{"id":"https://openalex.org/W2147788440","doi":"https://doi.org/10.1186/1751-0473-9-1","title":"TrigNER: automatically optimized biomedical event trigger recognition on scientific documents","display_name":"TrigNER: automatically optimized biomedical event trigger recognition on scientific documents","publication_year":2014,"publication_date":"2014-01-08","ids":{"openalex":"https://openalex.org/W2147788440","doi":"https://doi.org/10.1186/1751-0473-9-1","mag":"2147788440","pmid":"https://pubmed.ncbi.nlm.nih.gov/24401704"},"language":"en","primary_location":{"id":"doi:10.1186/1751-0473-9-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-9-1","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-9-1","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"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":"Source Code for Biology and Medicine","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-9-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072967999","display_name":"David Campos","orcid":"https://orcid.org/0000-0002-3448-2111"},"institutions":[{"id":"https://openalex.org/I60858718","display_name":"University of Aveiro","ror":"https://ror.org/00nt41z93","country_code":"PT","type":"education","lineage":["https://openalex.org/I60858718"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"David Campos","raw_affiliation_strings":["IEETA/DETI, University of Aveiro, 3810-193, Aveiro, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IEETA/DETI, University of Aveiro, 3810-193, Aveiro, Portugal","institution_ids":["https://openalex.org/I60858718"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059728213","display_name":"Quoc-Chinh Bui","orcid":null},"institutions":[{"id":"https://openalex.org/I913958620","display_name":"Erasmus University Rotterdam","ror":"https://ror.org/057w15z03","country_code":"NL","type":"education","lineage":["https://openalex.org/I913958620"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Quoc-Chinh Bui","raw_affiliation_strings":["Department of Medical Informatics, Erasmus Medical Centre Rotterdam, Rotterdam, Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Informatics, Erasmus Medical Centre Rotterdam, Rotterdam, Netherlands","institution_ids":["https://openalex.org/I913958620"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073280030","display_name":"S\u00e9rgio Matos","orcid":"https://orcid.org/0000-0003-1941-3983"},"institutions":[{"id":"https://openalex.org/I60858718","display_name":"University of Aveiro","ror":"https://ror.org/00nt41z93","country_code":"PT","type":"education","lineage":["https://openalex.org/I60858718"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"S\u00e9rgio Matos","raw_affiliation_strings":["IEETA/DETI, University of Aveiro, 3810-193, Aveiro, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IEETA/DETI, University of Aveiro, 3810-193, Aveiro, Portugal","institution_ids":["https://openalex.org/I60858718"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040524956","display_name":"Jos\u00e9 Lu\u00eds Oliveira","orcid":"https://orcid.org/0000-0002-6672-6176"},"institutions":[{"id":"https://openalex.org/I60858718","display_name":"University of Aveiro","ror":"https://ror.org/00nt41z93","country_code":"PT","type":"education","lineage":["https://openalex.org/I60858718"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Jos\u00e9 Lu\u00eds Oliveira","raw_affiliation_strings":["IEETA/DETI, University of Aveiro, 3810-193, Aveiro, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IEETA/DETI, University of Aveiro, 3810-193, Aveiro, Portugal","institution_ids":["https://openalex.org/I60858718"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5072967999"],"corresponding_institution_ids":["https://openalex.org/I60858718"],"apc_list":null,"apc_paid":null,"fwci":2.6524,"has_fulltext":true,"cited_by_count":51,"citation_normalized_percentile":{"value":0.90606072,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"9","issue":"1","first_page":"1","last_page":"1"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9897000193595886,"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":0.9897000193595886,"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/T13083","display_name":"Advanced Text Analysis Techniques","score":0.0031999999191612005,"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/T10028","display_name":"Topic Modeling","score":0.0015999999595806003,"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":0.7421781420707703},{"id":"https://openalex.org/keywords/event","display_name":"Event (particle physics)","score":0.6241322159767151},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5729113221168518},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.41990649700164795},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32537150382995605}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7421781420707703},{"id":"https://openalex.org/C2779662365","wikidata":"https://www.wikidata.org/wiki/Q5416694","display_name":"Event (particle physics)","level":2,"score":0.6241322159767151},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5729113221168518},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.41990649700164795},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32537150382995605},{"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/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1186/1751-0473-9-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-9-1","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-9-1","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"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":"Source Code for Biology and Medicine","raw_type":"journal-article"},{"id":"pmid:24401704","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24401704","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":"Source code for biology and medicine","raw_type":null},{"id":"pmh:eur:oai:repub.eur.nl:71451","is_oa":true,"landing_page_url":"http://hdl.handle.net/1765/71451","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Source Code for Biology and Medicine, 9(1)","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:europepmc.org:2895674","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3896761","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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3896761","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3896761","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"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":"Source