{"id":"https://openalex.org/W4316041281","doi":"https://doi.org/10.3389/frai.2022.1051724","title":"Clinical concept recognition: Evaluation of existing systems on EHRs","display_name":"Clinical concept recognition: Evaluation of existing systems on EHRs","publication_year":2023,"publication_date":"2023-01-13","ids":{"openalex":"https://openalex.org/W4316041281","doi":"https://doi.org/10.3389/frai.2022.1051724","pmid":"https://pubmed.ncbi.nlm.nih.gov/36714202"},"language":"en","primary_location":{"id":"doi:10.3389/frai.2022.1051724","is_oa":true,"landing_page_url":"https://doi.org/10.3389/frai.2022.1051724","pdf_url":"https://www.frontiersin.org/articles/10.3389/frai.2022.1051724/pdf","source":{"id":"https://openalex.org/S4210197006","display_name":"Frontiers in Artificial Intelligence","issn_l":"2624-8212","issn":["2624-8212"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Artificial Intelligence","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/articles/10.3389/frai.2022.1051724/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079554685","display_name":"Juan Antonio Lossio-Ventura","orcid":"https://orcid.org/0000-0003-0996-2356"},"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/I4210158500","display_name":"National Institute of Mental Health","ror":"https://ror.org/04xeg9z08","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210158500"]},{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Juan Antonio Lossio-Ventura","raw_affiliation_strings":["Biomedical Informatics Research, Stanford University, Stanford, CA, United States","National Institute of Mental Health, National Institutes of Health, Bethesda, MD, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Informatics Research, Stanford University, Stanford, CA, United States","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"National Institute of Mental Health, National Institutes of Health, Bethesda, MD, United States","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210158500"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088482976","display_name":"Ran Sun","orcid":"https://orcid.org/0000-0002-5181-3242"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ran Sun","raw_affiliation_strings":["Biomedical Informatics Research, Stanford University, Stanford, CA, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Informatics Research, Stanford University, Stanford, CA, United States","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056324335","display_name":"Sebastien Boussard","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sebastien Boussard","raw_affiliation_strings":["College of Engineering, Boston University, Boston, MA, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Engineering, Boston University, Boston, MA, United States","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023944464","display_name":"Tina Hernandez\u2010Boussard","orcid":"https://orcid.org/0000-0001-6553-3455"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tina Hernandez-Boussard","raw_affiliation_strings":["Biomedical Informatics Research, Stanford University, Stanford, CA, United States","Department of Biomedical Data Sciences, Stanford University, Stanford, CA, United States","Department of Surgery, Stanford University, Stanford, CA, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Informatics Research, Stanford University, Stanford, CA, United States","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Biomedical Data Sciences, Stanford University, Stanford, CA, United States","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Surgery, Stanford University, Stanford, CA, United States","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5079554685"],"corresponding_institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210158500","https://openalex.org/I97018004"],"apc_list":{"value":2125,"currency":"USD","value_usd":2125},"apc_paid":{"value":2125,"currency":"USD","value_usd":2125},"fwci":0.749,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.6613566,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"5","issue":null,"first_page":"1051724","last_page":"1051724"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.4278999865055084,"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":0.4278999865055084,"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":0.28040000796318054,"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":0.10490000247955322,"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":0.495199590921402},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3786372244358063},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3232213258743286}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.495199590921402},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3786372244358063},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3232213258743286}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/frai.2022.1051724","is_oa":true,"landing_page_url":"https://doi.org/10.3389/frai.2022.1051724","pdf_url":"https://www.frontiersin.org/articles/10.3389/frai.2022.1051724/pdf","source":{"id":"https://openalex.org/S4210197006","display_name":"Frontiers in Artificial Intelligence","issn_l":"2624-8212","issn":["2624-8212"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Artificial Intelligence","raw_type":"journal-article"},{"id":"pmid:36714202","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36714202","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":"Frontiers in artificial intelligence","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9880223","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9880223","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9880223/pdf/frai-05-1051724.