{"id":"https://openalex.org/W2113031313","doi":"https://doi.org/10.1093/jamia/ocv102","title":"A method for systematic discovery of adverse drug events from clinical notes","display_name":"A method for systematic discovery of adverse drug events from clinical notes","publication_year":2015,"publication_date":"2015-07-31","ids":{"openalex":"https://openalex.org/W2113031313","doi":"https://doi.org/10.1093/jamia/ocv102","mag":"2113031313","pmid":"https://pubmed.ncbi.nlm.nih.gov/26232442"},"language":"en","primary_location":{"id":"doi:10.1093/jamia/ocv102","is_oa":true,"landing_page_url":"https://doi.org/10.1093/jamia/ocv102","pdf_url":"https://academic.oup.com/jamia/article-pdf/22/6/1196/17376791/ocv102.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/22/6/1196/17376791/ocv102.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044802363","display_name":"Guan Wang","orcid":"https://orcid.org/0000-0003-2341-3054"},"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":"Guan Wang","raw_affiliation_strings":["Stanford University, Center for Biomedical Informatics, Stanford, California, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanford University, Center for Biomedical Informatics, Stanford, California, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102792254","display_name":"Kenneth Jung","orcid":"https://orcid.org/0000-0001-8203-2513"},"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":"Kenneth Jung","raw_affiliation_strings":["Stanford University, Center for Biomedical Informatics, Stanford, California, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanford University, Center for Biomedical Informatics, Stanford, California, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046047290","display_name":"Rainer Winnenburg","orcid":"https://orcid.org/0000-0002-2770-2809"},"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":"Rainer Winnenburg","raw_affiliation_strings":["Stanford University, Center for Biomedical Informatics, Stanford, California, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanford University, Center for Biomedical Informatics, 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 University, Center for Biomedical Informatics, Stanford, California, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanford University, Center for Biomedical Informatics, Stanford, California, USA","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I97018004"],"apc_list":{"value":3967,"currency":"USD","value_usd":3967},"apc_paid":null,"fwci":3.9159,"has_fulltext":true,"cited_by_count":75,"citation_normalized_percentile":{"value":0.94247514,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"22","issue":"6","first_page":"1196","last_page":"1204"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9976000189781189,"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":0.9976000189781189,"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/T11943","display_name":"Pharmacovigilance and Adverse Drug Reactions","score":0.9779999852180481,"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/T10350","display_name":"Electronic Health Records Systems","score":0.9577999711036682,"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/drug-discovery","display_name":"Drug discovery","score":0.6576097011566162},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4970104992389679},{"id":"https://openalex.org/keywords/adverse-effect","display_name":"Adverse effect","score":0.4965861439704895},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.4767882823944092},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3964756727218628},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.37080925703048706},{"id":"https://openalex.org/keywords/intensive-care-medicine","display_name":"Intensive care medicine","score":0.32069164514541626},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.25742387771606445},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.24005568027496338},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11279758810997009}],"concepts":[{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.6576097011566162},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4970104992389679},{"id":"https://openalex.org/C197934379","wikidata":"https://www.wikidata.org/wiki/Q2047938","display_name":"Adverse effect","level":2,"score":0.4965861439704895},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.4767882823944092},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3964756727218628},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.37080925703048706},{"id":"https://openalex.org/C177713679","wikidata":"https://www.wikidata.org/wiki/Q679690","display_name":"Intensive care medicine","level":1,"score":0.32069164514541626},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.25742387771606445},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.24005568027496338},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11279758810997009}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":"D011358","descriptor_name":"Product Surveillance, Postmarketing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D011358","descriptor_name":"Product Surveillance, Postmarketing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D011358","descriptor_name":"Product Surveillance, Postmarketing","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":"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":true},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","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},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/jamia/ocv102","is_oa":true,"landing_page_url":"https://doi.org/10.1093/jamia/ocv102","pdf_url":"https://academic.oup.com/jamia/article-pdf/22/6/1196/17376791/ocv102.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:26232442","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26232442","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:pubmedcentral.nih.gov:4921953","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4921953","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":"doi:10.1093/jamia/ocv102","is_oa":true,"landing_page_url":"https://doi.org/10.1093/jamia/ocv102","pdf_url":"https://academic.oup.com/jamia/article-pdf/22/6/1196/17376791/ocv102.