{"id":"https://openalex.org/W2232325453","doi":"https://doi.org/10.1136/amiajnl-2013-001612","title":"Mining clinical text for signals of adverse drug-drug interactions","display_name":"Mining clinical text for signals of adverse drug-drug interactions","publication_year":2013,"publication_date":"2013-10-25","ids":{"openalex":"https://openalex.org/W2232325453","doi":"https://doi.org/10.1136/amiajnl-2013-001612","mag":"2232325453","pmid":"https://pubmed.ncbi.nlm.nih.gov/24158091"},"language":"en","primary_location":{"id":"doi:10.1136/amiajnl-2013-001612","is_oa":true,"landing_page_url":"https://doi.org/10.1136/amiajnl-2013-001612","pdf_url":"https://academic.oup.com/jamia/article-pdf/21/2/353/6114478/21-2-353.pdf","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":"bronze","oa_url":"https://academic.oup.com/jamia/article-pdf/21/2/353/6114478/21-2-353.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088004913","display_name":"Srinivasan Iyer","orcid":"https://orcid.org/0000-0002-6186-2603"},"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":true,"raw_author_name":"Srinivasan V Iyer","raw_affiliation_strings":["Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043102729","display_name":"Rave Harpaz","orcid":null},"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":"Rave Harpaz","raw_affiliation_strings":["Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059906626","display_name":"Paea LePendu","orcid":"https://orcid.org/0000-0001-7358-931X"},"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":"Paea LePendu","raw_affiliation_strings":["Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030710827","display_name":"Anna Bauer\u2010Mehren","orcid":"https://orcid.org/0000-0001-8905-9161"},"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":"Anna Bauer-Mehren","raw_affiliation_strings":["Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041175834","display_name":"Nigam H. Shah","orcid":"https://orcid.org/0000-0001-9385-7158"},"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":"Nigam H Shah","raw_affiliation_strings":["Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5088004913"],"corresponding_institution_ids":["https://openalex.org/I97018004"],"apc_list":{"value":3967,"currency":"USD","value_usd":3967},"apc_paid":null,"fwci":6.772,"has_fulltext":false,"cited_by_count":174,"citation_normalized_percentile":{"value":0.98021357,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"21","issue":"2","first_page":"353","last_page":"362"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11943","display_name":"Pharmacovigilance and Adverse Drug Reactions","score":0.9520999789237976,"subfield":{"id":"https://openalex.org/subfields/3005","display_name":"Toxicology"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11943","display_name":"Pharmacovigilance and Adverse Drug Reactions","score":0.9520999789237976,"subfield":{"id":"https://openalex.org/subfields/3005","display_name":"Toxicology"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.025200000032782555,"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/T13702","display_name":"Machine Learning in Healthcare","score":0.006200000178068876,"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/drug","display_name":"Drug","score":0.7767418622970581},{"id":"https://openalex.org/keywords/adverse-effect","display_name":"Adverse effect","score":0.46383604407310486},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.4630480110645294},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.447897732257843},{"id":"https://openalex.org/keywords/adverse-drug-reaction","display_name":"Adverse drug reaction","score":0.43458032608032227},{"id":"https://openalex.org/keywords/intensive-care-medicine","display_name":"Intensive care medicine","score":0.33398354053497314},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.2857365608215332}],"concepts":[{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.7767418622970581},{"id":"https://openalex.org/C197934379","wikidata":"https://www.wikidata.org/wiki/Q2047938","display_name":"Adverse effect","level":2,"score":0.46383604407310486},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.4630480110645294},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.447897732257843},{"id":"https://openalex.org/C2780542314","wikidata":"https://www.wikidata.org/wiki/Q45959","display_name":"Adverse