{"id":"https://openalex.org/W2979946792","doi":"https://doi.org/10.1093/jamia/ocz141","title":"Extracting medications and associated adverse drug events using a natural language processing system combining knowledge base and deep learning","display_name":"Extracting medications and associated adverse drug events using a natural language processing system combining knowledge base and deep learning","publication_year":2019,"publication_date":"2019-07-24","ids":{"openalex":"https://openalex.org/W2979946792","doi":"https://doi.org/10.1093/jamia/ocz141","mag":"2979946792","pmid":"https://pubmed.ncbi.nlm.nih.gov/31591641"},"language":"en","primary_location":{"id":"doi:10.1093/jamia/ocz141","is_oa":false,"landing_page_url":"https://doi.org/10.1093/jamia/ocz141","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/7489056","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100336360","display_name":"Long Chen","orcid":"https://orcid.org/0000-0001-6148-9709"},"institutions":[{"id":"https://openalex.org/I4210086396","display_name":"Med Data Quest (United States)","ror":"https://ror.org/00w3t2881","country_code":"US","type":"company","lineage":["https://openalex.org/I4210086396"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Long Chen","raw_affiliation_strings":["Med Data Quest, Inc, La Jolla, California, USA"],"affiliations":[{"raw_affiliation_string":"Med Data Quest, Inc, La Jolla, California, USA","institution_ids":["https://openalex.org/I4210086396"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087377548","display_name":"\u88d5\u4e8c \u6c60\u8c37","orcid":"https://orcid.org/0000-0002-1704-1744"},"institutions":[{"id":"https://openalex.org/I4210086396","display_name":"Med Data Quest (United States)","ror":"https://ror.org/00w3t2881","country_code":"US","type":"company","lineage":["https://openalex.org/I4210086396"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yu Gu","raw_affiliation_strings":["Med Data Quest, Inc, La Jolla, California, USA"],"affiliations":[{"raw_affiliation_string":"Med Data Quest, Inc, La Jolla, California, USA","institution_ids":["https://openalex.org/I4210086396"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110768736","display_name":"Xin Ji","orcid":null},"institutions":[{"id":"https://openalex.org/I4210086396","display_name":"Med Data Quest (United States)","ror":"https://ror.org/00w3t2881","country_code":"US","type":"company","lineage":["https://openalex.org/I4210086396"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xin Ji","raw_affiliation_strings":["Med Data Quest, Inc, La Jolla, California, USA"],"affiliations":[{"raw_affiliation_string":"Med Data Quest, Inc, La Jolla, California, USA","institution_ids":["https://openalex.org/I4210086396"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101727179","display_name":"Zhiyong Sun","orcid":"https://orcid.org/0000-0001-9510-4897"},"institutions":[{"id":"https://openalex.org/I4210086396","display_name":"Med Data Quest (United States)","ror":"https://ror.org/00w3t2881","country_code":"US","type":"company","lineage":["https://openalex.org/I4210086396"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhiyong Sun","raw_affiliation_strings":["Med Data Quest, Inc, La Jolla, California, USA"],"affiliations":[{"raw_affiliation_string":"Med Data Quest, Inc, La Jolla, California, USA","institution_ids":["https://openalex.org/I4210086396"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073204856","display_name":"Haodan Li","orcid":null},"institutions":[{"id":"https://openalex.org/I4210086396","display_name":"Med Data Quest (United States)","ror":"https://ror.org/00w3t2881","country_code":"US","type":"company","lineage":["https://openalex.org/I4210086396"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Haodan Li","raw_affiliation_strings":["Med Data Quest, Inc, La Jolla, California, USA"],"affiliations":[{"raw_affiliation_string":"Med Data Quest, Inc, La Jolla, California, USA","institution_ids":["https://openalex.org/I4210086396"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070895035","display_name":"Yuan Gao","orcid":"https://orcid.org/0000-0002-0628-4484"},"institutions":[{"id":"https://openalex.org/I4210086396","display_name":"Med Data Quest (United States)","ror":"https://ror.org/00w3t2881","country_code":"US","type":"company","lineage":["https://openalex.org/I4210086396"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuan Gao","raw_affiliation_strings":["Med Data Quest, Inc, La Jolla, California, USA"],"affiliations":[{"raw_affiliation_string":"Med Data Quest, Inc, La Jolla, California, USA","institution_ids":["https://openalex.org/I4210086396"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101682935","display_name":"Yang Huang","orcid":"https://orcid.org/0000-0002-9551-4447"},"institutions":[{"id":"https://openalex.org/I4210086396","display_name":"Med Data Quest (United States)","ror":"https://ror.org/00w3t2881","country_code":"US","type":"company","lineage":["https://openalex.org/I4210086396"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yang Huang","raw_affiliation_strings":["Med Data Quest, Inc, La Jolla, California, USA"],"affiliations":[{"raw_affiliation_string":"Med Data Quest, Inc, La Jolla, California, USA","institution_ids":["https://openalex.org/I4210086396"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5100336360"],"corresponding_institution_ids":["https://openalex.org/I4210086396"],"apc_list":{"value":3967,"currency":"USD","value_usd":3967},"apc_paid":null,"fwci":2.8278,"has_fulltext":false,"cited_by_count":72,"citation_normalized_percentile":{"value":0.91699116,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"27","issue":"1","first_page":"56","last_page":"64"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9936000108718872,"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":0.9936000108718872,"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":0.9866999983787537,"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/T12574","display_name":"Clinical Reasoning and Diagnostic Skills","score":0.9782999753952026,"subfield":{"id":"https://openalex.org/subfields/2714","display_name":"Family