Code Biol Med","raw_type":"Text"},{"id":"pmh:oai:repub.eur.nl:71451","is_oa":true,"landing_page_url":"http://repub.eur.nl/pub/71451","pdf_url":null,"source":{"id":"https://openalex.org/S4306400997","display_name":"RePub (Erasmus University, Rotterdam)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I913958620","host_organization_name":"Erasmus University Rotterdam","host_organization_lineage":["https://openalex.org/I913958620"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Source Code for Biology and Medicine vol. 9 no. 1","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/1751-0473-9-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-9-1","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-9-1","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"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":"Source Code for Biology and Medicine","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.5}],"awards":[{"id":"https://openalex.org/G1578237752","display_name":null,"funder_award_id":"COMPETE","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G2222338232","display_name":null,"funder_award_id":"FCOMP-01-0124-FEDER-022682","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G706141057","display_name":null,"funder_award_id":"PEst-C/EEI/UI0127/2011","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G8868700560","display_name":null,"funder_award_id":"FCOMP-01-0124-FEDER","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"}],"funders":[{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2147788440.pdf","grobid_xml":"https://content.openalex.org/works/W2147788440.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W76749362","https://openalex.org/W154351976","https://openalex.org/W189514790","https://openalex.org/W1989375079","https://openalex.org/W1992593537","https://openalex.org/W2003185534","https://openalex.org/W2032566933","https://openalex.org/W2047782770","https://openalex.org/W2048140075","https://openalex.org/W2065963191","https://openalex.org/W2075655036","https://openalex.org/W2087616798","https://openalex.org/W2088634345","https://openalex.org/W2103017472","https://openalex.org/W2108706252","https://openalex.org/W2108791029","https://openalex.org/W2124772738","https://openalex.org/W2147880316","https://openalex.org/W2148853951","https://openalex.org/W2169528473","https://openalex.org/W2250628044","https://openalex.org/W2252132714","https://openalex.org/W2912026815","https://openalex.org/W4230872509"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655","https://openalex.org/W2359140296"],"abstract_inverted_index":{"BACKGROUND:":[0],"Cellular":[1],"events":[2,29],"play":[3],"a":[4,59,100,105,115,133,148,175,227,272],"central":[5],"role":[6],"in":[7,63,219,262],"the":[8,31,38,41,64,69,85,90,93,97,157,171,181,208,220,263,285],"understanding":[9],"of":[10,25,27,40,47,52,87,92,99,127,200,211,230,265],"biological":[11],"processes":[12],"and":[13,20,81,96,143,160,178,189,232,248,259,293,300,304],"functions,":[14],"providing":[15],"insight":[16],"on":[17,73,236,297],"both":[18],"physiological":[19],"pathogenesis":[21],"mechanisms.":[22],"Automatic":[23],"extraction":[24,66],"mentions":[26],"such":[28],"from":[30],"literature":[32],"represents":[33],"an":[34,56,281],"important":[35,61,282],"contribution":[36,177,283],"to":[37,154,207,255,284,291],"progress":[39],"biomedical":[42,120,266,286],"domain,":[43],"allowing":[44],"faster":[45,294],"updating":[46],"existing":[48,234],"knowledge.":[49],"The":[50,196,250],"identification":[51],"trigger":[53,106,122,239],"words":[54],"indicating":[55],"event":[57,65,102,121,165,213,238,267,295],"is":[58,152,280,309],"very":[60],"step":[62,77],"pipeline,":[67],"since":[68],"following":[70],"task(s)":[71],"rely":[72],"its":[74,270],"output.":[75],"This":[76,307],"presents":[78],"various":[79,201,237],"complex":[80,258],"unsolved":[82],"challenges,":[83],"namely":[84,241],"selection":[86,98],"informative":[88],"features,":[89],"representation":[91],"textual":[94],"context,":[95],"specific":[101],"type":[103],"for":[104,119,163,192],"word":[107],"given":[108],"this":[109,278],"context.":[110],"RESULTS:":[111],"We":[112,276],"propose":[113],"TrigNER,":[114],"machine":[116],"learning-based":[117],"solution":[118,252,308],"recognition,":[123],"which":[124],"takes":[125],"advantage":[126],"Conditional":[128],"Random":[129],"Fields":[130],"(CRFs)":[131],"with":[132],"high-end":[134],"feature":[135,158],"set,":[136],"including":[137],"linguistic-based,":[138],"orthographic,":[139],"morphological,":[140],"local":[141],"context":[142],"dependency":[144,193],"parsing":[145,194],"features.":[146,195],"Additionally,":[147],"completely":[149],"configurable":[150],"algorithm":[151],"used":[153],"automatically":[155,169,179],"optimize":[156],"set":[159],"training":[161],"parameters":[162],"each":[164,204,212],"type.":[166,214],"Thus,":[167],"it":[168],"selects":[170],"features":[172],"that":[173],"have":[174],"positive":[176],"optimizes":[180],"CRF":[182,202],"model":[183],"order,":[184],"n-grams":[185],"sizes,":[186],"vertex":[187],"information":[188],"maximum":[190],"hops":[191],"final":[197],"output":[198],"consists":[199],"models,":[203],"one":[205],"optimized":[206,260],"linguistic":[209],"characteristics":[210],"CONCLUSIONS:":[215],"TrigNER":[216],"was":[217],"tested":[218],"BioNLP":[221],"2009":[222],"shared":[223],"task":[224],"corpus,":[225],"achieving":[226],"total":[228],"F-measure":[229],"62.7":[231],"outperforming":[233],"solutions":[235],"types,":[240],"gene":[242],"expression,":[243],"transcription,":[244],"protein":[245],"catabolism,":[246],"phosphorylation":[247],"binding.":[249],"proposed":[251],"allows":[253],"researchers":[254],"easily":[256],"apply":[257],"techniques":[261],"recognition":[264,296],"triggers,":[268],"making":[269],"application":[271],"simple":[273],"routine":[274],"task.":[275],"believe":[277],"work":[279],"text":[287],"mining":[288],"community,":[289],"contributing":[290],"improved":[292],"scientific":[298],"articles,":[299],"consequent":[301],"hypothesis":[302],"generation":[303],"knowledge":[305],"discovery.":[306],"freely":[310],"available":[311],"as":[312],"open":[313],"source":[314],"at":[315],"http://bioinformatics.ua.pt/trigner.":[316]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":10},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":3}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}