{"id":"https://openalex.org/W3092431239","doi":"https://doi.org/10.48550/arxiv.2010.03550","title":"Understanding Clinical Trial Reports: Extracting Medical Entities and Their Relations","display_name":"Understanding Clinical Trial Reports: Extracting Medical Entities and Their Relations","publication_year":2020,"publication_date":"2020-10-07","ids":{"openalex":"https://openalex.org/W3092431239","doi":"https://doi.org/10.48550/arxiv.2010.03550","mag":"3092431239","pmid":"https://pubmed.ncbi.nlm.nih.gov/34457164","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/8378650"},"language":"en","primary_location":{"id":"pmh:oai:pubmedcentral.nih.gov:8378650","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8378650","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,"listed_in":[],"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":"AMIA Jt Summits Transl Sci Proc","raw_type":"Text"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["arxiv","datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8378650","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044071498","display_name":"Benjamin Nye","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I12912129","display_name":"Northeastern University","ror":"https://ror.org/04t5xt781","country_code":"US","type":"education","lineage":["https://openalex.org/I12912129"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nye, Benjamin E.","raw_affiliation_strings":["Northeastern University , Boston , MA ;","1 Northeastern University, Boston, MA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Northeastern University , Boston , MA ;","institution_ids":["https://openalex.org/I12912129"]},{"raw_affiliation_string":"1 Northeastern University, Boston, MA","institution_ids":["https://openalex.org/I12912129"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068459156","display_name":"Jay DeYoung","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I12912129","display_name":"Northeastern University","ror":"https://ror.org/04t5xt781","country_code":"US","type":"education","lineage":["https://openalex.org/I12912129"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"DeYoung, Jay","raw_affiliation_strings":["Northeastern University , Boston , MA ;","Northeastern University, Boston, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Northeastern University , Boston , MA ;","institution_ids":["https://openalex.org/I12912129"]},{"raw_affiliation_string":"Northeastern University, Boston, United States","institution_ids":["https://openalex.org/I12912129"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Lehman, Eric","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I12912129","display_name":"Northeastern University","ror":"https://ror.org/04t5xt781","country_code":"US","type":"education","lineage":["https://openalex.org/I12912129"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lehman, Eric","raw_affiliation_strings":["Northeastern University , Boston , MA ;","Northeastern University, Boston, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Northeastern University , Boston , MA ;","institution_ids":["https://openalex.org/I12912129"]},{"raw_affiliation_string":"Northeastern University, Boston, United States","institution_ids":["https://openalex.org/I12912129"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032571629","display_name":"Ani Nenkova","orcid":"https://orcid.org/0000-0002-5825-7875","observed_orcids":["https://orcid.org/0000-0002-5825-7875"]},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nenkova, Ani","raw_affiliation_strings":["University of Pennsylvania , Philadelphia , PA ;","2 University of Pennsylvania Philadelphia PA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Pennsylvania , Philadelphia , PA ;","institution_ids":["https://openalex.org/I79576946"]},{"raw_affiliation_string":"2 University of Pennsylvania Philadelphia PA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036860076","display_name":"Iain James Marshall","orcid":"https://orcid.org/0000-0003-2594-2654","observed_orcids":["https://orcid.org/0000-0003-2594-2654"]},"institutions":[{"id":"https://openalex.org/I183935753","display_name":"King's College London","ror":"https://ror.org/0220mzb33","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I183935753"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Marshall, Iain J.","raw_affiliation_strings":["King's College London , London","3 #N# King\u2019s College London ,  London ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"King's College London , London","institution_ids":["https://openalex.org/I183935753"]},{"raw_affiliation_string":"3 #N# King\u2019s College London ,  London ,","institution_ids":["https://openalex.org/I183935753"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036790226","display_name":"Byron Wallace","orcid":"https://orcid.org/0000-0003-2409-7735","observed_orcids":["https://orcid.org/0000-0003-2409-7735"]},"institutions":[{"id":"https://openalex.org/I12912129","display_name":"Northeastern University","ror":"https://ror.org/04t5xt781","country_code":"US","type":"education","lineage":["https://openalex.org/I12912129"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wallace, Byron C.","raw_affiliation_strings":["Northeastern University , Boston , MA ;","Northeastern University, Boston, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Northeastern University , Boston , MA ;","institution_ids":["https://openalex.org/I12912129"]},{"raw_affiliation_string":"Northeastern University, Boston, United States","institution_ids":["https://openalex.org/I12912129"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.032,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.80291971,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":98},"biblio":{"volume":"2021","issue":null,"first_page":"485","last_page":"494"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/2718","display_name":"Health Informatics"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/2718","display_name":"Health Informatics"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.0008999999845400453,"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/T13083","display_name":"Advanced Text Analysis Techniques","score":0.00019999999494757503,"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/clinical-trial-reports","display_name":"clinical trial reports","score":0.9869999885559082},{"id":"https://openalex.org/keywords/medical-entity-extraction","display_name":"medical entity extraction","score":0.7720000147819519},{"id":"https://openalex.org/keywords/relation-extraction","display_name":"relation extraction","score":0.875},{"id":"https://openalex.org/keywords/drug-repurposing","display_name":"drug repurposing","score":0.6240000128746033},{"id":"https://openalex.org/keywords/cancer","display_name":"cancer","score":0.7099999785423279},{"id":"https://openalex.org/keywords/evidence-extraction","display_name":"evidence