{"id":"https://openalex.org/W2112670696","doi":"https://doi.org/10.1093/bioinformatics/bti414","title":"POSBIOTM--NER: a trainable biomedical named-entity recognition system","display_name":"POSBIOTM--NER: a trainable biomedical named-entity recognition system","publication_year":2005,"publication_date":"2005-04-06","ids":{"openalex":"https://openalex.org/W2112670696","doi":"https://doi.org/10.1093/bioinformatics/bti414","mag":"2112670696","pmid":"https://pubmed.ncbi.nlm.nih.gov/15814561"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti414","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti414","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/11/2794/48971189/bioinformatics_21_11_2794.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/21/11/2794/48971189/bioinformatics_21_11_2794.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101453734","display_name":"Yu Song","orcid":"https://orcid.org/0000-0001-8727-1097"},"institutions":[{"id":"https://openalex.org/I123900574","display_name":"Pohang University of Science and Technology","ror":"https://ror.org/04xysgw12","country_code":"KR","type":"education","lineage":["https://openalex.org/I123900574"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Y. Song","raw_affiliation_strings":["Department of CSE, POSTECH Pohang, 790-784, Korea. songyu@postech.ac.kr","Department of CSE, POSTECH Pohang, 790-784, Korea#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of CSE, POSTECH Pohang, 790-784, Korea. songyu@postech.ac.kr","institution_ids":["https://openalex.org/I123900574"]},{"raw_affiliation_string":"Department of CSE, POSTECH Pohang, 790-784, Korea#TAB#","institution_ids":["https://openalex.org/I123900574"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100728165","display_name":"Edward Kim","orcid":"https://orcid.org/0000-0002-7715-4054"},"institutions":[{"id":"https://openalex.org/I123900574","display_name":"Pohang University of Science and Technology","ror":"https://ror.org/04xysgw12","country_code":"KR","type":"education","lineage":["https://openalex.org/I123900574"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"E. Kim","raw_affiliation_strings":["Department of CSE, POSTECH  Pohang, 790-784, Korea","Department of CSE, POSTECH Pohang, 790-784, Korea#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of CSE, POSTECH  Pohang, 790-784, Korea","institution_ids":["https://openalex.org/I123900574"]},{"raw_affiliation_string":"Department of CSE, POSTECH Pohang, 790-784, Korea#TAB#","institution_ids":["https://openalex.org/I123900574"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023749697","display_name":"G. G. Lee","orcid":"https://orcid.org/0000-0002-7024-345X"},"institutions":[{"id":"https://openalex.org/I123900574","display_name":"Pohang University of Science and Technology","ror":"https://ror.org/04xysgw12","country_code":"KR","type":"education","lineage":["https://openalex.org/I123900574"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"G. G. Lee","raw_affiliation_strings":["Department of CSE, POSTECH  Pohang, 790-784, Korea","Department of CSE, POSTECH Pohang, 790-784, Korea#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of CSE, POSTECH  Pohang, 790-784, Korea","institution_ids":["https://openalex.org/I123900574"]},{"raw_affiliation_string":"Department of CSE, POSTECH Pohang, 790-784, Korea#TAB#","institution_ids":["https://openalex.org/I123900574"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030042887","display_name":"Byoung-Kee Yi","orcid":"https://orcid.org/0000-0002-7699-9629"},"institutions":[{"id":"https://openalex.org/I123900574","display_name":"Pohang University of Science and Technology","ror":"https://ror.org/04xysgw12","country_code":"KR","type":"education","lineage":["https://openalex.org/I123900574"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"B.-k. Yi","raw_affiliation_strings":["Department of CSE, POSTECH  Pohang, 790-784, Korea","Department of CSE, POSTECH Pohang, 790-784, Korea#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of CSE, POSTECH  Pohang, 790-784, Korea","institution_ids":["https://openalex.org/I123900574"]},{"raw_affiliation_string":"Department of CSE, POSTECH Pohang, 790-784, Korea#TAB#","institution_ids":["https://openalex.org/I123900574"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5101453734"],"corresponding_institution_ids":["https://openalex.org/I123900574"],"apc_list":null,"apc_paid":null,"fwci":0.8615,"has_fulltext":false,"cited_by_count":35,"citation_normalized_percentile":{"value":0.71439944,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"21","issue":"11","first_page":"2794","last_page":"2796"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998000264167786,"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":0.9998000264167786,"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/T10181","display_name":"Natural Language Processing Techniques","score":0.9972000122070312,"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":0.9959999918937683,"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/named-entity-recognition","display_name":"Named-entity recognition","score":0.9291780591011047},{"id":"https://openalex.org/keywords/conditional-random-field","display_name":"Conditional