{"id":"https://openalex.org/W2115562276","doi":"https://doi.org/10.1186/1758-2946-7-s1-s9","title":"Incorporating domain knowledge in chemical and biomedical named entity recognition with word representations","display_name":"Incorporating domain knowledge in chemical and biomedical named entity recognition with word representations","publication_year":2015,"publication_date":"2015-01-19","ids":{"openalex":"https://openalex.org/W2115562276","doi":"https://doi.org/10.1186/1758-2946-7-s1-s9","mag":"2115562276","pmid":"https://pubmed.ncbi.nlm.nih.gov/25810780"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-7-s1-s9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-7-s1-s9","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-7-S1-S9","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-7-S1-S9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062473985","display_name":"Tsendsuren Munkhdalai","orcid":"https://orcid.org/0000-0002-8783-4993"},"institutions":[{"id":"https://openalex.org/I163753206","display_name":"Chungbuk National University","ror":"https://ror.org/02wnxgj78","country_code":"KR","type":"education","lineage":["https://openalex.org/I163753206"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Tsendsuren Munkhdalai","raw_affiliation_strings":["Database/Bioinformatics Laboratory, School of Electrical & Computer Engineering, Chungbuk National University, Cheongju, South Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Database/Bioinformatics Laboratory, School of Electrical & Computer Engineering, Chungbuk National University, Cheongju, South Korea","institution_ids":["https://openalex.org/I163753206"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101641185","display_name":"Meijing Li","orcid":"https://orcid.org/0000-0002-3626-9066"},"institutions":[{"id":"https://openalex.org/I163753206","display_name":"Chungbuk National University","ror":"https://ror.org/02wnxgj78","country_code":"KR","type":"education","lineage":["https://openalex.org/I163753206"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Meijing Li","raw_affiliation_strings":["Database/Bioinformatics Laboratory, School of Electrical & Computer Engineering, Chungbuk National University, Cheongju, South Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Database/Bioinformatics Laboratory, School of Electrical & Computer Engineering, Chungbuk National University, Cheongju, South Korea","institution_ids":["https://openalex.org/I163753206"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086221076","display_name":"Khuyagbaatar Batsuren","orcid":"https://orcid.org/0000-0002-6819-5444"},"institutions":[{"id":"https://openalex.org/I163753206","display_name":"Chungbuk National University","ror":"https://ror.org/02wnxgj78","country_code":"KR","type":"education","lineage":["https://openalex.org/I163753206"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Khuyagbaatar Batsuren","raw_affiliation_strings":["Database/Bioinformatics Laboratory, School of Electrical & Computer Engineering, Chungbuk National University, Cheongju, South Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Database/Bioinformatics Laboratory, School of Electrical & Computer Engineering, Chungbuk National University, Cheongju, South Korea","institution_ids":["https://openalex.org/I163753206"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020963205","display_name":"Hyeon Ah Park","orcid":null},"institutions":[{"id":"https://openalex.org/I163753206","display_name":"Chungbuk National University","ror":"https://ror.org/02wnxgj78","country_code":"KR","type":"education","lineage":["https://openalex.org/I163753206"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Hyeon Ah Park","raw_affiliation_strings":["Database/Bioinformatics Laboratory, School of Electrical & Computer Engineering, Chungbuk National University, Cheongju, South Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Database/Bioinformatics Laboratory, School of Electrical & Computer Engineering, Chungbuk National University, Cheongju, South Korea","institution_ids":["https://openalex.org/I163753206"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060163419","display_name":"Nak Hyeon Choi","orcid":null},"institutions":[{"id":"https://openalex.org/I163753206","display_name":"Chungbuk National University","ror":"https://ror.org/02wnxgj78","country_code":"KR","type":"education","lineage":["https://openalex.org/I163753206"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Nak Hyeon Choi","raw_affiliation_strings":["Database/Bioinformatics Laboratory, School of Electrical & Computer Engineering, Chungbuk National University, Cheongju, South Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Database/Bioinformatics Laboratory, School of Electrical & Computer Engineering, Chungbuk National University, Cheongju, South Korea","institution_ids":["https://openalex.org/I163753206"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043932631","display_name":"Keun Ho Ryu","orcid":"https://orcid.org/0000-0003-0394-9054"},"institutions":[{"id":"https://openalex.org/I163753206","display_name":"Chungbuk