{"id":"https://openalex.org/W4394789579","doi":"https://doi.org/10.1093/bib/bbae132","title":"Surveying biomedical relation extraction: a critical examination of current datasets and the proposal of a new resource","display_name":"Surveying biomedical relation extraction: a critical examination of current datasets and the proposal of a new resource","publication_year":2024,"publication_date":"2024-03-27","ids":{"openalex":"https://openalex.org/W4394789579","doi":"https://doi.org/10.1093/bib/bbae132","pmid":"https://pubmed.ncbi.nlm.nih.gov/38609331"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae132","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae132","pdf_url":"https://academic.oup.com/bib/article-pdf/25/3/bbae132/57221564/bbae132.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/25/3/bbae132/57221564/bbae132.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034137404","display_name":"Ming-Siang Huang","orcid":null},"institutions":[{"id":"https://openalex.org/I143578492","display_name":"Asia University","ror":"https://ror.org/038a1tp19","country_code":"TW","type":"education","lineage":["https://openalex.org/I143578492"]},{"id":"https://openalex.org/I165441096","display_name":"National Health Research Institutes","ror":"https://ror.org/02r6fpx29","country_code":"TW","type":"nonprofit","lineage":["https://openalex.org/I165441096"]},{"id":"https://openalex.org/I4210105785","display_name":"Intelligent Systems Research (United States)","ror":"https://ror.org/01reevc91","country_code":"US","type":"company","lineage":["https://openalex.org/I4210105785"]}],"countries":["TW","US"],"is_corresponding":false,"raw_author_name":"Ming-Siang Huang","raw_affiliation_strings":["Asia University , College of Information and Electrical Engineering, , Taichung , Taiwan","Asia University , Department of Computer Science and Information Engineering, , New Taipei City , Taiwan","Department of Computer Science and Information Engineering , College of Information and Electrical Engineering, , Taichung , Taiwan","Intelligent Agent Systems Laboratory , Department of Computer Science and Information Engineering, , New Taipei City , Taiwan","National Institute of Cancer Research, National Health Research Institutes , Tainan , Taiwan","Intelligent Agent Systems Laboratory, Department of Computer Science and Information Engineering, Asia University, New Taipei City, Taiwan","Department of Computer Science and Information Engineering, College of Information and Electrical Engineering, Asia University, Taichung, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Asia University , College of Information and Electrical Engineering, , Taichung , Taiwan","institution_ids":["https://openalex.org/I143578492"]},{"raw_affiliation_string":"Asia University , Department of Computer Science and Information Engineering, , New Taipei City , Taiwan","institution_ids":["https://openalex.org/I143578492"]},{"raw_affiliation_string":"Department of Computer Science and Information Engineering , College of Information and Electrical Engineering, , Taichung , Taiwan","institution_ids":[]},{"raw_affiliation_string":"Intelligent Agent Systems Laboratory , Department of Computer Science and Information Engineering, , New Taipei City , Taiwan","institution_ids":["https://openalex.org/I4210105785"]},{"raw_affiliation_string":"National Institute of Cancer Research, National Health Research Institutes , Tainan , Taiwan","institution_ids":["https://openalex.org/I165441096"]},{"raw_affiliation_string":"Intelligent Agent Systems Laboratory, Department of Computer Science and Information Engineering, Asia University, New Taipei City, Taiwan","institution_ids":["https://openalex.org/I143578492"]},{"raw_affiliation_string":"Department of Computer Science and Information Engineering, College of Information and Electrical Engineering, Asia University, Taichung, Taiwan","institution_ids":["https://openalex.org/I143578492"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037000720","display_name":"Jen-Chieh Han","orcid":"https://orcid.org/0000-0003-0998-4539"},"institutions":[{"id":"https://openalex.org/I22265921","display_name":"National Central University","ror":"https://ror.org/00944ve71","country_code":"TW","type":"education","lineage":["https://openalex.org/I22265921"]},{"id":"https://openalex.org/I4210098366","display_name":"Institute of Information Science, Academia Sinica","ror":"https://ror.org/00z83z196","country_code":"TW","type":"facility","lineage":["https://openalex.org/I4210098366","https://openalex.org/I84653119"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Jen-Chieh Han","raw_affiliation_strings":["Intelligent Information Service Research Laboratory , Department