extraction","score":0.7059999704360962}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7721686363220215},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.6573902368545532},{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.6378467082977295},{"id":"https://openalex.org/C535046627","wikidata":"https://www.wikidata.org/wiki/Q30612","display_name":"Clinical trial","level":2,"score":0.5677269101142883},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5376198887825012},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.501507043838501},{"id":"https://openalex.org/C2777466982","wikidata":"https://www.wikidata.org/wiki/Q5227287","display_name":"Data extraction","level":3,"score":0.48256316781044006},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.45719611644744873},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.43443599343299866},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3926160931587219},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3739774227142334},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36587387323379517},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3258529305458069},{"id":"https://openalex.org/C2779473830","wikidata":"https://www.wikidata.org/wiki/Q1540899","display_name":"MEDLINE","level":2,"score":0.2752164602279663},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.14728274941444397},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","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/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","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}],"mesh":[{"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}],"locations_count":6,"locations":[{"id":"pmh:oai:pubmedcentral.nih.gov:8378650","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8378650","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,"listed_in":[],"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":"AMIA Jt Summits Transl Sci Proc","raw_type":"Text"},{"id":"pmid:34457164","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34457164","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,"listed_in":[],"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":"AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science","raw_type":"Journal Article"},{"id":"pmh:oai:arXiv.org:2010.03550","doi":null,"is_oa":true,"landing_page_url":"http://arxiv.org/abs/2010.03550","pdf_url":"https://arxiv.org/pdf/2010.03550","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":null,"raw_type":"text"},{"id":"mag:3092431239","doi":null,"is_oa":true,"landing_page_url":"http://arxiv.org/pdf/2010.03550.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"arXiv (Cornell University)","raw_type":null},{"id":"pmh:oai:kclpure.kcl.ac.uk:publications/23547e33-c54f-4d5b-9155-8b9e1094e651","doi":null,"is_oa":false,"landing_page_url":"https://kclpure.kcl.ac.uk/portal/en/publications/23547e33-c54f-4d5b-9155-8b9e1094e651","pdf_url":null,"source":{"id":"https://openalex.org/S4306400216","display_name":"Research Portal (King's College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I183935753","host_organization_name":"King's College London","host_organization_lineage":["https://openalex.org/I183935753"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nye, B E, DeYoung, J, Lehman, E, Nenkova, A, Marshall, I J & Wallace, B C 2021, 'Understanding Clinical Trial Reports : Extracting Medical Entities and Their Relations', AMIA ... Annual Symposium proceedings. AMIA Symposium, vol. 2021, pp. 485-494.","raw_type":"info:eu-repo/semantics/article"},{"id":"doi:10.48550/arxiv.2010.03550","doi":"https://doi.org/10.48550/arxiv.2010.03550","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2010.03550","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:8378650","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8378650","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,"listed_in":[],"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":"AMIA Jt Summits Transl Sci Proc","raw_type":"Text"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.5683000087738037}],"study_designs":[],"awards":[{"id":"https://openalex.org/G3272463826","display_name":"CAREER: Structured Scientific Evidence Extraction: Models and Corpora","funder_award_id":"1750978","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3092431239.pdf","grobid_xml":"https://content.openalex.org/works/W3092431239.grobid-xml"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W1522301498","https://openalex.org/W2005958938","https://openalex.org/W2026981750","https://openalex.org/W2146668368","https://openalex.org/W2250668331","https://openalex.org/W2251520281","https://openalex.org/W2346452181","https://openalex.org/W2600659824","https://openalex.org/W2788914818","https://openalex.org/W2798373858","https://openalex.org/W2799125718","https://openalex.org/W2885925344","https://openalex.org/W2896457183","https://openalex.org/W2907265599","https://openalex.org/W2934100103","https://openalex.org/W2963404965","https://openalex.org/W2963718112","https://openalex.org/W2970771982","https://openalex.org/W2972140869","https://openalex.org/W3004071925","https://openalex.org/W3023421484"],"related_works":["https://openalex.org/W4286980122","https://openalex.org/W3026948875","https://openalex.org/W2938589277","https://openalex.org/W3023421484","https://openalex.org/W7083213613","https://openalex.org/W4281293036","https://openalex.org/W4389519532","https://openalex.org/W366435148","https://openalex.org/W4404784046","https://openalex.org/W4225436579"],"abstract_inverted_index":{"task":[0],"of":[1,81,102],"both":[2],"(a)":[3],"extracting":[4],"treatments":[5],"and":[6,39],"outcomes":[7],"from":[8],"full-text":[9],"articles":[10],"describing":[11],"clinical":[12],"trials":[13],"(entity":[14],"identification)":[15],"and,":[16],"(b)":[17],"inferring":[18],"the":[19,23,28,82,99],"reported":[20],"results":[21,47,65],"for":[22,36,96],"former":[24],"with":[25,84],"respect":[26],"to":[27,88],"latter":[29],"(relation":[30],"extraction).":[31],"We":[32,55],"introduce":[33],"new":[34,59],"data":[35],"this":[37],"task,":[38],"evaluate":[40],"models":[41],"that":[42,69,92],"have":[43],"recently":[44],"achieved":[45],"state-of-the-art":[46],"on":[48],"similar":[49],"tasks":[50],"in":[51],"Natural":[52],"Language":[53],"Processing.":[54],"then":[56],"propose":[57],"a":[58,78,85],"method":[60],"motivated":[61],"by":[62],"how":[63],"trial":[64],"are":[66],"typically":[67],"presented":[68],"outperforms":[70],"these":[71],"purely":[72],"data-driven":[73],"baselines.":[74],"Finally,":[75],"we":[76],"run":[77],"fielded":[79],"evaluation":[80],"model":[83],"non-profit":[86],"seeking":[87],"identify":[89],"existing":[90],"drugs":[91],"might":[93],"be":[94],"re-purposed":[95],"cancer,":[97],"showing":[98],"potential":[100],"utility":[101],"end-to-end":[103],"evidence":[104],"extraction":[105],"systems.":[106]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":5}],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2020-10-15T00:00:00"}
