{"id":"https://openalex.org/W2416643236","doi":null,"title":"Sophia: A Expedient UMLS Concept Extraction Annotator.","display_name":"Sophia: A Expedient UMLS Concept Extraction Annotator.","publication_year":2014,"publication_date":"2014-01-01","ids":{"openalex":"https://openalex.org/W2416643236","mag":"2416643236","pmid":"https://pubmed.ncbi.nlm.nih.gov/25954351","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/4420011"},"language":"en","primary_location":{"id":"pmh:oai:pubmedcentral.nih.gov:4420011","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4420011","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,"listed_in":[],"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":"AMIA Annu Symp Proc","raw_type":"Text"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4420011","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007564242","display_name":"Guy Divita","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]},{"id":"https://openalex.org/I4210089864","display_name":"VA Salt Lake City Healthcare System","ror":"https://ror.org/007fyq698","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1322918889","https://openalex.org/I2799886695","https://openalex.org/I4210089864","https://openalex.org/I4210113540"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Guy Divita","raw_affiliation_strings":["VA Salt Lake City Health Care System and University of Utah School of Medicine, Salt Lake City, UT"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"VA Salt Lake City Health Care System and University of Utah School of Medicine, Salt Lake City, UT","institution_ids":["https://openalex.org/I223532165","https://openalex.org/I4210089864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047536976","display_name":"Qing Treitler Zeng","orcid":"https://orcid.org/0000-0002-3439-7179","observed_orcids":["https://orcid.org/0000-0002-3439-7179"]},"institutions":[{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]},{"id":"https://openalex.org/I4210089864","display_name":"VA Salt Lake City Healthcare System","ror":"https://ror.org/007fyq698","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1322918889","https://openalex.org/I2799886695","https://openalex.org/I4210089864","https://openalex.org/I4210113540"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qing T Zeng","raw_affiliation_strings":["VA Salt Lake City Health Care System and University of Utah School of Medicine, Salt Lake City, UT"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"VA Salt Lake City Health Care System and University of Utah School of Medicine, Salt Lake City, UT","institution_ids":["https://openalex.org/I223532165","https://openalex.org/I4210089864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005755665","display_name":"Adi V. Gundlapalli","orcid":"https://orcid.org/0000-0002-7423-7903","observed_orcids":["https://orcid.org/0000-0002-7423-7903"]},"institutions":[{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]},{"id":"https://openalex.org/I4210089864","display_name":"VA Salt Lake City Healthcare System","ror":"https://ror.org/007fyq698","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1322918889","https://openalex.org/I2799886695","https://openalex.org/I4210089864","https://openalex.org/I4210113540"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adi V Gundlapalli","raw_affiliation_strings":["VA Salt Lake City Health Care System and University of Utah School of Medicine, Salt Lake City, UT"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"VA Salt Lake City Health Care System and University of Utah School of Medicine, Salt Lake City, UT","institution_ids":["https://openalex.org/I223532165","https://openalex.org/I4210089864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037435182","display_name":"Scott L. DuVall","orcid":"https://orcid.org/0000-0002-4898-3865","observed_orcids":["https://orcid.org/0000-0002-4898-3865"]},"institutions":[{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]},{"id":"https://openalex.org/I4210089864","display_name":"VA Salt Lake City Healthcare System","ror":"https://ror.org/007fyq698","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1322918889","https://openalex.org/I2799886695","https://openalex.org/I4210089864","https://openalex.org/I4210113540"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Scott Duvall","raw_affiliation_strings":["VA Salt Lake City Health Care System and University of Utah School of Medicine, Salt Lake City, UT"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"VA Salt Lake City Health Care System and University of Utah School of Medicine, Salt Lake City, UT","institution_ids":["https://openalex.org/I223532165","https://openalex.org/I4210089864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069032571","display_name":"Jonathan R. Nebeker","orcid":"https://orcid.org/0000-0001-5355-5008","observed_orcids":["https://orcid.org/0000-0001-5355-5008"]},"institutions":[{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]},{"id":"https://openalex.org/I4210089864","display_name":"VA Salt Lake City Healthcare System","ror":"https://ror.org/007fyq698","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1322918889","https://openalex.org/I2799886695","https://openalex.org/I4210089864","https://openalex.org/I4210113540"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan Nebeker","raw_affiliation_strings":["VA Salt Lake City Health Care System and University of Utah School of Medicine, Salt Lake City, UT"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"VA Salt Lake City Health Care System and University of Utah School of Medicine, Salt Lake City, UT","institution_ids":["https://openalex.org/I223532165","https://openalex.org/I4210089864"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078072232","display_name":"Matthew H. Samore","orcid":"https://orcid.org/0000-0002-4862-9196","observed_orcids":["https://orcid.org/0000-0002-4862-9196"]},"institutions":[{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]},{"id":"https://openalex.org/I4210089864","display_name":"VA Salt Lake City Healthcare System","ror":"https://ror.org/007fyq698","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1322918889","https://openalex.org/I2799886695","https://openalex.org/I4210089864","https://openalex.org/I4210113540"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew H Samore","raw_affiliation_strings":["VA Salt Lake City Health Care System and University of Utah School of Medicine, Salt Lake City, UT"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"VA Salt Lake City Health Care System and University of Utah School of Medicine, Salt Lake