drug reaction","level":3,"score":0.43458032608032227},{"id":"https://openalex.org/C177713679","wikidata":"https://www.wikidata.org/wiki/Q679690","display_name":"Intensive care medicine","level":1,"score":0.33398354053497314},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.2857365608215332}],"mesh":[{"descriptor_ui":"D004347","descriptor_name":"Drug Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004347","descriptor_name":"Drug Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004347","descriptor_name":"Drug Interactions","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":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1136/amiajnl-2013-001612","is_oa":true,"landing_page_url":"https://doi.org/10.1136/amiajnl-2013-001612","pdf_url":"https://academic.oup.com/jamia/article-pdf/21/2/353/6114478/21-2-353.pdf","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:24158091","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24158091","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:3306858","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3932451","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":null,"raw_type":"Text"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt8v1489sh","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/8v1489sh","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of the American Medical Informatics Association, vol 21, iss 2","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1136/amiajnl-2013-001612","is_oa":true,"landing_page_url":"https://doi.org/10.1136/amiajnl-2013-001612","pdf_url":"https://academic.oup.com/jamia/article-pdf/21/2/353/6114478/21-2-353.pdf","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"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.6299999952316284}],"awards":[{"id":"https://openalex.org/G1362058311","display_name":null,"funder_award_id":"R01 GM101430","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2225135173","display_name":null,"funder_award_id":"U54 HG004028","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G8000693649","display_name":null,"funder_award_id":"GM101430","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320307856","display_name":"World Health Organization","ror":"https://ror.org/01f80g185"},{"id":"https://openalex.org/F4320308757","display_name":"Foundation for Anesthesia Education and Research","ror":"https://ror.org/04d16a047"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320333491","display_name":"Palo Alto Medical Foundation","ror":null},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2232325453.pdf"},"referenced_works_count":64,"referenced_works":["https://openalex.org/W27189800","https://openalex.org/W45588658","https://openalex.org/W91361357","https://openalex.org/W311004003","https://openalex.org/W1492818624","https://openalex.org/W1616099694","https://openalex.org/W1960737837","https://openalex.org/W1967555951","https://openalex.org/W1969879564","https://openalex.org/W1981809734","https://openalex.org/W1989986729","https://openalex.org/W1994929347","https://openalex.org/W1995077739","https://openalex.org/W2002430005","https://openalex.org/W2004281677","https://openalex.org/W2007138823","https://openalex.org/W2009313526","https://openalex.org/W2012487908","https://openalex.org/W2019515024","https://openalex.org/W2021372314","https://openalex.org/W2021805817","https://openalex.org/W2021920492","https://openalex.org/W2023141245","https://openalex.org/W2026447576","https://openalex.org/W2029592334","https://openalex.org/W2031299502","https://openalex.org/W2038397660","https://openalex.org/W2039594635","https://openalex.org/W2040555718","https://openalex.org/W2057881684","https://openalex.org/W2065176229","https://openalex.org/W2088263677","https://openalex.org/W2091582819","https://openalex.org/W2093015714","https://openalex.org/W2098730643","https://openalex.org/W2103018059","https://openalex.org/W2106417713","https://openalex.org/W2107516065","https://openalex.org/W2109482131","https://openalex.org/W2110922423","https://openalex.org/W2112656327","https://openalex.org/W2115259143","https://openalex.org/W2117397379","https://openalex.org/W2118415328","https://openalex.org/W2119002393","https://openalex.org/W2122532950","https://openalex.org/W2126344780","https://