National University","ror":"https://ror.org/02wnxgj78","country_code":"KR","type":"education","lineage":["https://openalex.org/I163753206"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Keun Ho Ryu","raw_affiliation_strings":["Database/Bioinformatics Laboratory, School of Electrical & Computer Engineering, Chungbuk National University, Cheongju, South Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Database/Bioinformatics Laboratory, School of Electrical & Computer Engineering, Chungbuk National University, Cheongju, South Korea","institution_ids":["https://openalex.org/I163753206"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5043932631"],"corresponding_institution_ids":["https://openalex.org/I163753206"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":4.3677,"has_fulltext":true,"cited_by_count":46,"citation_normalized_percentile":{"value":0.95074432,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"7","issue":"S1","first_page":"S9","last_page":"S9"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.8504999876022339,"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":0.8504999876022339,"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":0.11110000312328339,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.007000000216066837,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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":0.8786419630050659},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8536646366119385},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6202128529548645},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.6172524094581604},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.6165424585342407},{"id":"https://openalex.org/keywords/conditional-random-field","display_name":"Conditional random field","score":0.6152625679969788},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.47368812561035156},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.47009631991386414},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.4131661355495453},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.14170798659324646}],"concepts":[{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.8786419630050659},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8536646366119385},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6202128529548645},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.6172524094581604},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.6165424585342407},{"id":"https://openalex.org/C152565575","wikidata":"https://www.wikidata.org/wiki/Q1124538","display_name":"Conditional random field","level":2,"score":0.6152625679969788},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.47368812561035156},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.47009631991386414},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.4131661355495453},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.14170798659324646},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","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}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/1758-2946-7-s1-s9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-7-s1-s9","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-7-S1-S9","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:25810780","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25810780","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":"Journal of cheminformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:3334616","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4331699","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:10.1186/1758-2946-7-s1-s9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-7-s1-s9","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-7-S1-S9","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Quality Education","score":0.7300000190734863,"id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G1366621873","display_name":null,"funder_award_id":"2008-0062611","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"},{"id":"https://openalex.org/G2552964249","display_name":null,"funder_award_id":"2013R1A2A2A01068923","funder_id":"https://openalex.org/F4320322030","funder_display_name":"Ministry of Science, ICT and Future Planning"},{"id":"https://openalex.org/G5184896402","display_name":null,"funder_award_id":"2008-0062611","funder_id":"https://openalex.org/F4320320671","funder_display_name":"National Research Foundation"},{"id":"https://openalex.org/G7522479510","display_name":null,"funder_award_id":"2013R1A2A2A01068923","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"},{"id":"https://openalex.org/G8313445081","display_name":null,"funder_award_id":"2008-0062611","funder_id":"https://openalex.org/F4320322030","funder_display_name":"Ministry of Science, ICT and Future Planning"}],"funders":[{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320322030","display_name":"Ministry of Science, ICT and Future Planning","ror":"https://ror.org/032e49973"},{"id":"https://openalex.org/F4320322120","display_name":"National Research Foundation of Korea","ror":"https://ror.org/013aysd81"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2115562276.pdf","grobid_xml":"https://content.openalex.org/works/W2115562276.