{"id":"https://openalex.org/W2161853863","doi":"https://doi.org/10.1109/tcbb.2014.2366770","title":"Curatable Named-Entity Recognition Using Semantic Relations","display_name":"Curatable Named-Entity Recognition Using Semantic Relations","publication_year":2014,"publication_date":"2014-11-03","ids":{"openalex":"https://openalex.org/W2161853863","doi":"https://doi.org/10.1109/tcbb.2014.2366770","mag":"2161853863","pmid":"https://pubmed.ncbi.nlm.nih.gov/26357317"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2014.2366770","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2014.2366770","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084428660","display_name":"Yi-Yu Hsu","orcid":"https://orcid.org/0000-0003-4286-3181"},"institutions":[{"id":"https://openalex.org/I91807558","display_name":"National Cheng Kung University","ror":"https://ror.org/01b8kcc49","country_code":"TW","type":"education","lineage":["https://openalex.org/I91807558"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Yi-Yu Hsu","raw_affiliation_strings":["Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan, R.O.C"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan, R.O.C","institution_ids":["https://openalex.org/I91807558"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101898313","display_name":"Hung\u2010Yu Kao","orcid":"https://orcid.org/0000-0002-8890-8544"},"institutions":[{"id":"https://openalex.org/I91807558","display_name":"National Cheng Kung University","ror":"https://ror.org/01b8kcc49","country_code":"TW","type":"education","lineage":["https://openalex.org/I91807558"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Hung-Yu Kao","raw_affiliation_strings":["Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan, R.O.C"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan, R.O.C","institution_ids":["https://openalex.org/I91807558"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I91807558"],"apc_list":null,"apc_paid":null,"fwci":0.698,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.70498591,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"12","issue":"4","first_page":"785","last_page":"792"},"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/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"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9898999929428101,"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/named-entity-recognition","display_name":"Named-entity recognition","score":0.9097000956535339},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7813257575035095},{"id":"https://openalex.org/keywords/crfs","display_name":"CRFS","score":0.7754561901092529},{"id":"https://openalex.org/keywords/conditional-random-field","display_name":"Conditional random field","score":0.6678122878074646},{"id":"https://openalex.org/keywords/uniprot","display_name":"UniProt","score":0.6108404994010925},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5470590591430664},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.5364336371421814},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.49603113532066345},{"id":"https://openalex.org/keywords/latent-dirichlet-allocation","display_name":"Latent Dirichlet allocation","score":0.46273335814476013},{"id":"https://openalex.org/keywords/entity-linking","display_name":"Entity linking","score":0.4351913630962372},{"id":"https://openalex.org/keywords/topic-model","display_name":"Topic model","score":0.32597678899765015},{"id":"https://openalex.org/keywords/knowledge-base","display_name":"Knowledge base","score":0.17901864647865295},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09823867678642273}],"concepts":[{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.9097000956535339},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7813257575035095},{"id":"https://openalex.org/C2775953691","wikidata":"https://www.wikidata.org/wiki/Q5013874","display_name":"CRFS","level":3,"score":0.7754561901092529},{"id":"https://openalex.org/C152565575","wikidata":"https://www.wikidata.org/wiki/Q1124538","display_name":"Conditional random field","level":2,"score":0.6678122878074646},{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.6108404994010925},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5470590591430664},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5364336371421814},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.49603113532066345},{"id":"https://openalex.org/C500882744","wikidata":"https://www.wikidata.org/wiki/Q269236","display_name":"Latent Dirichlet allocation","level":3,"score":0.46273335814476013},{"id":"https://openalex.org/C96711827","wikidata":"https://www.wikidata.org/wiki/Q17012245","display_name":"Entity linking","level":3,"score":0.4351913630962372},{"id":"https://openalex.org/C171686336","wikidata":"https://www.wikidata.org/wiki/Q3532085","display_name":"Topic model","level":2,"score":0.32597678899765015},{"id":"https://openalex.org/C4554734","wikidata":"https://www.wikidata.org/wiki/Q593744","display_name":"Knowledge