{"id":"https://openalex.org/W2100276951","doi":"https://doi.org/10.1186/1471-2105-16-s16-s4","title":"TEES 2.2: Biomedical Event Extraction for Diverse Corpora","display_name":"TEES 2.2: Biomedical Event Extraction for Diverse Corpora","publication_year":2015,"publication_date":"2015-10-30","ids":{"openalex":"https://openalex.org/W2100276951","doi":"https://doi.org/10.1186/1471-2105-16-s16-s4","mag":"2100276951","pmid":"https://pubmed.ncbi.nlm.nih.gov/26551925"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-16-s16-s4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-16-s16-s4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-16-S16-S4","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","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-16-S16-S4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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":true,"raw_author_name":"Jari Bj\u00f6rne","raw_affiliation_strings":["Department of Information Technology, University of Turku, Joukahaisenkatu 3-5, 20520, Turku, Finland","Turku Centre for Computer Science (TUCS), Joukahaisenkatu 3-5, 20520, Turku, Finland","Department of Information Technology, University of Turku, Turku, Finland","Turku Centre for Computer Science (TUCS), Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information Technology, University of Turku, Joukahaisenkatu 3-5, 20520, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":"Turku Centre for Computer Science (TUCS), Joukahaisenkatu 3-5, 20520, Turku, Finland","institution_ids":["https://openalex.org/I183173800"]},{"raw_affiliation_string":"Department of Information Technology, University of Turku, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":"Turku Centre for Computer Science (TUCS), Turku, Finland","institution_ids":["https://openalex.org/I183173800"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5105839982","display_name":"Tapio Salakoski","orcid":null},"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":"Tapio Salakoski","raw_affiliation_strings":["Department of Information Technology, University of Turku, Joukahaisenkatu 3-5, 20520, Turku, Finland","Turku Centre for Computer Science (TUCS), Joukahaisenkatu 3-5, 20520, Turku, Finland","Department of Information Technology, University of Turku, Turku, Finland","Turku Centre for Computer Science (TUCS), Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information Technology, University of Turku, Joukahaisenkatu 3-5, 20520, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":"Turku Centre for Computer Science (TUCS), Joukahaisenkatu 3-5, 20520, Turku, Finland","institution_ids":["https://openalex.org/I183173800"]},{"raw_affiliation_string":"Department of Information Technology, University of Turku, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":"Turku Centre for Computer Science (TUCS), Turku, Finland","institution_ids":["https://openalex.org/I183173800"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5049143500"],"corresponding_institution_ids":["https://openalex.org/I155660961","https://openalex.org/I183173800"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.7916,"has_fulltext":true,"cited_by_count":51,"citation_normalized_percentile":{"value":0.84907026,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"16","issue":"S16","first_page":"S4","last_page":"S4"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9915000200271606,"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":0.9915000200271606,"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":0.0017000000225380063,"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":0.0008999999845400453,"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/event","display_name":"Event (particle physics)","score":0.5513173341751099},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5442836284637451},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.521524965763092},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4659985303878784},{"id":"https://openalex.org/keywords/extraction","display_name":"Extraction (chemistry)","score":0.4392086863517761},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3606697916984558},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.35842257738113403},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3401775360107422},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12068083882331848},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.06576091051101685},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.058741241693496704}],"concepts":[{"id":"https://openalex.org/C2779662365","wikidata":"https://www.wikidata.org/wiki/Q5416694","display_name":"Event (particle physics)","level":2,"score":0.5513173341751099},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5442836284637451},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.521524965763092},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4659985303878784},{"id":"https://openalex.org/C4725764","wikidata":"https://www.wikidata.org/wiki/Q844704","display_name":"Extraction (chemistry)","level":2,"score":0.4392086863517761},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3606697916984558},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.35842257738113403},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3401775360107422},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12068083882331848},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.06576091051101685},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.058741241693496704},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1186/1471-2105-16-s16-s4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-16-s16-s4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-16-S16-S4","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":"pmid:26551925","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26551925","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:3620876","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4642046","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-16-s16-s4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-16-s16-s4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-16-S16-S4","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":[{"score":0.6299999952316284,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"},{"id":"https://openalex.org/F4320323313","display_name":"Turun Yliopisto","ror":"https://ror.org/05vghhr25"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2100276951.pdf","grobid_xml":"https://content.openalex.org/works/W2100276951.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W8550301","https://openalex.org/W76749362","https://openalex.org/W122290181","https://openalex.org/W150863218","https://openalex.org/W165790511","https://openalex.org/W241117969","https://openalex.org/W1510526001","https://openalex.org/W1594031697","https://openalex.org/W1830777114","https://openalex.org/W1934889228","https://openalex.org/W2027383523","https://openalex.org/W2032566933","https://openalex.org/W2052947212","https://openalex.org/W2069805705","https://openalex.org/W2092269560","https://openalex.org/W2095023795","https://openalex.org/W2097300420","https://openalex.org/W2098722636","https://openalex.org/W2101234009","https://openalex.org/W2103448252","https://openalex.org/W2105842272","https://openalex.org/W2108791029","https://openalex.org/W2121844933","https://openalex.org/W2125765581","https://openalex.org/W2128036577","https://openalex.org/W2145107779","https://openalex.org/W2145428772","https://openalex.org/W2179494026","https://openalex.org/W2250204381","https://openalex.org/W2250469303","https://openalex.org/W2250591852","https://openalex.org/W2250619635","https://openalex.org/W2250765544","https://openalex.org/W2251279337","https://openalex.org/W2251431888","https://openalex.org/W2251814321","https://openalex.org/W2252057336","https://openalex.org/W2252145363","https://openalex.org/W2608050011","https://openalex.org/W2771576526","https://openalex.org/W2914431807","https://openalex.org/W2916147465","https://openalex.org/W2916355958","https://openalex.org/W2923652028","https://openalex.org/W3085162807","https://openalex.org/W4244006029","https://openalex.org/W4301101316"],"related_works":["https://openalex.org/W2415545834","https://openalex.org/W2069695727","https://openalex.org/W2377297411","https://openalex.org/W1802639773","https://openalex.org/W2118505788","https://openalex.org/W4254166511","https://openalex.org/W3148217948","https://openalex.org/W2150084125","https://openalex.org/W1542823905","https://openalex.org/W1490878237"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,45,75,129,206],"Turku":[2],"Event":[3],"Extraction":[4],"System":[5],"(TEES)":[6],"is":[7,138,164,190],"a":[8,26,37,67,90,120,170],"text":[9,71],"mining":[10,72],"program":[11],"developed":[12,100],"for":[13,93,101,131,211],"the":[14,29,34,55,82,103,114,132,145,155,159,167,183,195,198,201,212,230,247,255],"extraction":[15,261],"of":[16,36,54,58,69,107,126,135,147,154,173,197,246,258],"events,":[17],"complex":[18],"biomedical":[19,70,259],"relationships,":[20],"from":[21,238],"scientific":[22],"literature.":[23],"Based":[24],"on":[25],"graph-generation":[27],"approach,":[28],"system":[30,47,77,130,208,234],"detects":[31],"events":[32],"with":[33,178],"use":[35],"rich":[38],"feature":[39,203],"set":[40],"built":[41],"via":[42],"dependency":[43],"parsing.":[44],"TEES":[46,76,179,202,207,232],"has":[48,217],"achieved":[49],"record":[50],"performance":[51,222],"in":[52,66,86,123,141,180,200,223,254],"several":[53,224],"shared":[56,226,241],"tasks":[57,242],"its":[59],"domain,":[60],"and":[61,117,216,251],"continues":[62],"to":[63,81,88,113,119,144,152,182,193,235],"be":[64],"used":[65,192],"variety":[68,172],"tasks.":[73,128,157,227],"RESULTS:":[74],"was":[78,99,209],"quickly":[79],"adapted":[80],"BioNLP'13":[83,156],"Shared":[84,214],"Task":[85,215],"order":[87],"provide":[89],"public":[91],"baseline":[92],"derived":[94],"systems.":[95],"An":[96],"automated":[97,133],"approach":[98],"learning":[102,134,162,175],"underlying":[104],"annotation":[105,136],"rules":[106,137],"event":[108,260],"type,":[109],"allowing":[110],"immediate":[111],"adaptation":[112,151],"various":[115],"subtasks,":[116],"leading":[118],"first":[121],"place":[122],"four":[124],"out":[125],"eight":[127],"further":[139],"enhanced":[140],"this":[142],"paper":[143],"point":[146],"requiring":[148],"no":[149],"manual":[150],"any":[153],"Further,":[158],"scikit-learn":[160,187],"machine":[161,174],"library":[163],"integrated":[165],"into":[166],"system,":[168],"bringing":[169],"wide":[171],"methods":[176,250],"usable":[177],"addition":[181],"default":[184],"SVM.":[185],"A":[186],"ensemble":[188],"method":[189],"also":[191],"analyze":[194],"importances":[196],"features":[199],"sets.":[204],"CONCLUSIONS:":[205],"introduced":[210],"BioNLP'09":[213],"since":[218],"then":[219],"demonstrated":[220],"good":[221],"other":[225],"By":[228],"applying":[229],"current":[231],"2.2":[233],"multiple":[236],"corpora":[237],"these":[239],"past":[240],"an":[243],"overarching":[244],"analysis":[245],"most":[248],"promising":[249],"possible":[252],"pitfalls":[253],"evolving":[256],"field":[257],"are":[262],"presented.":[263]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2012,"cited_by_count":4}],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2025-10-10T00:00:00"}