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W55204438","https://openalex.org/W103980920","https://openalex.org/W1423339008","https://openalex.org/W1583837637","https://openalex.org/W1614298861","https://openalex.org/W2004111828","https://openalex.org/W2008639146","https://openalex.org/W2021331223","https://openalex.org/W2051999173","https://openalex.org/W2101553882","https://openalex.org/W2103316358","https://openalex.org/W2103320915","https://openalex.org/W2107005506","https://openalex.org/W2114361266","https://openalex.org/W2117479478","https://openalex.org/W2119091936","https://openalex.org/W2121227244","https://openalex.org/W2121244856","https://openalex.org/W2121802207","https://openalex.org/W2127008962","https://openalex.org/W2127239015","https://openalex.org/W2134967412","https://openalex.org/W2141252530","https://openalex.org/W2142016317","https://openalex.org/W2145870108","https://openalex.org/W2147154106","https://openalex.org/W2149369282","https://openalex.org/W2152398020","https://openalex.org/W2158139315","https://openalex.org/W2165647706","https://openalex.org/W2171374484","https://openalex.org/W2172240666","https://openalex.org/W2559997609","https://openalex.org/W2733628661","https://openalex.org/W3082731548","https://openalex.org/W4300022934","https://openalex.org/W4392051461"],"related_works":["https://openalex.org/W4250494529","https://openalex.org/W1964783010","https://openalex.org/W2399696375","https://openalex.org/W45206245","https://openalex.org/W2211396092","https://openalex.org/W2061834489","https://openalex.org/W3088215229","https://openalex.org/W2078793151","https://openalex.org/W3047727388","https://openalex.org/W2759598007"],"abstract_inverted_index":{"BACKGROUND:":[0],"Chemical":[1,233,238],"and":[2,34,75,106,170,202,223,237,244,267],"biomedical":[3,50,152,174,268],"Named":[4],"Entity":[5,234],"Recognition":[6],"(NER)":[7],"is":[8,186,198,272],"an":[9,32,161,221,224,246],"essential":[10],"prerequisite":[11],"task":[12],"before":[13],"effective":[14],"text":[15,24,39,90,101,117],"mining":[16,40],"can":[17,165,203],"begin":[18],"for":[19,89,103,110],"biochemical-text":[20],"data.":[21,146],"Exploiting":[22],"unlabeled":[23,61],"data":[25,62,102],"to":[26,42,65,76,135,140,168],"leverage":[27,77],"system":[28,78,138,163,183,271],"performance":[29,263],"has":[30],"been":[31],"active":[33],"challenging":[35],"research":[36],"topic":[37],"in":[38,46,63,118,133,144,264],"due":[41],"the":[43,47,115,119,121,137,156,181,211,228,250,255],"recent":[44],"growth":[45],"amount":[48,99],"of":[49,100,180,190,231,254],"literature.":[51],"We":[52,148,176],"present":[53],"a":[54,70,97,151],"semi-supervised":[55],"learning":[56,92],"method":[57,82,123],"that":[58,164],"efficiently":[59],"exploits":[60],"order":[64,134],"incorporate":[66],"domain":[67],"knowledge":[68],"into":[69,206],"named":[71],"entity":[72],"recognition":[73],"model":[74],"performance.":[79],"The":[80],"proposed":[81,122,157],"includes":[83],"Natural":[84],"Language":[85],"Processing":[86],"(NLP)":[87],"tasks":[88,143],"preprocessing,":[91],"word":[93],"representation":[94],"features":[95],"from":[96],"large":[98],"feature":[104],"extraction,":[105],"conditional":[107],"random":[108],"fields":[109],"token":[111],"classification.":[112],"Other":[113],"than":[114],"free":[116],"domain,":[120],"does":[124],"not":[125],"rely":[126],"on":[127,227,249],"any":[128,131],"lexicon":[129],"nor":[130],"dictionary":[132],"keep":[136],"applicable":[139],"other":[141,207],"NER":[142,153,172],"bio-text":[145],"RESULTS:":[147],"extended":[149],"BANNER,":[150],"system,":[154],"with":[155],"method.":[158],"This":[159],"yields":[160],"integrated":[162],"be":[166,204],"applied":[167],"chemical":[169,266],"drug":[171],"or":[173],"NER.":[175,269],"call":[177],"our":[178],"branch":[179],"BANNER":[182,212],"BANNER-CHEMDNER,":[184],"which":[185],"scalable":[187],"over":[188],"millions":[189],"documents,":[191],"processing":[192],"about":[193],"530":[194],"documents":[195],"per":[196],"minute,":[197],"configurable":[199],"via":[200],"XML,":[201],"plugged":[205],"systems":[208],"by":[209],"using":[210],"Unstructured":[213],"Information":[214],"Management":[215],"Architecture":[216],"(UIMA)":[217],"interface.":[218],"BANNER-CHEMDNER":[219,270],"achieved":[220,245],"85.68%":[222],"86.47%":[225],"F-measure":[226,248],"testing":[229,252],"sets":[230],"CHEMDNER":[232],"Mention":[235],"(CEM)":[236],"Document":[239],"Indexing":[240],"(CDI)":[241],"subtasks,":[242],"respectively,":[243],"87.04%":[247],"official":[251],"set":[253],"BioCreative":[256],"II":[257],"gene":[258],"mention":[259],"task,":[260],"showing":[261],"remarkable":[262],"both":[265],"available":[273],"at:":[274],"https://bitbucket.org/tsendeemts/banner-chemdner.":[275]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":10},{"year":2015,"cited_by_count":4}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
