2020-08-07","ids":{"openalex":"https://openalex.org/W3092040890","doi":"https://doi.org/10.1093/jamia/ocaa205","mag":"3092040890","pmid":"https://pubmed.ncbi.nlm.nih.gov/33029619"},"language":"en","primary_location":{"id":"doi:10.1093/jamia/ocaa205","is_oa":false,"landing_page_url":"https://doi.org/10.1093/jamia/ocaa205","pdf_url":null,"source":{"id":"https://openalex.org/S129839026","display_name":"Journal of the American Medical Informatics Association","issn_l":"1067-5027","issn":["1067-5027","1527-974X"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of the American Medical Informatics Association","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7647370","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040635806","display_name":"Maxwell Weinzierl","orcid":"https://orcid.org/0000-0002-8049-7453"},"institutions":[{"id":"https://openalex.org/I162577319","display_name":"The University of Texas at Dallas","ror":"https://ror.org/049emcs32","country_code":"US","type":"education","lineage":["https://openalex.org/I162577319"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Maxwell A Weinzierl","raw_affiliation_strings":["Human Language Technology Research Institute, Department of Computer Science, Erik Jonsson School of Engineering & Computer Science, University of Texas at Dallas, Richardson, Texas, USA"],"raw_orcid":"https://orcid.org/0000-0002-8049-7453","affiliations":[{"raw_affiliation_string":"Human Language Technology Research Institute, Department of Computer Science, Erik Jonsson School of Engineering & Computer Science, University of Texas at Dallas, Richardson, Texas, USA","institution_ids":["https://openalex.org/I162577319"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087477366","display_name":"Ram\u00f3n Maldonado","orcid":null},"institutions":[{"id":"https://openalex.org/I162577319","display_name":"The University of Texas at Dallas","ror":"https://ror.org/049emcs32","country_code":"US","type":"education","lineage":["https://openalex.org/I162577319"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ramon Maldonado","raw_affiliation_strings":["Human Language Technology Research Institute, Department of Computer Science, Erik Jonsson School of Engineering & Computer Science, University of Texas at Dallas, Richardson, Texas, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Human Language Technology Research Institute, Department of Computer Science, Erik Jonsson School of Engineering & Computer Science, University of Texas at Dallas, Richardson, Texas, USA","institution_ids":["https://openalex.org/I162577319"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014682058","display_name":"Sanda M. Harabagiu","orcid":"https://orcid.org/0000-0002-8186-1501"},"institutions":[{"id":"https://openalex.org/I162577319","display_name":"The University of Texas at Dallas","ror":"https://ror.org/049emcs32","country_code":"US","type":"education","lineage":["https://openalex.org/I162577319"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sanda M Harabagiu","raw_affiliation_strings":["Human Language Technology Research Institute, Department of Computer Science, Erik Jonsson School of Engineering & Computer Science, University of Texas at Dallas, Richardson, Texas, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Human Language Technology Research Institute, Department of Computer Science, Erik Jonsson School of Engineering & Computer Science, University of Texas at Dallas, Richardson, Texas, USA","institution_ids":["https://openalex.org/I162577319"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5040635806"],"corresponding_institution_ids":["https://openalex.org/I162577319"],"apc_list":{"value":3967,"currency":"USD","value_usd":3967},"apc_paid":null,"fwci":0.4882,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.6249292,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"27","issue":"10","first_page":"1556","last_page":"1567"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.4474000036716461,"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":0.4474000036716461,"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":0.4431999921798706,"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/T13702","display_name":"Machine Learning in Healthcare","score":0.01810000091791153,"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":0.928943395614624},{"id":"https://openalex.org/keywords/relationship-extraction","display_name":"Relationship extraction","score":0.9110798835754395},{"id":"https://openalex.org/keywords/relation","display_name":"Relation (database)","score":0.8296062350273132},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7493767738342285},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.6092851161956787},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5671510696411133},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.40175727009773254},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.15799754858016968}],"concepts":[{"id":"https://openalex.org/C69505689","wikidata":"https://www.wikidata.org/wiki/Q455338","display_name":"Unified Medical Language System","level":2,"score":0.928943395614624},{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.9110798835754395},{"id":"https://openalex.org/C25343380","wikidata":"https://www.wikidata.org/wiki/Q277521","display_name":"Relation (database)","level":2,"score":0.8296062350273132},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7493767738342285},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.6092851161956787},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5671510696411133},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.40175727009773254},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.15799754858016968}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/jamia/ocaa205","is_oa":false,"landing_page_url":"https://doi.org/10.1093/jamia/ocaa205","pdf_url":null,"source":{"id":"https://openalex.org/S129839026","display_name":"Journal of the American Medical Informatics Association","issn_l":"1067-5027","issn":["1067-5027","1527-974X"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of the American Medical Informatics Association","raw_type":"journal-article"},{"id":"pmid:33029619","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33029619","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":"Journal of the American Medical Informatics Association : JAMIA","raw_type":null},{"id":"pmh:oai:europepmc.org:7386742","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC7647370","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:7647370","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7647370","pdf_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Am Med Inform Assoc","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:7647370","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7647370","pdf_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Am Med Inform Assoc","raw_type":"Text"},"sustainable_development_goals":[{"display_name":"Quality Education","score":0.7799999713897705,"id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W848063403","https://openalex.org/W1550258693","https://openalex.org/W2104381725","https://openalex.org/W2119717200","https://openalex.org/W2129367118","https://openalex.org/W2159583324","https://openalex.org/W2159636537","https://openalex.org/W2168041406","https://openalex.org/W2170189740","https://openalex.org/W2187089797","https://openalex.org/W2252979829","https://openalex.org/W2753068549","https://openalex.org/W2765742249","https://openalex.org/W2804220263","https://openalex.org/W2896457183","https://openalex.org/W2997253122","https://openalex.org/W3099032418"],"related_works":["https://openalex.org/W3092040890","https://openalex.org/W3107474891","https://openalex.org/W2528512298","https://openalex.org/W2368651715","https://openalex.org/W3163741274","https://openalex.org/W3166593409","https://openalex.org/W2751754833","https://openalex.org/W3201556757","https://openalex.org/W1515542156","https://openalex.org/W3002472320"],"abstract_inverted_index":{"OBJECTIVE:":[0],"We":[1,233],"explored":[2],"how":[3],"knowledge":[4,49,56,103,184],"embeddings":[5,50,104],"(KEs)":[6],"learned":[7,37],"from":[8,43],"the":[9,17,44,91,99,135,138,148,153,161,180,187,204,218,235],"Unified":[10],"Medical":[11],"Language":[12],"System":[13],"(UMLS)":[14],"Metathesaurus":[15,189,220],"impact":[16,162],"quality":[18],"of":[19,26,34,73,78,118,126,137,163,170,182,198,206],"relation":[20,41,84,100,116,141,145,210,223,244],"extraction":[21,101,142,146,211,224,245],"on":[22,143,227,246],"2":[23,144,195,247],"diverse":[24],"sets":[25],"biomedical":[27,79,228],"texts.":[28],"MATERIALS":[29],"AND":[30],"METHODS:":[31],"Two":[32],"forms":[33,197],"KEs":[35,66,113,208],"were":[36],"for":[38,76,115,243],"concepts":[39,80],"and":[40,52,83,120,152,172],"types":[42,85,117],"UMLS":[45,92,188,219],"Metathesaurus,":[46],"namely":[47],"lexicalized":[48],"(LKEs)":[51],"unlexicalized":[53,65,112,130],"KEs.":[54],"A":[55],"embedding":[57],"encoder":[58],"(KEE)":[59],"enabled":[60],"learning":[61],"either":[62,109,127],"LKEs":[63,75,110,128,164,215],"or":[64,111,129],"as":[67,69],"well":[68],"neural":[70],"models":[71],"capable":[72],"producing":[74],"mentions":[77],"in":[81,90,132,140,186,190,209,221],"texts":[82,229],"that":[86],"are":[87],"not":[88,177],"encoded":[89,185],"Metathesaurus.":[93],"This":[94],"allowed":[95],"us":[96],"to":[97],"design":[98],"with":[102],"(REKE)":[105],"system,":[106,237],"which":[107,238],"incorporates":[108],"produced":[114],"interest":[119],"their":[121],"arguments.":[122],"RESULTS:":[123],"The":[124],"incorporation":[125],"KE":[131],"REKE":[133,176,236],"advances":[134],"state":[136],"art":[139],"datasets:":[147],"2010":[149],"i2b2/VA":[150],"dataset":[151],"2013":[154],"Drug-Drug":[155],"Interaction":[156],"Extraction":[157],"Challenge":[158],"corpus.":[159],"Moreover,":[160],"is":[165],"superior,":[166],"achieving":[167],"F1":[168],"scores":[169],"78.2":[171],"82.0,":[173],"respectively.":[174],"DISCUSSION:":[175],"only":[178],"highlights":[179],"importance":[181],"incorporating":[183,207],"a":[191,222],"novel":[192],"way,":[193],"through":[194],"possible":[196],"KEs,":[199],"but":[200],"it":[201],"also":[202],"showcases":[203],"subtleties":[205],"systems.":[212],"CONCLUSIONS:":[213],"Incorporating":[214],"informed":[216],"by":[217],"system":[225],"operating":[226],"shows":[230],"significant":[231],"promise.":[232],"present":[234],"establishes":[239],"new":[240],"state-of-the-art":[241],"results":[242],"datasets":[248],"when":[249],"using":[250],"LKEs.":[251]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