of Computer Science and Information Engineering, , Taoyuan , Taiwan","National Central University , Department of Computer Science and Information Engineering, , Taoyuan , Taiwan","Intelligent Information Service Research Laboratory, Department of Computer Science and Information Engineering, National Central University, Taoyuan, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Intelligent Information Service Research Laboratory , Department of Computer Science and Information Engineering, , Taoyuan , Taiwan","institution_ids":["https://openalex.org/I4210098366"]},{"raw_affiliation_string":"National Central University , Department of Computer Science and Information Engineering, , Taoyuan , Taiwan","institution_ids":["https://openalex.org/I22265921"]},{"raw_affiliation_string":"Intelligent Information Service Research Laboratory, Department of Computer Science and Information Engineering, National Central University, Taoyuan, Taiwan","institution_ids":["https://openalex.org/I22265921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101336306","display_name":"Pei-Yen Lin","orcid":null},"institutions":[{"id":"https://openalex.org/I143578492","display_name":"Asia University","ror":"https://ror.org/038a1tp19","country_code":"TW","type":"education","lineage":["https://openalex.org/I143578492"]},{"id":"https://openalex.org/I4210105785","display_name":"Intelligent Systems Research (United States)","ror":"https://ror.org/01reevc91","country_code":"US","type":"company","lineage":["https://openalex.org/I4210105785"]}],"countries":["TW","US"],"is_corresponding":false,"raw_author_name":"Pei-Yen Lin","raw_affiliation_strings":["Asia University , Department of Computer Science and Information Engineering, , New Taipei City , Taiwan","Intelligent Agent Systems Laboratory , Department of Computer Science and Information Engineering, , New Taipei City , Taiwan","Intelligent Agent Systems Laboratory, Department of Computer Science and Information Engineering, Asia University, New Taipei City, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Asia University , Department of Computer Science and Information Engineering, , New Taipei City , Taiwan","institution_ids":["https://openalex.org/I143578492"]},{"raw_affiliation_string":"Intelligent Agent Systems Laboratory , Department of Computer Science and Information Engineering, , New Taipei City , Taiwan","institution_ids":["https://openalex.org/I4210105785"]},{"raw_affiliation_string":"Intelligent Agent Systems Laboratory, Department of Computer Science and Information Engineering, Asia University, New Taipei City, Taiwan","institution_ids":["https://openalex.org/I143578492"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102648475","display_name":"Yu-Ting You","orcid":null},"institutions":[{"id":"https://openalex.org/I143578492","display_name":"Asia University","ror":"https://ror.org/038a1tp19","country_code":"TW","type":"education","lineage":["https://openalex.org/I143578492"]},{"id":"https://openalex.org/I4210105785","display_name":"Intelligent Systems Research (United States)","ror":"https://ror.org/01reevc91","country_code":"US","type":"company","lineage":["https://openalex.org/I4210105785"]}],"countries":["TW","US"],"is_corresponding":false,"raw_author_name":"Yu-Ting You","raw_affiliation_strings":["Asia University , Department of Computer Science and Information Engineering, , New Taipei City , Taiwan","Intelligent Agent Systems Laboratory , Department of Computer Science and Information Engineering, , New Taipei City , Taiwan","Intelligent Agent Systems Laboratory, Department of Computer Science and Information Engineering, Asia University, New Taipei City, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Asia University , Department of Computer Science and Information Engineering, , New Taipei City , Taiwan","institution_ids":["https://openalex.org/I143578492"]},{"raw_affiliation_string":"Intelligent Agent Systems Laboratory , Department of Computer Science and Information Engineering, , New Taipei City , Taiwan","institution_ids":["https://openalex.org/I4210105785"]},{"raw_affiliation_string":"Intelligent Agent Systems Laboratory, Department of Computer Science and Information Engineering, Asia University, New Taipei City, Taiwan","institution_ids":["https://openalex.org/I143578492"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030771512","display_name":"Richard Tzong\u2010Han Tsai","orcid":"https://orcid.org/0000-0003-0513-107X"},"institutions":[{"id":"https://openalex.org/I22265921","display_name":"National Central University","ror":"https://ror.org/00944ve71","country_code":"TW","type":"education","lineage":["https://openalex.org/I22265921"]},{"id":"https://openalex.org/I4210098366","display_name":"Institute