{"id":"https://openalex.org/W2090274024","doi":"https://doi.org/10.1186/1471-2105-11-s5-o2","title":"Event extraction on PubMed scale","display_name":"Event extraction on PubMed scale","publication_year":2010,"publication_date":"2010-10-01","ids":{"openalex":"https://openalex.org/W2090274024","doi":"https://doi.org/10.1186/1471-2105-11-s5-o2","mag":"2090274024"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-11-s5-o2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s5-o2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S5-O2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S5-O2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019929457","display_name":"Filip Ginter","orcid":"https://orcid.org/0000-0002-5484-6103"},"institutions":[{"id":"https://openalex.org/I1323252656","display_name":"Information Technology University","ror":"https://ror.org/00ngv8j44","country_code":"PK","type":"education","lineage":["https://openalex.org/I1323252656"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI","PK"],"is_corresponding":true,"raw_author_name":"Filip Ginter","raw_affiliation_strings":["Department of Information Technology, University of Turku, Finland","Dept. of Inf. Technol., Univ. of Turku, Finland"],"affiliations":[{"raw_affiliation_string":"Department of Information Technology, University of Turku, Finland","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":"Dept. of Inf. Technol., Univ. of Turku, Finland","institution_ids":["https://openalex.org/I1323252656"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049143500","display_name":"Jari Bj\u00f6rne","orcid":"https://orcid.org/0000-0003-1722-6404"},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Jari Bj\u00f6rne","raw_affiliation_strings":["Department of Information Technology, University of Turku, Finland","Turku Centre for Computer Science (TUCS), Finland","Department of Information Technology, University of Turku, , Finland"],"affiliations":[{"raw_affiliation_string":"Department of Information Technology, University of Turku, Finland","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":"Turku Centre for Computer Science (TUCS), Finland","institution_ids":["https://openalex.org/I183173800"]},{"raw_affiliation_string":"Department of Information Technology, University of Turku, , Finland","institution_ids":["https://openalex.org/I155660961"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066925770","display_name":"Sampo Pyysalo","orcid":"https://orcid.org/0000-0002-6279-5000"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]},{"id":"https://openalex.org/I161296585","display_name":"Tokyo University of Science","ror":"https://ror.org/05sj3n476","country_code":"JP","type":"education","lineage":["https://openalex.org/I161296585"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Sampo Pyysalo","raw_affiliation_strings":["Department of Computer Science, University of Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Tokyo, Japan","institution_ids":["https://openalex.org/I74801974","https://openalex.org/I161296585"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5019929457"],"corresponding_institution_ids":["https://openalex.org/I1323252656","https://openalex.org/I155660961"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.1352,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.54451372,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":"11","issue":"S5","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":0.9998999834060669,"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":0.9998999834060669,"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":0.9879999756813049,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.98580002784729,"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/computer-science","display_name":"Computer science","score":0.8731437921524048},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7951502799987793},{"id":"https://openalex.org/keywords/event","display_name":"Event (particle physics)","score":0.761117696762085},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.6028628349304199},{"id":"https://openalex.org/keywords/parsing","display_name":"Parsing","score":0.5785018801689148},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5627942085266113},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5159279108047485},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5150518417358398},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.4959891736507416},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.46812334656715393},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.46646177768707275},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.43164244294166565},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.39580610394477844},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3846394419670105},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.18433406949043274},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.18390530347824097},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10094863176345825}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8731437921524048},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7951502799987793},{"id":"https://openalex.org/C2779662365","wikidata":"https://www.wikidata.org/wiki/Q5416694","display_name":"Event (particle