random field","score":0.918263852596283},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.84307861328125},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.656353771686554},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.632846474647522},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.5398999452590942},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.45895108580589294},{"id":"https://openalex.org/keywords/conjunction","display_name":"Conjunction (astronomy)","score":0.45469537377357483},{"id":"https://openalex.org/keywords/linguistics","display_name":"Linguistics","score":0.09114551544189453},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.07003739476203918}],"concepts":[{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.9291780591011047},{"id":"https://openalex.org/C152565575","wikidata":"https://www.wikidata.org/wiki/Q1124538","display_name":"Conditional random field","level":2,"score":0.918263852596283},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.84307861328125},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.656353771686554},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.632846474647522},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.5398999452590942},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.45895108580589294},{"id":"https://openalex.org/C59656382","wikidata":"https://www.wikidata.org/wiki/Q191536","display_name":"Conjunction (astronomy)","level":2,"score":0.45469537377357483},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.09114551544189453},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.07003739476203918},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"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/C1276947","wikidata":"https://www.wikidata.org/wiki/Q333","display_name":"Astronomy","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/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","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/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bti414","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti414","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/11/2794/48971189/bioinformatics_21_11_2794.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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:15814561","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15814561","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:oasis.postech.ac.kr:2014.oak/24578","is_oa":false,"landing_page_url":"https://oasis.postech.ac.kr/handle/2014.oak/24578","pdf_url":null,"source":{"id":"https://openalex.org/S4306401965","display_name":"Open Access System for Information Sharing (Pohang University of Science and Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I123900574","host_organization_name":"Pohang University of Science and Technology","host_organization_lineage":["https://openalex.org/I123900574"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti414","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti414","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/11/2794/48971189/bioinformatics_21_11_2794.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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":[{"display_name":"Quality Education","score":0.5799999833106995,"id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2112670696.pdf","grobid_xml":"https://content.openalex.org/works/W2112670696.grobid-xml"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W2047782770","https://openalex.org/W2127479124","https://openalex.org/W2130260860","https://openalex.org/W2135912801","https://openalex.org/W2147880316","https://openalex.org/W2163107094"],"related_works":["https://openalex.org/W2078793151","https://openalex.org/W4288762748","https://openalex.org/W3003390203","https://openalex.org/W2751906762","https://openalex.org/W2510663906","https://openalex.org/W2886890203","https://openalex.org/W2411964588","https://openalex.org/W4313594223","https://openalex.org/W136407171","https://openalex.org/W2759598007"],"abstract_inverted_index":{"POSBIOTM-NER":[0,8],"is":[1],"a":[2],"trainable":[3],"biomedical":[4],"named-entity":[5],"recognition":[6],"system.":[7],"can":[9],"be":[10,67],"automatically":[11],"trained":[12,37,46],"and":[13,29,56],"adapted":[14],"to":[15],"new":[16],"datasets":[17],"without":[18],"performance":[19],"degradation,":[20],"using":[21],"CRF":[22],"(conditional":[23],"random":[24],"field)":[25],"machine":[26],"learning":[27],"techniques":[28],"automatic":[30],"linguistic":[31],"feature":[32],"analysis.":[33],"Currently,":[34],"we":[35],"have":[36],"our":[38,60],"system":[39],"on":[40,48,53,59],"three":[41],"different":[42],"datasets.":[43],"GENIA-NER":[44],"was":[45],"based":[47,52,58],"GENIA":[49],"Corpus,":[50],"GENE-NER":[51],"BioCreative":[54],"data":[55],"GPCR-NER":[57],"own":[61],"POSBIOTM/NE":[62],"corpus,":[63],"respectively,":[64],"which":[65],"would":[66],"used":[68],"in":[69],"GPCR-related":[70],"pathway":[71],"extraction.":[72]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":2}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