of Information Science, Academia Sinica","ror":"https://ror.org/00z83z196","country_code":"TW","type":"facility","lineage":["https://openalex.org/I4210098366","https://openalex.org/I84653119"]},{"id":"https://openalex.org/I4210150355","display_name":"Research Center for Humanities and Social Sciences, Academia Sinica","ror":"https://ror.org/05n4swm55","country_code":"TW","type":"facility","lineage":["https://openalex.org/I4210150355","https://openalex.org/I84653119"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Richard Tzong-Han Tsai","raw_affiliation_strings":["Center for Geographic Information Science, Research Center for Humanities and Social Sciences, Academia Sinica , Taipei , Taiwan","Intelligent Information Service Research Laboratory , Department of Computer Science and Information Engineering, , Taoyuan , Taiwan","National Central University , Department of Computer Science and Information Engineering, , Taoyuan , Taiwan","Center for Geographic Information Science, Research Center for Humanities and Social Sciences, Academia Sinica, Taipei, Taiwan","Intelligent Information Service Research Laboratory, Department of Computer Science and Information Engineering, National Central University, Taoyuan, Taiwan"],"raw_orcid":"https://orcid.org/0000-0003-0513-107X","affiliations":[{"raw_affiliation_string":"Center for Geographic Information Science, Research Center for Humanities and Social Sciences, Academia Sinica , Taipei , Taiwan","institution_ids":["https://openalex.org/I4210150355"]},{"raw_affiliation_string":"Intelligent Information Service Research Laboratory , Department of Computer Science and Information Engineering, , Taoyuan , Taiwan","institution_ids":["https://openalex.org/I4210098366"]},{"raw_affiliation_string":"National Central University , Department of Computer Science and Information Engineering, , Taoyuan , Taiwan","institution_ids":["https://openalex.org/I22265921"]},{"raw_affiliation_string":"Center for Geographic Information Science, Research Center for Humanities and Social Sciences, Academia Sinica, Taipei, Taiwan","institution_ids":["https://openalex.org/I4210150355"]},{"raw_affiliation_string":"Intelligent Information Service Research Laboratory, Department of Computer Science and Information Engineering, National Central University, Taoyuan, Taiwan","institution_ids":["https://openalex.org/I22265921"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5119558606","display_name":"Wen\u2212Lian Hsu","orcid":"https://orcid.org/0000-0001-7061-3513"},"institutions":[{"id":"https://openalex.org/I143578492","display_name":"Asia University","ror":"https://ror.org/038a1tp19","country_code":"TW","type":"education","lineage":["https://openalex.org/I143578492"]},{"id":"https://openalex.org/I4210105785","display_name":"Intelligent Systems Research (United States)","ror":"https://ror.org/01reevc91","country_code":"US","type":"company","lineage":["https://openalex.org/I4210105785"]}],"countries":["TW","US"],"is_corresponding":true,"raw_author_name":"Wen-Lian Hsu","raw_affiliation_strings":["Asia University , College of Information and Electrical Engineering, , Taichung , Taiwan","Asia University , Department of Computer Science and Information Engineering, , New Taipei City , Taiwan","Department of Computer Science and Information Engineering , College of Information and Electrical Engineering, , Taichung , Taiwan","Intelligent Agent Systems Laboratory , Department of Computer Science and Information Engineering, , New Taipei City , Taiwan","Department of Computer Science and Information Engineering, College of Information and Electrical Engineering, Asia University, Taichung, Taiwan","Intelligent Agent Systems Laboratory, Department of Computer Science and Information Engineering, Asia University, New Taipei City, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Asia University , College of Information and Electrical Engineering, , Taichung , Taiwan","institution_ids":["https://openalex.org/I143578492"]},{"raw_affiliation_string":"Asia University , Department of Computer Science and Information Engineering, , New Taipei City , Taiwan","institution_ids":["https://openalex.org/I143578492"]},{"raw_affiliation_string":"Department of Computer Science and Information Engineering , College of Information and Electrical Engineering, , Taichung , Taiwan","institution_ids":[]},{"raw_affiliation_string":"Intelligent Agent Systems Laboratory , Department of Computer Science and Information Engineering, , New Taipei City , Taiwan","institution_ids":["https://openalex.org/I4210105785"]},{"raw_affiliation_string":"Department of Computer Science and Information Engineering, College