{"id":"https://openalex.org/W2097300420","doi":"https://doi.org/10.1093/bioinformatics/bts487","title":"A robust approach to extract biomedical events from literature","display_name":"A robust approach to extract biomedical events from literature","publication_year":2012,"publication_date":"2012-08-01","ids":{"openalex":"https://openalex.org/W2097300420","doi":"https://doi.org/10.1093/bioinformatics/bts487","mag":"2097300420","pmid":"https://pubmed.ncbi.nlm.nih.gov/22859502"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts487","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts487","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/20/2654/520992/bts487.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/28/20/2654/520992/bts487.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059728213","display_name":"Quoc-Chinh Bui","orcid":null},"institutions":[{"id":"https://openalex.org/I887064364","display_name":"University of Amsterdam","ror":"https://ror.org/04dkp9463","country_code":"NL","type":"education","lineage":["https://openalex.org/I887064364"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Quoc-Chinh Bui","raw_affiliation_strings":["Computational Science, Informatics Institute, Faculty of Science, University of Amsterdam, The Netherlands","Computational Science, Informatics Institute, Faculty of Science, University of Amsterdam, The Netherlands#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Science, Informatics Institute, Faculty of Science, University of Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I887064364"]},{"raw_affiliation_string":"Computational Science, Informatics Institute, Faculty of Science, University of Amsterdam, The Netherlands#TAB#","institution_ids":["https://openalex.org/I887064364"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016657852","display_name":"P.M.A. Sloot","orcid":"https://orcid.org/0000-0002-3848-5395"},"institutions":[{"id":"https://openalex.org/I887064364","display_name":"University of Amsterdam","ror":"https://ror.org/04dkp9463","country_code":"NL","type":"education","lineage":["https://openalex.org/I887064364"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Peter M.A. Sloot","raw_affiliation_strings":["Computational Science, Informatics Institute, Faculty of Science, University of Amsterdam, The Netherlands","Computational Science, Informatics Institute, Faculty of Science, University of Amsterdam, The Netherlands#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Science, Informatics Institute, Faculty of Science, University of Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I887064364"]},{"raw_affiliation_string":"Computational Science, Informatics Institute, Faculty of Science, University of Amsterdam, The Netherlands#TAB#","institution_ids":["https://openalex.org/I887064364"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5059728213"],"corresponding_institution_ids":["https://openalex.org/I887064364"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.589,"has_fulltext":false,"cited_by_count":32,"citation_normalized_percentile":{"value":0.82732465,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"28","issue":"20","first_page":"2654","last_page":"2661"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9950000047683716,"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":0.9950000047683716,"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":0.0020000000949949026,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.00039999998989515007,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8398589491844177},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.667625904083252},{"id":"https://openalex.org/keywords/binary-relation","display_name":"Binary relation","score":0.5868868231773376},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5719965696334839},{"id":"https://openalex.org/keywords/binary-number","display_name":"Binary number","score":0.5639225840568542},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.5528669357299805},{"id":"https://openalex.org/keywords/event","display_name":"Event (particle physics)","score":0.5093287229537964},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.501528263092041},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.4636709690093994},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4484970271587372},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.44121822714805603},{"id":"https://openalex.org/keywords/template","display_name":"Template","score":0.4318579435348511},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3510703146457672},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.18125659227371216},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12542185187339783},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.12477180361747742},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.07779562473297119}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8398589491844177},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.667625904083252},{"id":"https://openalex.org/C65180967","wikidata":"https://www.wikidata.org/wiki/Q130901","display_name":"Binary relation","level":2,"score":0.5868868231773376},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5719965696334839},{"id":"https://openalex.org/C48372109","wikidata":"https://www.wikidata.org/wiki/Q3913","display_name":"Binary number","level":2,"score":0.5639225840568542},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.5528669357299805},{"id":"https://openalex.org/C2779662365","wikidata":"https://www.wikidata.org/wiki/Q5416694","display_name":"Event (particle physics)","level":2,"score":0.5093287229537964},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.501528263092041},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.4636709690093994},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4484970271587372},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.44121822714805603},{"id":"https://openalex.org/C82714645","wikidata":"https://www.wikidata.org/wiki/Q438331","display_name":"Template","level":2,"score":0.4318579435348511},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3510703146457672},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.18125659227371216},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12542185187339783},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.12477180361747742},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.07779562473297119},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"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},{"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/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C94375191","wikidata":"https://www.wikidata.org/wiki/Q11205","display_name":"Arithmetic","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/bts487","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts487","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/20/2654/520992/bts487.