Practice"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6776387691497803},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6241796612739563},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.6169745922088623},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.6055824160575867},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5640572309494019},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5610090494155884},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.4802672863006592},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4669918119907379},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.46335911750793457},{"id":"https://openalex.org/keywords/knowledge-base","display_name":"Knowledge base","score":0.46283626556396484},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.4416520893573761},{"id":"https://openalex.org/keywords/relationship-extraction","display_name":"Relationship extraction","score":0.4345383942127228}],"concepts":[{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6776387691497803},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6241796612739563},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.6169745922088623},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.6055824160575867},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5640572309494019},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5610090494155884},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.4802672863006592},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4669918119907379},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.46335911750793457},{"id":"https://openalex.org/C4554734","wikidata":"https://www.wikidata.org/wiki/Q593744","display_name":"Knowledge base","level":2,"score":0.46283626556396484},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.4416520893573761},{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.4345383942127228},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"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":"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":"D009323","descriptor_name":"Natural Language Processing","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":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","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":false},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D033262","descriptor_name":"Narration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D033262","descriptor_name":"Narration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D033262","descriptor_name":"Narration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","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":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":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/jamia/ocz141","is_oa":false,"landing_page_url":"https://doi.org/10.1093/jamia/ocz141","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:31591641","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31591641","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:7489056","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7489056","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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:7489056","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7489056","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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","id":"https://metadata.un.org/sdg/4","score":0.6700000166893005}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W86609720","https://openalex.org/W1919684990","https://openalex.org/W1974754328","https://openalex.org/W1979496029","https://openalex.org/W1991287461","https://openalex.org/W2007867931","https://openalex.org/W2053106197","https://openalex.org/W2097960255","https://openalex.org/W2114039834","https://openalex.org/W2122402213","https://openalex.org/W2126166543","https://openalex.org/W2140302476","https://openalex.org/W2141869602","https://openalex.org/W2146089916","https://openalex.org/W2166858912","https://openalex.org/W2168041406","https://openalex.org/W2251622960","https://openalex.org/W2293023260","https://openalex.org/W2396881363","https://openalex.org/W2410444648","https://openalex.org/W2416810581","https://openalex.org/W2460367506","https://openalex.org/W2469314752","https://openalex.org/W2513378248","https://openalex.org/W2517194566","https://openalex.org/W2595551253","https://openalex.org/W2615822908","https://openalex.org/W2735580341","https://openalex.org/W2750779823","https://openalex.org/W2751936342","https://openalex.org/W2759609474","https://openalex.org/W2768488789","https://openalex.org/W2801154470","https://openalex.org/W2808393080","https://openalex.org/W2963641259","https://openalex.org/W2964217331","https://openalex.org/W4229779919","https://openalex.org/W4244978678","https://openalex.org/W4293236771","https://openalex.org/W4294457161","https://openalex.org/W4378951071","https://openalex.org/W6603505381","https://openalex.org/W6696884364","https://openalex.org/W6716195970","https://openalex.org/W6718816867","https://openalex.org/W6720120379","https://openalex.org/W6752597651"],"related_works":["https://openalex.org/W2334378031","https://openalex.org/W842810586","https://openalex.org/W2916255597","https://openalex.org/W4319940250","https://openalex.org/W3095980030","https://openalex.org/W2352298027","https://openalex.org/W2092919065","https://openalex.org/W3138801416","https://openalex.org/W3198510869","https://openalex.org/W4379379356"],"abstract_inverted_index":{"We":[0],"demonstrate":[1],"the":[2,6],"generic":[3],"approaches":[4],"and":[5,35,50],"practice":[7],"of":[8,33],"connecting":[9],"general":[10],"purposed":[11],"clinical":[12],"NLP":[13,29],"system":[14,30],"to":[15,46],"task-specific":[16],"requirements":[17],"with":[18],"deep":[19],"learning":[20],"methods.":[21],"Our":[22],"results":[23],"indicate":[24],"that":[25],"a":[26],"well-designed":[27],"hybrid":[28],"is":[31],"capable":[32],"ADE":[34],"medication-related":[36],"information":[37],"extraction,":[38],"which":[39],"can":[40],"be":[41],"used":[42],"in":[43],"real-world":[44],"applications":[45],"support":[47],"ADE-related":[48],"researches":[49],"medical":[51],"decisions.":[52]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":18},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":16},{"year":2020,"cited_by_count":10}],"updated_date":"2026-03-08T08:50:53.379069","created_date":"2025-10-10T00:00:00"}