of Information and Electrical Engineering, Asia University, Taichung, Taiwan","institution_ids":["https://openalex.org/I143578492"]},{"raw_affiliation_string":"Intelligent Agent Systems Laboratory, Department of Computer Science and Information Engineering, Asia University, New Taipei City, Taiwan","institution_ids":["https://openalex.org/I143578492"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5030771512","https://openalex.org/A5119558606"],"corresponding_institution_ids":["https://openalex.org/I143578492","https://openalex.org/I22265921","https://openalex.org/I4210098366","https://openalex.org/I4210105785","https://openalex.org/I4210150355"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":2.917,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.9126492,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"25","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9993000030517578,"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":0.9993000030517578,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.995199978351593,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9901000261306763,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7764825820922852},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6951523423194885},{"id":"https://openalex.org/keywords/relation","display_name":"Relation (database)","score":0.5999826192855835},{"id":"https://openalex.org/keywords/relationship-extraction","display_name":"Relationship extraction","score":0.5960772633552551},{"id":"https://openalex.org/keywords/variety","display_name":"Variety (cybernetics)","score":0.5904840230941772},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.5854169130325317},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5529888272285461},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5165228247642517},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5049622654914856},{"id":"https://openalex.org/keywords/event","display_name":"Event (particle physics)","score":0.47323310375213623},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4710659384727478},{"id":"https://openalex.org/keywords/resource","display_name":"Resource (disambiguation)","score":0.4627774655818939},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.4597416818141937},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.35043442249298096},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.34455782175064087},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.24596798419952393},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.11081796884536743},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10776764154434204}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7764825820922852},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6951523423194885},{"id":"https://openalex.org/C25343380","wikidata":"https://www.wikidata.org/wiki/Q277521","display_name":"Relation (database)","level":2,"score":0.5999826192855835},{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.5960772633552551},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.5904840230941772},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.5854169130325317},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5529888272285461},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5165228247642517},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5049622654914856},{"id":"https://openalex.org/C2779662365","wikidata":"https://www.wikidata.org/wiki/Q5416694","display_name":"Event (particle physics)","level":2,"score":0.47323310375213623},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4710659384727478},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.4627774655818939},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.4597416818141937},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.35043442249298096},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.34455782175064087},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.24596798419952393},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.11081796884536743},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10776764154434204},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"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/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","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},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"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":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae132","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae132","pdf_url":"https://academic.oup.com/bib/article-pdf/25/3/bbae132/57221564/bbae132.