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22859502","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22859502","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:dare.uva.nl:openaire_cris_publications/8a0d5781-d491-47ce-b449-1ff571a66aa3","is_oa":false,"landing_page_url":"https://dare.uva.nl/personal/pure/en/publications/a-robust-approach-to-extract-biomedical-events-from-literature(8a0d5781-d491-47ce-b449-1ff571a66aa3).html","pdf_url":null,"source":{"id":"https://openalex.org/S4306400088","display_name":"UvA-DARE (University of Amsterdam)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I887064364","host_organization_name":"University of Amsterdam","host_organization_lineage":["https://openalex.org/I887064364"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bui, Q C & Sloot, P M A 2012, 'A robust approach to extract biomedical events from literature', Bioinformatics, vol. 28, no. 20, pp. 2654-2661. https://doi.org/10.1093/bioinformatics/bts487","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:dare.uva.nl:publications/8a0d5781-d491-47ce-b449-1ff571a66aa3","is_oa":false,"landing_page_url":"https://handle.uba.uva.nl/personal/pure/en/publications/a-robust-approach-to-extract-biomedical-events-from-literature(8a0d5781-d491-47ce-b449-1ff571a66aa3).html","pdf_url":null,"source":{"id":"https://openalex.org/S4306400088","display_name":"UvA-DARE (University of Amsterdam)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I887064364","host_organization_name":"University of Amsterdam","host_organization_lineage":["https://openalex.org/I887064364"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bui, Q C & Sloot, P M A 2012, 'A robust approach to extract biomedical events from literature', Bioinformatics, vol. 28, no. 20, pp. 2654-2661. https://doi.org/10.1093/bioinformatics/bts487","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:dr.ntu.edu.sg:10356/96085","is_oa":false,"landing_page_url":"https://hdl.handle.net/10356/96085","pdf_url":null,"source":{"id":"https://openalex.org/S4306402609","display_name":"DR-NTU (Nanyang Technological University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I172675005","host_organization_name":"Nanyang Technological University","host_organization_lineage":["https://openalex.org/I172675005"],"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":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts487","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts487","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/20/2654/520992/bts487.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2097300420.pdf"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W136394213","https://openalex.org/W154351976","https://openalex.org/W1508671669","https://openalex.org/W1777768792","https://openalex.org/W1877040722","https://openalex.org/W1898214464","https://openalex.org/W1925121078","https://openalex.org/W1975481163","https://openalex.org/W1977223481","https://openalex.org/W1995672001","https://openalex.org/W2003185534","https://openalex.org/W2032566933","https://openalex.org/W2056478778","https://openalex.org/W2068094441","https://openalex.org/W2075322787","https://openalex.org/W2075655036","https://openalex.org/W2103320915","https://openalex.org/W2106560678","https://openalex.org/W2108706252","https://openalex.org/W2110408238","https://openalex.org/W2115936127","https://openalex.org/W2121368442","https://openalex.org/W2122139846","https://openalex.org/W2129769245","https://openalex.org/W2135186741","https://openalex.org/W2138275182","https://openalex.org/W2155598164","https://openalex.org/W2169961254","https://openalex.org/W2171283231","https://openalex.org/W2251450145","https://openalex.org/W2252226131","https://openalex.org/W6605508192","https://openalex.org/W6606243021","https://openalex.org/W6630492222","https://openalex.org/W6639278583","https://openalex.org/W6639642803","https://openalex.org/W6640092400","https://openalex.org/W6644100520","https://openalex.org/W6677987329","https://openalex.org/W6679478935","https://openalex.org/W6680588392","https://openalex.org/W6682553958","https://openalex.org/W6691960683"],"related_works":["https://openalex.org/W2121300814","https://openalex.org/W4234406076","https://openalex.org/W1886613375","https://openalex.org/W4236081792","https://openalex.org/W4250583430","https://openalex.org/W2010731026","https://openalex.org/W2360893094","https://openalex.org/W4390787808","https://openalex.org/W2379390860","https://openalex.org/W2391083822"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1],"abundance":[2],"of":[3,85,141,161],"biomedical":[4,16,47,65,78],"literature":[5],"has":[6],"attracted":[7],"significant":[8],"interest":[9],"in":[10,159],"novel":[11,74],"methods":[12,55,114],"to":[13,76,105,117,149],"automatically":[14],"extract":[15,58,77,106],"relations":[17,30,41,62],"from":[18,80],"the":[19,45,89,110,119,125,150],"literature.":[20],"Until":[21],"recently,":[22],"most":[23],"research":[24],"was":[25],"focused":[26],"on":[27,100],"extracting":[28],"binary":[29,40],"such":[31],"as":[32,64],"protein-protein":[33],"interactions":[34],"and":[35,60,130,143],"drug-disease":[36],"relations.":[37],"However,":[38],"these":[39],"cannot":[42],"fully":[43],"represent":[44],"original":[46],"data.":[48],"Therefore,":[49],"there":[50],"is":[51,168],"a":[52,73],"need":[53],"for":[54,170],"that":[56],"can":[57],"fine-grained":[59],"complex":[61],"known":[63],"events.":[66],"RESULTS:":[67],"In":[68,88,109],"this":[69],"article":[70],"we":[71,136],"propose":[72],"method":[75,83],"events":[79],"text.":[81],"Our":[82,165],"consists":[84],"two":[86],"phases.":[87],"first":[90],"phase,":[91,112],"training":[92],"data":[93],"are":[94,103,115,147],"mapped":[95],"into":[96],"structured":[97],"representations.":[98],"Based":[99],"that,":[101],"templates":[102],"used":[104],"rules":[107],"automatically.":[108],"second":[111],"extraction":[113,128],"developed":[116],"process":[118],"obtained":[120],"rules.":[121],"When":[122],"evaluated":[123],"against":[124],"Genia":[126],"event":[127],"abstract":[129],"full-text":[131],"test":[132],"datasets":[133],"(Task":[134],"1),":[135],"obtain":[137],"results":[138],"with":[139],"F-scores":[140],"52.34":[142],"53.34,":[144],"respectively,":[145],"which":[146],"comparable":[148],"state-of-the-art":[151],"systems.":[152],"Furthermore,":[153],"our":[154],"system":[155],"achieves":[156],"superior":[157],"performance":[158],"terms":[160],"computational":[162],"efficiency.":[163],"AVAILABILITY:":[164],"source":[166],"code":[167],"available":[169],"academic":[171],"use":[172],"at":[173],"http://dl.dropbox.com/u/10256952/BioEvent.zip.":[174]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":4}],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2025-10-10T00:00:00"}
