{"id":"https://openalex.org/W4378072589","doi":"https://doi.org/10.48550/arxiv.2305.13395","title":"BioDEX: Large-Scale Biomedical Adverse Drug Event Extraction for Real-World Pharmacovigilance","display_name":"BioDEX: Large-Scale Biomedical Adverse Drug Event Extraction for Real-World Pharmacovigilance","publication_year":2023,"publication_date":"2023-05-22","ids":{"openalex":"https://openalex.org/W4378072589","doi":"https://doi.org/10.48550/arxiv.2305.13395"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2305.13395","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2305.13395","pdf_url":"https://arxiv.org/pdf/2305.13395","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":null},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2305.13395","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031474902","display_name":"Karel D\u2019Oosterlinck","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"D'Oosterlinck, Karel","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102792763","display_name":"Fran\u00e7ois Remy","orcid":"https://orcid.org/0000-0003-4775-6975"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Remy, Fran\u00e7ois","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004214531","display_name":"Johannes Deleu","orcid":"https://orcid.org/0000-0001-8277-2415"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Deleu, Johannes","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075509168","display_name":"Thomas Demeester","orcid":"https://orcid.org/0000-0002-9901-5768"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Demeester, Thomas","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084742757","display_name":"Chris Develder","orcid":"https://orcid.org/0000-0003-2707-4176"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Develder, Chris","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011614450","display_name":"Klim Zaporojets","orcid":"https://orcid.org/0000-0003-4988-978X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zaporojets, Klim","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083561499","display_name":"Aneiss Ghodsi","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ghodsi, Aneiss","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059013252","display_name":"Simon Ellershaw","orcid":"https://orcid.org/0000-0002-1851-0047"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ellershaw, Simon","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029122049","display_name":"Jack Collins","orcid":"https://orcid.org/0000-0001-8281-2085"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Collins, Jack","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5042601761","display_name":"Christopher Potts","orcid":"https://orcid.org/0000-0002-7978-6055"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Potts, Christopher","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5031474902"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11943","display_name":"Pharmacovigilance and Adverse Drug Reactions","score":0.9890000224113464,"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":0.9890000224113464,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9571999907493591,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T11492","display_name":"Academic integrity and plagiarism","score":0.9542999863624573,"subfield":{"id":"https://openalex.org/subfields/3311","display_name":"Safety Research"},"field":{"id":"https://openalex.org/fields/33","display_name":"Social Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pharmacovigilance","display_name":"Pharmacovigilance","score":0.8027203679084778},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.6542478203773499},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6379711627960205},{"id":"https://openalex.org/keywords/event","display_name":"Event (particle physics)","score":0.5297411680221558},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5223858952522278},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.4387246072292328},{"id":"https://openalex.org/keywords/adverse-drug-reaction","display_name":"Adverse drug reaction","score":0.41683071851730347},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.40205299854278564},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.39474061131477356},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3934207558631897},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.32710927724838257},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.1455002725124359},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09024035930633545}],"concepts":[{"id":"https://openalex.org/C57658597","wikidata":"https://www.wikidata.org/wiki/Q1550789","display_name":"Pharmacovigilance","level":3,"score":0.8027203679084778},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.6542478203773499},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6379711627960205},{"id":"https://openalex.org/C2779662365","wikidata":"https://www.wikidata.org/wiki/Q5416694","display_name":"Event (particle