{"id":"https://openalex.org/W2741379117","doi":"https://doi.org/10.18653/v1/w17-2310","title":"End-to-End System for Bacteria Habitat Extraction","display_name":"End-to-End System for Bacteria Habitat Extraction","publication_year":2017,"publication_date":"2017-01-01","ids":{"openalex":"https://openalex.org/W2741379117","doi":"https://doi.org/10.18653/v1/w17-2310","mag":"2741379117"},"language":"en","primary_location":{"id":"doi:10.18653/v1/w17-2310","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/w17-2310","pdf_url":"https://www.aclweb.org/anthology/W17-2310.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioNLP 2017","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.aclweb.org/anthology/W17-2310.pdf","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086256360","display_name":"Farrokh Mehryary","orcid":"https://orcid.org/0000-0002-5555-2828"},"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"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Farrokh Mehryary","raw_affiliation_strings":[". The University of Turku Graduate School (UTUGS), University of Turku, Finland",". Turku NLP Group, Department of FT, University of Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":". The University of Turku Graduate School (UTUGS), University of Turku, Finland","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":". Turku NLP Group, Department of FT, University of Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058939594","display_name":"Kai Hakala","orcid":"https://orcid.org/0000-0001-8943-7011"},"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"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Kai Hakala","raw_affiliation_strings":[". The University of Turku Graduate School (UTUGS), University of Turku, Finland",". Turku NLP Group, Department of FT, University of Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":". The University of Turku Graduate School (UTUGS), University of Turku, Finland","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":". Turku NLP Group, Department of FT, University of Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000080545","display_name":"Suwisa Kaewphan","orcid":"https://orcid.org/0000-0001-8534-1215"},"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":"Suwisa Kaewphan","raw_affiliation_strings":[". The University of Turku Graduate School (UTUGS), University of Turku, Finland",". Turku NLP Group, Department of FT, University of Turku, Finland",". Turku Centre for Computer Science (TUCS), Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":". The University of Turku Graduate School (UTUGS), University of Turku, Finland","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":". Turku NLP Group, Department of FT, 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"]}]},{"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"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Jari Bj\u00f6rne","raw_affiliation_strings":[". Turku NLP Group, Department of FT, University of Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":". Turku NLP Group, Department of FT, University of Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]},{"author_position":"middle","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":[". Turku Centre for Computer Science (TUCS), Finland",". Turku NLP Group, Department of FT, University of Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":". Turku Centre for Computer Science (TUCS), Finland","institution_ids":["https://openalex.org/I183173800"]},{"raw_affiliation_string":". Turku NLP Group, Department of FT, University of Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019929457","display_name":"Filip Ginter","orcid":"https://orcid.org/0000-0002-5484-6103"},"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"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Filip Ginter","raw_affiliation_strings":[". Turku NLP Group, Department of FT, University of Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":". Turku NLP Group, Department of FT, University of Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"80","last_page":"90"},"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/T10028","display_name":"Topic Modeling","score":0.9975000023841858,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9860000014305115,"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":0.8036257028579712},{"id":"https://openalex.org/keywords/normalization","display_name":"Normalization (sociology)","score":0.7545052170753479},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5903931856155396},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5710710287094116},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.5680498480796814},{"id":"https://openalex.org/keywords/relationship-extraction","display_name":"Relationship extraction","score":0.5219061970710754},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.4365352392196655},{"id":"https://openalex.org/keywords/f1-score","display_name":"F1 score","score":0.43024903535842896},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4085691571235657},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.32975712418556213},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.13116678595542908},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.07791122794151306}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8036257028579712},{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.7545052170753479},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5903931856155396},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5710710287094116},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.5680498480796814},{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.5219061970710754},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.4365352392196655},{"id":"https://openalex.org/C148524875","wikidata":"https://www.wikidata.org/wiki/Q6975395","display_name":"F1 score","level":2,"score":0.43024903535842896},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4085691571235657},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.32975712418556213},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.13116678595542908},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.07791122794151306},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.18653/v1/w17-2310","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/w17-2310","pdf_url":"https://www.aclweb.org/anthology/W17-2310.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioNLP 2017","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.18653/v1/w17-2310","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/w17-2310","pdf_url":"https://www.aclweb.org/anthology/W17-2310.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioNLP 2017","raw_type":"proceedings-article"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.6100000143051147,"id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2741379117.pdf","grobid_xml":"https://content.openalex.org/works/W2741379117.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W122290181","https://openalex.org/W1508977358","https://openalex.org/W1522301498","https://openalex.org/W1750263989","https://openalex.org/W1859283887","https://openalex.org/W1978394996","https://openalex.org/W2051718393","https://openalex.org/W2095705004","https://openalex.org/W2096765155","https://openalex.org/W2098162425","https://openalex.org/W2101234009","https://openalex.org/W2108791029","https://openalex.org/W2138627627","https://openalex.org/W2142016317","https://openalex.org/W2159583324","https://openalex.org/W2173188050","https://openalex.org/W2176568210","https://openalex.org/W2229453122","https://openalex.org/W2250232417","https://openalex.org/W2251279337","https://openalex.org/W2252145363","https://openalex.org/W2509401464","https://openalex.org/W2509884321","https://openalex.org/W2510327534","https://openalex.org/W2511500211","https://openalex.org/W2511570169","https://openalex.org/W2511964075","https://openalex.org/W2515582862","https://openalex.org/W2518463060","https://openalex.org/W2527896214","https://openalex.org/W2964121744","https://openalex.org/W2964217331"],"related_works":["https://openalex.org/W2064314529","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/W2489933339","https://openalex.org/W2572241437","https://openalex.org/W4379379356"],"abstract_inverted_index":{"We":[0,37,88],"introduce":[1],"an":[2],"end-to-end":[3],"system":[4,25,42],"capable":[5],"of":[6,60,72],"named-entity":[7],"detection,":[8],"normalization":[9,95],"and":[10,18,33,39,64],"relation":[11,65],"extraction":[12,66],"for":[13,85],"extracting":[14],"information":[15],"about":[16],"bacteria":[17],"their":[19],"habitats":[20],"from":[21],"biomedical":[22],"literature.":[23],"Our":[24],"is":[26],"based":[27],"on":[28,43,78],"deep":[29],"learning,":[30],"CRF":[31],"classifiers":[32],"vector":[34],"space":[35],"models.":[36],"train":[38],"evaluate":[40],"the":[41,44,57,69,73,86,94],"BioNLP":[45],"2016":[46],"Shared":[47,74],"Task":[48,75],"Bacteria":[49],"Biotope":[50],"data.":[51],"The":[52],"official":[53],"evaluation":[54],"shows":[55],"that":[56],"joint":[58],"performance":[59],"our":[61],"entity":[62],"detection":[63],"models":[67],"outperforms":[68],"winning":[70],"team":[71],"by":[76],"19pp":[77],"F-score,":[79],"establishing":[80],"a":[81],"new":[82],"top":[83],"score":[84],"task.":[87,96],"also":[89],"achieve":[90],"state-ofthe-art":[91],"results":[92],"in":[93]},"counts_by_year":[{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":1}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}