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38609331","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38609331","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11014787","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11014787","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11014787/pdf/bbae132.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae132","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae132","pdf_url":"https://academic.oup.com/bib/article-pdf/25/3/bbae132/57221564/bbae132.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5991234239","display_name":null,"funder_award_id":"MOST 108-2319-B-400-001","funder_id":"https://openalex.org/F4320309618","funder_display_name":"Ministry of Science and Technology"},{"id":"https://openalex.org/G737106015","display_name":null,"funder_award_id":"MOST 108-","funder_id":"https://openalex.org/F4320322795","funder_display_name":"Ministry of Science and Technology, Taiwan"},{"id":"https://openalex.org/G8224019631","display_name":null,"funder_award_id":"108-2319-B-400-001","funder_id":"https://openalex.org/F4320322795","funder_display_name":"Ministry of Science and Technology, Taiwan"}],"funders":[{"id":"https://openalex.org/F4320309618","display_name":"Ministry of Science and Technology","ror":"https://ror.org/02b207r52"},{"id":"https://openalex.org/F4320311039","display_name":"Ministry of Higher Education and Scientific Research","ror":"https://ror.org/00kab6t91"},{"id":"https://openalex.org/F4320321528","display_name":"Shanghai Educational Development Foundation","ror":"https://ror.org/0220qvk04"},{"id":"https://openalex.org/F4320322724","display_name":"Ministry of Education, India","ror":"https://ror.org/048xjjh50"},{"id":"https://openalex.org/F4320322795","display_name":"Ministry of Science and Technology, Taiwan","ror":"https://ror.org/02kv4zf79"},{"id":"https://openalex.org/F4320331164","display_name":"National Science and Technology Council","ror":"https://ror.org/00wnb9798"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4394789579.pdf"},"referenced_works_count":126,"referenced_works":["https://openalex.org/W46679369","https://openalex.org/W1473718842","https://openalex.org/W1516184288","https://openalex.org/W1541954861","https://openalex.org/W1578843544","https://openalex.org/W1850865022","https://openalex.org/W1914733988","https://openalex.org/W1966976587","https://openalex.org/W1998898494","https://openalex.org/W2004910511","https://openalex.org/W2009313526","https://openalex.org/W2016106370","https://openalex.org/W2016928406","https://openalex.org/W2020132970","https://openalex.org/W2048059249","https://openalex.org/W2052217781","https://openalex.org/W2064030835","https://openalex.org/W2080101247","https://openalex.org/W2097960255","https://openalex.org/W2098722636","https://openalex.org/W2100751507","https://openalex.org/W2101234009","https://openalex.org/W2107580398","https://openalex.org/W2109070394","https://openalex.org/W2112796553","https://openalex.org/W2113072832","https://openalex.org/W2114033138","https://openalex.org/W2114363816","https://openalex.org/W2115880858","https://openalex.org/W2119412782","https://openalex.org/W2121844933","https://openalex.org/W2122496897","https://openalex.org/W2129767020","https://openalex.org/W2136437513","https://openalex.org/W2149298154","https://openalex.org/W2149803936","https://openalex.org/W2152183901","https://openalex.org/W2152698860","https://openalex.org/W2154896031","https://openalex.org/W2155518941","https://openalex.org/W2159583324","https://openalex.org/W2160238006","https://openalex.org/W2163362093","https://openalex.org/W2165253681","https://openalex.org/W2166111585","https://openalex.org/W2166474856","https://openalex.org/W2168041406","https://openalex.org/W2169974160","https://openalex.org/W2170021941","https://openalex.org/W2170189740","https://openalex.org/W2171685287","https://openalex.org/W2264517602","https://openalex.org/W2313983271","https://openalex.org/W2346452181","https://openalex.org/W2389836769","https://openalex.org/W2396881363","https://openalex.org/W2406368917","https://openalex.org/W2497265084","https://openalex.org/W2516260054","https://openalex.org/W2518463060","https://openalex.org/W2564980658","https://openalex.org/W2579434750","https://openalex.org/W2600659824","https://openalex.org/W2604372572","https://openalex.org/W2664267452","https://openalex.org/W2768488789","https://openalex.org/W2774772126","https://openalex.org/W2784499877","https://openalex.org/W2795129839","https://openalex.org/W2801930304","https://openalex.org/W2809349863","https://openalex.org/W2895715183","https://openalex.org/W2896457183","https://openalex.org/W2908840510","https://openalex.org/W2911489562","https://openalex.org/W2914171828","