openalex.org/W2133629218","https://openalex.org/W2142572836","https://openalex.org/W2147845824","https://openalex.org/W2148288796","https://openalex.org/W2154048976","https://openalex.org/W2161554615","https://openalex.org/W2168528736","https://openalex.org/W2171548451","https://openalex.org/W2339812389","https://openalex.org/W2410165175","https://openalex.org/W2517346518","https://openalex.org/W3085323863","https://openalex.org/W3122049309","https://openalex.org/W4230604660","https://openalex.org/W4246192712","https://openalex.org/W4251624698","https://openalex.org/W4292198115"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W3031052312","https://openalex.org/W4389568370","https://openalex.org/W3032375762","https://openalex.org/W1995515455","https://openalex.org/W2080531066","https://openalex.org/W3108674512","https://openalex.org/W1506200166","https://openalex.org/W1489783725","https://openalex.org/W2148612803"],"abstract_inverted_index":{"BACKGROUND":[0],"AND":[1],"OBJECTIVE:":[2],"Electronic":[3],"health":[4],"records":[5],"(EHRs)":[6],"are":[7,32],"increasingly":[8],"being":[9],"used":[10],"to":[11,21,83,99,175,229],"complement":[12],"the":[13,60,158,171,184,235],"FDA":[14],"Adverse":[15],"Event":[16],"Reporting":[17],"System":[18],"(FAERS)":[19],"and":[20,38,71,107,170,194,233],"enable":[22],"active":[23],"pharmacovigilance.":[24],"Over":[25],"30%":[26],"of":[27,63,69,87,123,177,186,192,207,211,237],"all":[28],"adverse":[29,109,238],"drug":[30,70,200,218,243,255],"reactions":[31],"caused":[33],"by":[34,152],"drug-drug":[35],"interactions":[36],"(DDIs)":[37],"result":[39],"in":[40,253,261],"significant":[41,101],"morbidity":[42],"every":[43],"year,":[44],"making":[45],"their":[46],"early":[47,190],"identification":[48],"vital.":[49],"We":[50,66,93,182],"present":[51],"an":[52,222],"approach":[53],"for":[54,90,189,195,198],"identifying":[55,196],"DDI":[56,136,231],"signals":[57,232],"directly":[58,138,245],"from":[59,74,80,127,139,180,246],"textual":[61],"portion":[62],"EHRs.":[64],"METHODS:":[65],"recognize":[67],"mentions":[68,89],"event":[72,213],"concepts":[73],"over":[75],"50":[76],"million":[77],"clinical":[78,247,262],"notes":[79],"two":[81,166],"sites":[82],"create":[84],"a":[85,120,205],"timeline":[86],"concept":[88],"each":[91],"patient.":[92],"then":[94],"use":[95],"adjusted":[96],"disproportionality":[97],"ratios":[98],"identify":[100,230],"drug-drug-event":[102],"associations":[103,137],"among":[104,215,240],"1165":[105],"drugs":[106],"14":[108],"events.":[110],"To":[111],"validate":[112],"our":[113,117,153,187],"results,":[114],"we":[115,203],"evaluate":[116],"performance":[118,172],"on":[119,165,217,221,242],"gold":[121,154],"standard":[122,155],"1698":[124],"DDIs":[125,179,193],"curated":[126],"existing":[128],"knowledge":[129],"bases,":[130],"as":[131,133,150,258,260],"well":[132,259],"with":[134],"signaling":[135,178],"FAERS":[140],"using":[141],"established":[142],"methods.":[143],"RESULTS:":[144],"Our":[145],"method":[146,188],"achieves":[147],"good":[148],"performance,":[149],"measured":[151],"(area":[156],"under":[157],"receiver":[159],"operator":[160],"characteristic":[161],"(ROC)":[162],"curve":[163],">80%),":[164],"independent":[167],"EHR":[168,223],"datasets":[169],"is":[173,227],"comparable":[174],"that":[176],"FAERS.":[181],"demonstrate":[183],"utility":[185,252],"detection":[191],"alternatives":[197],"risky":[199],"combinations.":[201],"Finally,":[202],"publish":[204],"first":[206],"its":[208],"kind":[209],"database":[210],"population":[212],"rates":[214],"patients":[216,241],"combinations":[219],"based":[220],"corpus.":[224],"CONCLUSIONS:":[225],"It":[226],"feasible":[228],"estimate":[234],"rate":[236],"events":[239],"combinations,":[244],"text;":[248],"this":[249],"could":[250],"have":[251],"prioritizing":[254],"interaction":[256],"surveillance":[257],"decision":[263],"support.":[264]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":13},{"year":2023,"cited_by_count":11},{"year":2022,"cited_by_count":14},{"year":2021,"cited_by_count":12},{"year":2020,"cited_by_count":19},{"year":2019,"cited_by_count":20},{"year":2018,"cited_by_count":15},{"year":2017,"cited_by_count":20},{"year":2016,"cited_by_count":13},{"year":2015,"cited_by_count":19},{"year":2014,"cited_by_count":6}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