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":"Front Artif Intell","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:95c143504541402c8149993e14f2bfdf","is_oa":true,"landing_page_url":"https://doaj.org/article/95c143504541402c8149993e14f2bfdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Artificial Intelligence, Vol 5 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3389/frai.2022.1051724","is_oa":true,"landing_page_url":"https://doi.org/10.3389/frai.2022.1051724","pdf_url":"https://www.frontiersin.org/articles/10.3389/frai.2022.1051724/pdf","source":{"id":"https://openalex.org/S4210197006","display_name":"Frontiers in Artificial Intelligence","issn_l":"2624-8212","issn":["2624-8212"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Artificial Intelligence","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G122144234","display_name":null,"funder_award_id":"R01CA183962","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G3900556074","display_name":null,"funder_award_id":"R01 CA183962","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G603925452","display_name":null,"funder_award_id":"R01CA183962","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4316041281.pdf"},"referenced_works_count":67,"referenced_works":["https://openalex.org/W42510333","https://openalex.org/W49934205","https://openalex.org/W86609720","https://openalex.org/W102787101","https://openalex.org/W1504212872","https://openalex.org/W1521626219","https://openalex.org/W1602694398","https://openalex.org/W1637593105","https://openalex.org/W1666916593","https://openalex.org/W2082302018","https://openalex.org/W2095896451","https://openalex.org/W2114039834","https://openalex.org/W2114388055","https://openalex.org/W2122402213","https://openalex.org/W2123241698","https://openalex.org/W2125117006","https://openalex.org/W2136224372","https://openalex.org/W2137767404","https://openalex.org/W2139865360","https://openalex.org/W2143902665","https://openalex.org/W2146089916","https://openalex.org/W2159583324","https://openalex.org/W2168041406","https://openalex.org/W2239231358","https://openalex.org/W2250618585","https://openalex.org/W2283041611","https://openalex.org/W2345195116","https://openalex.org/W2396881363","https://openalex.org/W2406368917","https://openalex.org/W2543360016","https://openalex.org/W2582146834","https://openalex.org/W2606156285","https://openalex.org/W2735580341","https://openalex.org/W2757504960","https://openalex.org/W2768488789","https://openalex.org/W2769851464","https://openalex.org/W2783547086","https://openalex.org/W2787243831","https://openalex.org/W2789244308","https://openalex.org/W2803290558","https://openalex.org/W2809579039","https://openalex.org/W2891469329","https://openalex.org/W2915623326","https://openalex.org/W2930139824","https://openalex.org/W2946102094","https://openalex.org/W2950023917","https://openalex.org/W2967387394","https://openalex.org/W3004047707","https://openalex.org/W3004763623","https://openalex.org/W3025047276","https://openalex.org/W3042528607","https://openalex.org/W3100271366","https://openalex.org/W3106224367","https://openalex.org/W3122634526","https://openalex.org/W3169284847","https://openalex.org/W3172427031","https://openalex.org/W3173561451","https://openalex.org/W4220989182","https://openalex.org/W4381594492","https://openalex.org/W6601735882","https://openalex.org/W6602039197","https://openalex.org/W6603505381","https://openalex.org/W6604181502","https://openalex.org/W6636672007","https://openalex.org/W6748439432","https://openalex.org/W6784223880","https://openalex.org/W6796399376"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Objective:":[0],"The":[1,73,119],"adoption":[2],"of":[3,12,43,67,75,83,138,170,248,267],"electronic":[4],"health":[5],"records":[6],"(EHRs)":[7],"has":[8],"produced":[9],"enormous":[10],"amounts":[11],"data,":[13],"creating":[14],"research":[15,77],"opportunities":[16],"in":[17,70,141,191,205,221],"clinical":[18,30,89,154,235,270,287,298],"data":[19],"sciences.":[20],"Several":[21,228],"concept":[22,45,97,155,229,271,292],"recognition":[23,46,98,230,293],"systems":[24,68,85,140,220,231,252,282],"have":[25],"been":[26],"developed":[27,51],"to":[28,58,79,86,233,285,296],"facilitate":[29],"information":[31,194,236,299],"extraction":[32,255,272,279,300],"from":[33,91,237],"these":[34,139],"data.":[35,239],"While":[36],"studies":[37],"exist":[38,232],"that":[39,260],"compare":[40],"the":[41,71,81,127,131,136,159,185,263],"performance":[42,82,121,137,161],"many":[44],"systems,":[47,99],"they":[48],"are":[49],"typically":[50],"internally":[52],"and":[53,64,107,116,130,150,164,172,177,179,274],"may":[54],"be":[55],"biased":[56],"due":[57],"different":[59,254],"internal":[60],"implementations,":[61],"parameters":[62],"used,":[63],"limited":[65],"number":[66],"included":[69,112],"evaluations.":[72],"goal":[74],"this":[76],"is":[78],"evaluate":[80],"existing":[84],"retrieve":[87],"relevant":[88,295],"concepts":[90,110,224],"EHRs.":[92],"Methods:":[93],"We":[94],"investigated":[95],"six":[96,249],"including":[100,145],"CLAMP,":[101],"cTAKES,":[102],"MetaMap,":[103],"NCBO":[104,199,213],"Annotator,":[105],"QuickUMLS,":[106],"ScispaCy.":[108],"Clinical":[109],"extracted":[111],"procedures,":[113],"disorders,":[114],"medications,":[115],"anatomical":[117],"location.":[118],"system":[120,294],"was":[122],"evaluated":[123],"on":[124,162,175,182],"two":[125],"datasets:":[126],"2010":[128],"i2b2":[129],"MIMIC-III.":[132,183],"Additionally,":[133],"we":[134],"assessed":[135],"five":[142,186],"challenging":[143,187],"situations,":[144,188],"negation,":[146],"severity,":[147],"abbreviation,":[148],"ambiguity,":[149],"misspelling.":[151],"Results:":[152],"For":[153],"extraction,":[156],"CLAMP":[157,203,217,261],"achieved":[158],"best":[160],"exact":[163],"inexact":[165],"matching,":[166],"with":[167],"an":[168,243],"F-score":[169],"0.70":[171],"0.94,":[173],"respectively,":[174,181],"i2b2;":[176],"0.39":[178],"0.50,":[180],"Across":[184],"ScispaCy":[189],"excelled":[190],"extracting":[192,206,222],"abbreviation":[193],"(F-score:":[195,201,215],"0.86)":[196],"followed":[197,211],"by":[198,212,246],"Annotator":[200,214],"0.79).":[202],"outperformed":[204,218],"severity":[207],"terms":[208],"(F-score":[209,225],"0.73)":[210],"0.68).":[216],"other":[219,286],"negated":[223],"0.63).":[226],"Conclusions:":[227],"extract":[234],"unstructured":[238],"This":[240],"study":[241],"provides":[242,262,283],"external":[244],"evaluation":[245],"end-users":[247],"commonly":[250],"used":[251],"across":[253,281],"tasks.":[256],"Our":[257],"findings":[258],"suggest":[259],"most":[264],"comprehensive":[265],"set":[266],"annotations":[268],"for":[269],"tasks":[273,280],"associated":[275],"challenges.":[276],"Comparing":[277],"standard":[278],"guidance":[284],"researchers":[288],"when":[289],"selecting":[290],"a":[291],"their":[297],"task.":[301]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