City, UT","institution_ids":["https://openalex.org/I223532165","https://openalex.org/I4210089864"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.6935,"has_fulltext":false,"cited_by_count":31,"citation_normalized_percentile":{"value":0.8791627,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":99},"biblio":{"volume":"2014","issue":null,"first_page":"467","last_page":"76"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/2718","display_name":"Health Informatics"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/2718","display_name":"Health Informatics"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T13702","display_name":"Machine Learning in Healthcare","score":0.0003000000142492354,"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/T10350","display_name":"Electronic Health Records Systems","score":0.00019999999494757503,"subfield":{"id":"https://openalex.org/subfields/3605","display_name":"Health Information Management"},"field":{"id":"https://openalex.org/fields/36","display_name":"Health Professions"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/sophia","display_name":"Sophia","score":0.5929999947547913},{"id":"https://openalex.org/keywords/clinical-natural-language-processing","display_name":"clinical natural language processing","score":0.8119999766349792},{"id":"https://openalex.org/keywords/electronic-health-records","display_name":"electronic health records","score":0.8270000219345093},{"id":"https://openalex.org/keywords/department-of-veterans-affairs","display_name":"Department of Veterans Affairs","score":0.6259999871253967},{"id":"https://openalex.org/keywords/metamap","display_name":"MetaMap","score":0.7450000047683716},{"id":"https://openalex.org/keywords/ctakes","display_name":"cTAKES","score":0.9950000047683716},{"id":"https://openalex.org/keywords/benchmarking","display_name":"benchmarking","score":0.503000020980835}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.6492433547973633},{"id":"https://openalex.org/C100660578","wikidata":"https://www.wikidata.org/wiki/Q18733","display_name":"Recall","level":2,"score":0.6309554576873779},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.6111347079277039},{"id":"https://openalex.org/C69505689","wikidata":"https://www.wikidata.org/wiki/Q455338","display_name":"Unified Medical Language System","level":2,"score":0.5648506283760071},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5608606338500977},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.46700987219810486},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.4131464660167694},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.34721648693084717},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.07633832097053528},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D014481","descriptor_name":"United States","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014493","descriptor_name":"United States Department of Veterans Affairs","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":true},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"pmh:oai:pubmedcentral.nih.gov:4420011","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4420011","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,"listed_in":[],"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":"AMIA Annu Symp Proc","raw_type":"Text"},{"id":"pmid:25954351","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25954351","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,"listed_in":[],"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":"AMIA ... Annual Symposium proceedings. AMIA Symposium","raw_type":"Journal Article"},{"id":"mag:2416643236","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25954351","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,"listed_in":[],"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":null,"is_accepted":false,"is_published":false,"raw_source_name":"PubMed","raw_type":null}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:4420011","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4420011","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,"listed_in":[],"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":"AMIA Annu Symp Proc","raw_type":"Text"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W102264027","https://openalex.org/W133035964","https://openalex.org/W1550258693","https://openalex.org/W1602694398","https://openalex.org/W1637593105","https://openalex.org/W1829379010","https://openalex.org/W2146089916","https://openalex.org/W2161548889","https://openalex.org/W2164790407","https://openalex.org/W2168041406","https://openalex.org/W2409132800"],"related_works":["https://openalex.org/W3206589498","https://openalex.org/W763180640","https://openalex.org/W2415814795","https://openalex.org/W2604854480","https://openalex.org/W2899165272","https://openalex.org/W3090480605","https://openalex.org/W2911254434","https://openalex.org/W2891469329","https://openalex.org/W7204105101","https://openalex.org/W1851638456"],"abstract_inverted_index":{"An":[0],"opportunity":[1],"exists":[2],"for":[3,141],"meaningful":[4],"concept":[5,46],"extraction":[6,47,57,144],"and":[7,30,55,72,78,90,95,104,112,131],"indexing":[8],"from":[9],"large":[10],"corpora":[11],"of":[12,74,118],"clinical":[13],"notes":[14],"in":[15],"the":[16,69,132],"Veterans":[17],"Affairs":[18],"(VA)":[19],"electronic":[20],"medical":[21],"record.":[22],"Currently":[23],"available":[24],"tools":[25],"such":[26],"as":[27,86],"MetaMap,":[28],"cTAKES":[29,89,103,130],"HITex":[31],"do":[32],"not":[33],"scale":[34],"up":[35],"to":[36,51,88,102,116,124],"address":[37,56],"this":[38],"big":[39],"data":[40],"need.":[41],"Sophia,":[42],"a":[43,53,138],"rapid":[44],"UMLS":[45],"annotator":[48],"was":[49,100],"developed":[50],"fulfill":[52],"mandate":[54],"where":[58],"high":[59],"throughput":[60],"is":[61],"needed":[62],"while":[63],"preserving":[64],"performance.":[65],"We":[66],"report":[67],"on":[68,84],"development,":[70],"testing":[71],"benchmarking":[73],"Sophia":[75,80,123,136],"against":[76],"MetaMap":[77,91,108,134],"cTAKEs.":[79],"demonstrated":[81],"improved":[82],"performance":[83],"recall":[85],"compared":[87],"(0.71":[92],"vs":[93,110],"0.66":[94],"0.38).":[96],"The":[97],"overall":[98],"f-score":[99],"similar":[101],"an":[105],"improvement":[106],"over":[107],"(0.53":[109],"0.57":[111],"0.43).":[113],"With":[114],"regard":[115],"speed":[117],"processing":[119],"records,":[120],"we":[121],"noted":[122],"be":[125],"several":[126],"fold":[127],"faster":[128],"than":[129],"scaled-out":[133],"service.":[135],"offers":[137],"viable":[139],"alternative":[140],"high-throughput":[142],"information":[143],"tasks.":[145]},"counts_by_year":[{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":3}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}