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":[{"id":"https://metadata.un.org/sdg/10","score":0.6600000262260437,"display_name":"Reduced inequalities"}],"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/G2356014100","display_name":null,"funder_award_id":"R01 LM011369","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G7529942499","display_name":null,"funder_award_id":"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/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"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2113031313.pdf","grobid_xml":"https://content.openalex.org/works/W2113031313.grobid-xml"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W73222560","https://openalex.org/W112113049","https://openalex.org/W182767159","https://openalex.org/W256825336","https://openalex.org/W273955616","https://openalex.org/W311004003","https://openalex.org/W1512404644","https://openalex.org/W1569856620","https://openalex.org/W1596932914","https://openalex.org/W1934602670","https://openalex.org/W1969879564","https://openalex.org/W1979496029","https://openalex.org/W1985875788","https://openalex.org/W1994868616","https://openalex.org/W2000054710","https://openalex.org/W2003999719","https://openalex.org/W2013770071","https://openalex.org/W2024862171","https://openalex.org/W2029592334","https://openalex.org/W2034702096","https://openalex.org/W2040555718","https://openalex.org/W2084876550","https://openalex.org/W2088562998","https://openalex.org/W2097360283","https://openalex.org/W2107516065","https://openalex.org/W2110412254","https://openalex.org/W2110888938","https://openalex.org/W2119002393","https://openalex.org/W2122825543","https://openalex.org/W2138499964","https://openalex.org/W2139212933","https://openalex.org/W2139865360","https://openalex.org/W2148554370","https://openalex.org/W2149676192","https://openalex.org/W2160194473","https://openalex.org/W2161554615","https://openalex.org/W2162258226","https://openalex.org/W2164105883","https://openalex.org/W2168528736","https://openalex.org/W2911964244","https://openalex.org/W4229779919","https://openalex.org/W4294457161","https://openalex.org/W4294541781","https://openalex.org/W6602996861","https://openalex.org/W6609623229","https://openalex.org/W6610017368","https://openalex.org/W6610912112","https://openalex.org/W6616962000","https://openalex.org/W6630546887","https://openalex.org/W6635767022","https://openalex.org/W6640497426","https://openalex.org/W6683435780","https://openalex.org/W6684007453","https://openalex.org/W6684091441"],"related_works":["https://openalex.org/W2480711475","https://openalex.org/W4206379684","https://openalex.org/W2017438361","https://openalex.org/W4220709714","https://openalex.org/W2061997414","https://openalex.org/W1587522533","https://openalex.org/W2366105490","https://openalex.org/W4361215268","https://openalex.org/W2330883931","https://openalex.org/W35123684"],"abstract_inverted_index":{"OBJECTIVE:":[0],"Adverse":[1],"drug":[2,57],"events":[3],"(ADEs)":[4],"are":[5,66,96,190],"undesired":[6],"harmful":[7],"effects":[8],"resulting":[9,179],"from":[10,35,47],"use":[11],"of":[12,19,33,56,131,148,166,187,196,215,228],"a":[13,26,73,81,86,125,139,151,225],"medication,":[14],"and":[15,59,170],"occur":[16],"in":[17,102,119,180,192],"30%":[18],"hospitalized":[20],"patients.":[21],"The":[22,108,156],"authors":[23,109],"have":[24,200],"developed":[25],"data-mining":[27],"method":[28,43,112,137,211],"for":[29,99,116,174,219],"systematic,":[30],"automated":[31],"detection":[32],"ADEs":[34,91,220],"electronic":[36,222],"medical":[37,223],"records.":[38],"MATERIALS":[39],"AND":[40],"METHODS:":[41],"This":[42,136,210],"uses":[44,138],"the":[45,78,94,117,146,197,207,213,229],"text":[46],"9.5":[48],"million":[49],"clinical":[50],"notes,":[51],"along":[52],"with":[53],"prior":[54],"knowledge":[55],"usages":[58],"known":[60],"ADEs,":[61],"as":[62],"inputs.":[63],"These":[64],"inputs":[65],"further":[67,97],"processed":[68],"into":[69],"statistics":[70],"used":[71,159],"by":[72,93,113],"discriminative":[74],"classifier":[75,95,140,157],"which":[76,175],"outputs":[77],"probability":[79],"that":[80,141,199,202],"given":[82],"drug-disorder":[83,163],"pair":[84],"represents":[85],"valid":[87],"ADE":[88],"association.":[89],"Putative":[90],"identified":[92],"filtered":[98],"positive":[100],"support":[101,115],"2":[103],"independent,":[104],"complementary":[105],"data":[106,122],"sources.":[107],"evaluate":[110],"this":[111],"assessing":[114],"predictions":[118],"other":[120],"curated":[121],"sources,":[123],"including":[124],"manually":[126],"curated,":[127],"time-indexed":[128],"reference":[129],"standard":[130],"label":[132],"change":[133],"events.":[134],"RESULTS:":[135],"achieves":[142],"an":[143],"area":[144],"under":[145],"curve":[147],"0.94":[149],"on":[150,160],"held":[152],"out":[153],"test":[154],"set.":[155],"is":[158],"2,362,950":[161],"possible":[162],"pairs":[164],"comprised":[165],"1602":[167],"unique":[168,172],"drugs":[169],"1475":[171],"disorders":[173],"we":[176],"had":[177],"data,":[178],"240":[181],"high-confidence,":[182],"well-supported":[183],"drug-AE":[184],"associations.":[185],"Eighty-seven":[186],"them":[188],"(36%)":[189],"supported":[191],"at":[193],"least":[194],"one":[195],"resources":[198],"information":[201],"was":[203],"not":[204],"available":[205],"to":[206],"classifier.":[208],"CONCLUSION:":[209],"demonstrates":[212],"feasibility":[214],"systematic":[216],"post-marketing":[217],"surveillance":[218],"using":[221],"records,":[224],"key":[226],"component":[227],"learning":[230],"healthcare":[231],"system.":[232]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":11},{"year":2016,"cited_by_count":10}],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2025-10-10T00:00:00"}