physics)","level":2,"score":0.5297411680221558},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5223858952522278},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.4387246072292328},{"id":"https://openalex.org/C2780542314","wikidata":"https://www.wikidata.org/wiki/Q45959","display_name":"Adverse drug reaction","level":3,"score":0.41683071851730347},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.40205299854278564},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.39474061131477356},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3934207558631897},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.32710927724838257},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.1455002725124359},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09024035930633545},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:arXiv.org:2305.13395","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2305.13395","pdf_url":"https://arxiv.org/pdf/2305.13395","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":null},{"id":"pmh:oai:archive.ugent.be:01HH1WVF7CCNEDP5GTRQA8RVHR","is_oa":true,"landing_page_url":"http://hdl.handle.net/1854/LU-01HH1WVF7CCNEDP5GTRQA8RVHR","pdf_url":"https://biblio.ugent.be/publication/01HH1WVF7CCNEDP5GTRQA8RVHR/file/01HH1X2Z2E5BK3NH0DB5CD3EQY","source":{"id":"https://openalex.org/S4306400478","display_name":"Ghent University Academic Bibliography (Ghent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I32597200","host_organization_name":"Ghent University","host_organization_lineage":["https://openalex.org/I32597200"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"2023 Conference on Empirical Methods in Natural Language Processing (EMNLP 2023), Proceedings","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"doi:10.48550/arxiv.2305.13395","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2305.13395","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2305.13395","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2305.13395","pdf_url":"https://arxiv.org/pdf/2305.13395","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":null},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320313796","display_name":"Innovationsfonden","ror":"https://ror.org/00daj4111"},{"id":"https://openalex.org/F4320321730","display_name":"Fonds Wetenschappelijk Onderzoek","ror":"https://ror.org/03qtxy027"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2377282230","https://openalex.org/W2995438986","https://openalex.org/W2520672216","https://openalex.org/W1606297102","https://openalex.org/W2286265647","https://openalex.org/W1997934777","https://openalex.org/W2380560108","https://openalex.org/W2321554583","https://openalex.org/W2800221202","https://openalex.org/W2907807817"],"abstract_inverted_index":{"Timely":[0],"and":[1,20,71,97,117,181],"accurate":[2],"extraction":[3],"of":[4,37,59,68,89,100,105,131,136],"Adverse":[5],"Drug":[6,51],"Events":[7],"(ADE)":[8],"from":[9],"biomedical":[10,74],"literature":[11],"is":[12],"paramount":[13],"for":[14,48],"public":[15],"safety,":[16],"but":[17],"involves":[18],"slow":[19],"costly":[21],"manual":[22],"labor.":[23],"We":[24,42,143,164],"set":[25,104],"out":[26],"to":[27,147,167],"improve":[28],"drug":[29,60,112],"safety":[30,61,80],"monitoring":[31],"(pharmacovigilance,":[32],"PV)":[33],"through":[34],"the":[35,56,64,93,109,111,114,119,129,133,137],"use":[36],"Natural":[38],"Language":[39],"Processing":[40],"(NLP).":[41],"introduce":[43],"BioDEX,":[44],"a":[45,101,103],"large-scale":[46],"resource":[47],"Biomedical":[49],"adverse":[50],"Event":[52],"Extraction,":[53],"rooted":[54],"in":[55,63,170],"historical":[57],"output":[58],"reporting":[62],"U.S.":[65],"BioDEX":[66],"consists":[67],"65k":[69],"abstracts":[70],"19k":[72],"full-text":[73],"papers":[75],"with":[76],"256k":[77],"associated":[78],"document-level":[79],"reports":[81,91],"created":[82],"by":[83,108],"medical":[84],"experts.":[85],"The":[86],"core":[87,134],"features":[88],"these":[90,172],"include":[92],"reported":[94],"weight,":[95],"age,":[96],"biological":[98],"sex":[99],"patient,":[102,110],"drugs":[106],"taken":[107],"dosages,":[113],"reactions":[115],"experienced,":[116],"whether":[118],"reaction":[120],"was":[121],"life":[122],"threatening.":[123],"In":[124],"this":[125,162],"work,":[126],"we":[127],"consider":[128],"task":[130],"predicting":[132],"information":[135],"report":[138],"given":[139],"its":[140],"originating":[141],"paper.":[142],"estimate":[144],"human":[145],"performance":[146],"be":[148],"72.0%":[149],"F1,":[150,157],"whereas":[151],"our":[152],"best":[153],"model":[154],"achieves":[155],"62.3%":[156],"indicating":[158],"significant":[159],"headroom":[160],"on":[161],"task.":[163],"also":[165],"begin":[166],"explore":[168],"ways":[169],"which":[171],"models":[173],"could":[174],"help":[175],"professional":[176],"PV":[177],"reviewers.":[178],"Our":[179],"code":[180],"data":[182],"are":[183],"available:":[184],"https://github.com/KarelDO/BioDEX.":[185]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":1}],"updated_date":"2026-05-21T09:19:25.381259","created_date":"2023-05-25T00:00:00"}