base","level":2,"score":0.17901864647865295},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09823867678642273},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"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/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"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":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D043922","descriptor_name":"Toxicogenetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D043922","descriptor_name":"Toxicogenetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D043922","descriptor_name":"Toxicogenetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2014.2366770","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2014.2366770","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26357317","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26357317","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.5099999904632568}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W151243474","https://openalex.org/W1550258693","https://openalex.org/W1880262756","https://openalex.org/W2018737226","https://openalex.org/W2032729847","https://openalex.org/W2040298461","https://openalex.org/W2070412833","https://openalex.org/W2084377579","https://openalex.org/W2091940856","https://openalex.org/W2102575587","https://openalex.org/W2105481534","https://openalex.org/W2109555487","https://openalex.org/W2109943925","https://openalex.org/W2112156955","https://openalex.org/W2119091936","https://openalex.org/W2121652122","https://openalex.org/W2123579157","https://openalex.org/W2127008962","https://openalex.org/W2127239015","https://openalex.org/W2127480960","https://openalex.org/W2133280805","https://openalex.org/W2153635508","https://openalex.org/W2156909104","https://openalex.org/W2158994553","https://openalex.org/W2161132397","https://openalex.org/W2168066604","https://openalex.org/W2169918010","https://openalex.org/W4231510805","https://openalex.org/W6632766574","https://openalex.org/W6639619044","https://openalex.org/W6678490793","https://openalex.org/W6679915538"],"related_works":["https://openalex.org/W2151982765","https://openalex.org/W2061834489","https://openalex.org/W2045347339","https://openalex.org/W2398073356","https://openalex.org/W3087842898","https://openalex.org/W2166353137","https://openalex.org/W3121295082","https://openalex.org/W2362486597","https://openalex.org/W2784047400","https://openalex.org/W2161853863"],"abstract_inverted_index":{"Named-entity":[0,53],"recognition":[1,143],"(NER)":[2],"plays":[3],"an":[4],"important":[5],"role":[6],"in":[7,24,72,91,112,127,145,165],"the":[8,14,46,73,89,92,139,166,180,185],"development":[9],"of":[10,133],"biomedical":[11],"databases.":[12],"However,":[13],"existing":[15],"NER":[16,194],"tools":[17,144],"produce":[18],"multifarious":[19],"named-entities":[20,39],"which":[21],"may":[22],"result":[23],"both":[25],"curatable":[26,38],"and":[27,68,109,162,192],"non-curatable":[28],"markers.":[29],"To":[30,78],"facilitate":[31],"biocuration":[32,47],"with":[33,42,52],"a":[34,57,102,149,201],"straightforward":[35],"approach,":[36],"classifying":[37],"is":[40,56,98,157],"helpful":[41],"regard":[43],"to":[44,63,87,159],"accelerating":[45],"workflow.":[48],"Co-occurrence":[49],"Interaction":[50],"Nexus":[51],"Recognition":[54],"(CoINNER)":[55],"web-based":[58],"tool":[59],"that":[60,105],"allows":[61],"users":[62],"identify":[64],"genes,":[65],"chemicals,":[66],"diseases,":[67],"action":[69,169],"term":[70,170],"mentions":[71,90,111,164,171],"Comparative":[74],"Toxicogenomic":[75],"Database":[76],"(CTD).":[77],"further":[79],"discover":[80],"interactions,":[81],"CoINNER":[82,97,134,199],"uses":[83],"multiple":[84],"advanced":[85],"algorithms":[86],"recognize":[88],"BioCreative":[93,116,146,181],"IV":[94,182],"CTD":[95,183],"Track.":[96],"developed":[99,136],"based":[100,137,151],"on":[101,138,152],"prototype":[103],"system":[104,126],"annotated":[106],"gene,":[107],"chemical,":[108],"disease":[110,163,193],"PubMed":[113],"abstracts":[114],"at":[115],"2012":[117],"Track":[118],"I":[119],"(literature":[120],"triage).":[121],"We":[122],"extended":[123],"our":[124],"previous":[125],"developing":[128],"CoINNER.":[129],"The":[130],"pre-tagging":[131],"results":[132],"were":[135,172,195],"state-of-the-art":[140],"named":[141],"entity":[142],"III.":[147],"Next,":[148],"method":[150],"conditional":[153],"random":[154],"fields":[155],"(CRFs)":[156],"proposed":[158],"predict":[160],"chemical":[161],"articles.":[167],"Finally,":[168],"collected":[173],"by":[174],"latent":[175],"Dirichlet":[176],"allocation":[177],"(LDA).":[178],"At":[179],"Track,":[184],"best":[186],"F-measures":[187],"reached":[188],"for":[189],"gene/protein,":[190],"chemical/drug":[191],"54":[196],"percent":[197,203],"while":[198],"achieved":[200],"61.5":[202],"F-measure.":[204],"System":[205],"URL:":[206],"http://ikmbio.csie.ncku.edu.tw/coinner/":[207],"introduction.htm.":[208]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}