physics)","level":2,"score":0.761117696762085},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.6028628349304199},{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.5785018801689148},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5627942085266113},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5159279108047485},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5150518417358398},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.4959891736507416},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.46812334656715393},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.46646177768707275},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.43164244294166565},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.39580610394477844},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3846394419670105},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.18433406949043274},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.18390530347824097},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10094863176345825},{"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/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/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","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/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/1471-2105-11-s5-o2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s5-o2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S5-O2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:e43ffe2d54b34571a9f6dd922b895f67","is_oa":true,"landing_page_url":"https://doaj.org/article/e43ffe2d54b34571a9f6dd922b895f67","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 11, Iss Suppl 5, p O2 (2010)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2956389","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2956389","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-11-s5-o2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s5-o2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S5-O2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2090274024.pdf","grobid_xml":"https://content.openalex.org/works/W2090274024.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W122290181","https://openalex.org/W2032566933","https://openalex.org/W2052947212","https://openalex.org/W2103320915","https://openalex.org/W2107005506","https://openalex.org/W2108010925","https://openalex.org/W2798636932"],"related_works":["https://openalex.org/W3004288456","https://openalex.org/W4362496998","https://openalex.org/W2184397297","https://openalex.org/W1663435917","https://openalex.org/W2810079151","https://openalex.org/W2616159224","https://openalex.org/W2164881856","https://openalex.org/W2572241437","https://openalex.org/W2103320915","https://openalex.org/W3082330004"],"abstract_inverted_index":{"There":[0],"has":[1],"been":[2,173],"a":[3,30,47,72,176,197,267],"growing":[4],"interest":[5],"in":[6,17,40,75,90,279],"typed,":[7],"recursively":[8,148],"nested":[9],"events":[10,34,147,219],"as":[11,236],"the":[12,18,37,52,59,82,91,104,110,116,122,126,182,194,206,210,214,226,229,233,274,281],"target":[13],"for":[14,244],"information":[15],"extraction":[16,42,63,78,97,168,186,284],"biomedical":[19],"domain.":[20],"The":[21,96],"BioNLP'09":[22],"Shared":[23,127],"Task":[24],"on":[25,46],"Event":[26,118],"Extraction":[27,119],"[1]":[28],"provided":[29],"standard":[31,48],"definition":[32],"of":[33,61,86,94,101,125,132,136,140,144,161,209,217,228,232,277],"and":[35,68,84,115,170,201,241],"established":[36,58],"current":[38],"state-of-the-art":[39,102,178],"event":[41,54,62,77,167,185,263,283],"through":[43],"competitive":[44],"evaluation":[45],"dataset":[49,130,157,195],"derived":[50],"from":[51,81],"GENIA":[53],"corpus.\r\n\r\nWe":[55],"have":[56],"previously":[57],"scalability":[60],"to":[64,261],"large":[65],"corpora":[66],"[2]":[67],"here":[69],"we":[70,212],"present":[71],"follow-up":[73],"study":[74],"which":[76,141],"is":[79,99,158],"performed":[80],"titles":[83],"abstracts":[85],"all":[87,245],"17.8M":[88],"citations":[89],"2009":[92],"release":[93],"PubMed.":[95],"pipeline":[98,179],"composed":[100],"methods:":[103],"BANNER":[105],"named":[106,154,238,252],"entity":[107,239],"recognizer":[108],"[3],":[109],"McClosky-Charniak":[111],"domain-adapted":[112],"parser":[113],"[4],":[114],"Turku":[117],"System":[120],"[5],":[121],"winning":[123],"entry":[124],"Task.\r\n\r\nThe":[128],"resulting":[129],"consists":[131],"over":[133],"19.2M":[134],"instances":[135,143,240],"4.5M":[137],"unique":[138,146],"events,":[139],"2.1M":[142],"1.6M":[145],"involve":[149],"at":[150,222,249],"least":[151,250],"two":[152],"different":[153],"entities.":[155],"This":[156,254],"several":[159],"orders":[160],"magnitude":[162],"larger":[163],"than":[164],"any":[165],"previous":[166],"effort":[169],"--":[171],"having":[172],"obtained":[174],"by":[175,265],"demonstrably":[177],"\u2014":[180],"represents":[181],"most":[183],"accurate":[184],"output":[187,227],"achievable":[188],"with":[189,225],"presently":[190],"available":[191,221],"tools.":[192],"Compiling":[193],"was":[196],"technically":[198],"challenging":[199],"undertaking":[200],"required":[202],"roughly":[203],"8,300":[204],"CPU-hours.\r\n\r\nAs":[205],"primary":[207],"contribution":[208],"study,":[211],"make":[213],"entire":[215],"set":[216],"extracted":[218],"freely":[220],"http://bionlp.utu.fi,":[223],"together":[224],"individual":[230],"stages":[231],"pipeline,":[234],"such":[235],"36.5M":[237],"syntactic":[242],"analyzes":[243],"20M":[246],"sentences":[247],"containing":[248],"one":[251],"entity.":[253],"resource":[255],"will":[256],"facilitate":[257],"future":[258],"research":[259],"related":[260],"biological":[262],"networks":[264],"providing":[266],"standard,":[268],"publicly":[269],"available,":[270],"large-scale":[271],"dataset,":[272],"avoiding":[273],"unnecessary":[275],"duplication":[276],"efforts":[278],"executing":[280],"complex":[282],"pipeline.":[285]},"counts_by_year":[{"year":2014,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