https://openalex.org/W2914431807","https://openalex.org/W2919115771","https://openalex.org/W2923014074","https://openalex.org/W2923652028","https://openalex.org/W2962784628","https://openalex.org/W2963020213","https://openalex.org/W2963979492","https://openalex.org/W2964348125","https://openalex.org/W2967166693","https://openalex.org/W2970771982","https://openalex.org/W2971258845","https://openalex.org/W2979250794","https://openalex.org/W3046375318","https://openalex.org/W3070389369","https://openalex.org/W3087927280","https://openalex.org/W3096403953","https://openalex.org/W3098949126","https://openalex.org/W3100452049","https://openalex.org/W3104015140","https://openalex.org/W3120223152","https://openalex.org/W3127429900","https://openalex.org/W3178755335","https://openalex.org/W4200043367","https://openalex.org/W4211064852","https://openalex.org/W4213060373","https://openalex.org/W4220967417","https://openalex.org/W4233069070","https://openalex.org/W4251372957","https://openalex.org/W4283318325","https://openalex.org/W4294214983","https://openalex.org/W4401946486","https://openalex.org/W6601894380","https://openalex.org/W6634676396","https://openalex.org/W6638575559","https://openalex.org/W6675354045","https://openalex.org/W6677345342","https://openalex.org/W6678161147","https://openalex.org/W6678180858","https://openalex.org/W6682425626","https://openalex.org/W6684211172","https://openalex.org/W6684310905","https://openalex.org/W6704842505","https://openalex.org/W6713619925","https://openalex.org/W6739183500","https://openalex.org/W6750615492","https://openalex.org/W6751205706","https://openalex.org/W6755207826","https://openalex.org/W6755651582","https://openalex.org/W6764537895","https://openalex.org/W6767306326"],"related_works":["https://openalex.org/W842810586","https://openalex.org/W4319940250","https://openalex.org/W2352298027","https://openalex.org/W2092919065","https://openalex.org/W3138801416","https://openalex.org/W4236762297","https://openalex.org/W2369351710","https://openalex.org/W2594363579","https://openalex.org/W2572241437","https://openalex.org/W4379379356"],"abstract_inverted_index":{"Natural":[0],"language":[1,154],"processing":[2],"(NLP)":[3],"has":[4,101],"become":[5],"an":[6,134],"essential":[7],"technique":[8],"in":[9,41,104,175,187],"various":[10,199],"fields,":[11],"offering":[12],"a":[13,65,165],"wide":[14],"range":[15],"of":[16,44,57,67,136,146,194],"possibilities":[17],"for":[18,168],"analyzing":[19],"data":[20],"and":[21,36,47,93,132,151,190],"developing":[22],"diverse":[23],"NLP":[24],"tasks.":[25],"In":[26,122],"the":[27,31,42,72,80,105,127,137,144,147,158,195],"biomedical":[28],"domain,":[29],"understanding":[30,193],"complex":[32],"relationships":[33],"between":[34],"compounds":[35],"proteins":[37],"is":[38],"critical,":[39],"especially":[40],"context":[43],"signal":[45],"transduction":[46],"biochemical":[48],"pathways.":[49],"Among":[50],"these":[51],"relationships,":[52],"protein-protein":[53],"interactions":[54],"(PPIs)":[55],"are":[56,114],"particular":[58],"interest,":[59],"given":[60],"their":[61],"potential":[62],"to":[63,74,116,184],"trigger":[64],"variety":[66],"biological":[68],"reactions.":[69],"To":[70],"improve":[71],"ability":[73],"predict":[75,117],"PPI":[76,148],"events,":[77],"we":[78,125,142,182],"propose":[79],"protein":[81,172],"event":[82,173],"detection":[83,174],"dataset":[84,100],"(PEDD),":[85],"which":[86],"comprises":[87],"6823":[88],"abstracts,":[89],"39":[90],"488":[91],"sentences":[92],"182":[94],"937":[95],"gene":[96],"pairs.":[97],"Our":[98],"PEDD":[99],"been":[102],"utilized":[103],"AI":[106],"CUP":[107],"Biomedical":[108],"Paper":[109],"Analysis":[110],"competition,":[111],"where":[112],"systems":[113],"challenged":[115],"12":[118],"different":[119],"relation":[120,129],"types.":[121],"this":[123,179],"paper,":[124],"review":[126],"state-of-the-art":[128],"extraction":[130,149],"research":[131],"provide":[133,164],"overview":[135],"PEDD's":[138],"compilation":[139],"process.":[140],"Furthermore,":[141],"present":[143],"results":[145],"competition":[150],"evaluate":[152],"several":[153],"models'":[155],"performances":[156],"on":[157,171],"PEDD.":[159],"This":[160],"paper's":[161],"outcomes":[162],"will":[163],"valuable":[166],"roadmap":[167],"future":[169],"studies":[170],"NLP.":[176],"By":[177],"addressing":[178],"critical":[180],"challenge,":[181],"hope":[183],"enable":[185],"breakthroughs":[186],"drug":[188],"discovery":[189],"enhance":[191],"our":[192],"molecular":[196],"mechanisms":[197],"underlying":[198],"diseases.":[200]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":2}],"updated_date":"2026-05-30T09:04:40.226872","created_date":"2025-10-10T00:00:00"}
