{"id":"https://openalex.org/W2604019706","doi":"https://doi.org/10.1093/bioinformatics/btx172","title":"A transition-based joint model for disease named entity recognition and normalization","display_name":"A transition-based joint model for disease named entity recognition and normalization","publication_year":2017,"publication_date":"2017-03-24","ids":{"openalex":"https://openalex.org/W2604019706","doi":"https://doi.org/10.1093/bioinformatics/btx172","mag":"2604019706","pmid":"https://pubmed.ncbi.nlm.nih.gov/28369171"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx172","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx172","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/15/2363/25157980/btx172.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"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","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/15/2363/25157980/btx172.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063227535","display_name":"Yinxia Lou","orcid":"https://orcid.org/0000-0001-5500-5982"},"institutions":[{"id":"https://openalex.org/I37461747","display_name":"Wuhan University","ror":"https://ror.org/033vjfk17","country_code":"CN","type":"education","lineage":["https://openalex.org/I37461747"]},{"id":"https://openalex.org/I89381930","display_name":"Shangqiu Normal University","ror":"https://ror.org/008m8sh03","country_code":"CN","type":"education","lineage":["https://openalex.org/I89381930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yinxia Lou","raw_affiliation_strings":["Computer School, Wuhan University, Wuhan, China","School of Computer and Information Technology, Shangqiu Normal University, Shangqiu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer School, Wuhan University, Wuhan, China","institution_ids":["https://openalex.org/I37461747"]},{"raw_affiliation_string":"School of Computer and Information Technology, Shangqiu Normal University, Shangqiu, China","institution_ids":["https://openalex.org/I89381930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100333738","display_name":"Yue Zhang","orcid":"https://orcid.org/0000-0002-6327-5023"},"institutions":[{"id":"https://openalex.org/I152815399","display_name":"Singapore University of Technology and Design","ror":"https://ror.org/05j6fvn87","country_code":"SG","type":"education","lineage":["https://openalex.org/I152815399"]},{"id":"https://openalex.org/I89381930","display_name":"Shangqiu Normal University","ror":"https://ror.org/008m8sh03","country_code":"CN","type":"education","lineage":["https://openalex.org/I89381930"]}],"countries":["CN","SG"],"is_corresponding":false,"raw_author_name":"Yue Zhang","raw_affiliation_strings":["Singapore University of Technology and Design, Shangqiu Normal University, Shangqiu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Singapore University of Technology and Design, Shangqiu Normal University, Shangqiu, China","institution_ids":["https://openalex.org/I152815399","https://openalex.org/I89381930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035133018","display_name":"Qian Tao","orcid":"https://orcid.org/0000-0002-8416-7224"},"institutions":[{"id":"https://openalex.org/I4210101555","display_name":"Hubei University of Science and Technology","ror":"https://ror.org/018wg9441","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210101555"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tao Qian","raw_affiliation_strings":["College of Computer Science and Technology,Hubei University of Science and Technology, Xianning, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology,Hubei University of Science and Technology, Xianning, China","institution_ids":["https://openalex.org/I4210101555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100325881","display_name":"Fei Li","orcid":"https://orcid.org/0000-0003-1816-1761"},"institutions":[{"id":"https://openalex.org/I37461747","display_name":"Wuhan University","ror":"https://ror.org/033vjfk17","country_code":"CN","type":"education","lineage":["https://openalex.org/I37461747"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fei Li","raw_affiliation_strings":["Computer School, Wuhan University, Wuhan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer School, Wuhan University, Wuhan, China","institution_ids":["https://openalex.org/I37461747"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020111720","display_name":"Shufeng Xiong","orcid":"https://orcid.org/0000-0001-5727-1766"},"institutions":[{"id":"https://openalex.org/I151878197","display_name":"Pingdingshan University","ror":"https://ror.org/026c29h90","country_code":"CN","type":"education","lineage":["https://openalex.org/I151878197"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shufeng Xiong","raw_affiliation_strings":["Pingdingshan University, Pingdingshan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pingdingshan University, Pingdingshan, China","institution_ids":["https://openalex.org/I151878197"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113141320","display_name":"Donghong Ji","orcid":null},"institutions":[{"id":"https://openalex.org/I37461747","display_name":"Wuhan University","ror":"https://ror.org/033vjfk17","country_code":"CN","type":"education","lineage":["https://openalex.org/I37461747"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Donghong Ji","raw_affiliation_strings":["Computer School, Wuhan University, Wuhan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer School, Wuhan University, Wuhan, China","institution_ids":["https://openalex.org/I37461747"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5113141320"],"corresponding_institution_ids":["https://openalex.org/I37461747"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.9524,"has_fulltext":false,"cited_by_count":66,"citation_normalized_percentile":{"value":0.94794697,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"33","issue":"15","first_page":"2363","last_page":"2371"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.5241000056266785,"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":0.5241000056266785,"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":0.25209999084472656,"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/T13702","display_name":"Machine Learning in Healthcare","score":0.11779999732971191,"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/normalization","display_name":"Normalization (sociology)","score":0.8195654153823853},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7882754802703857},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.6613643169403076},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5877030491828918},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.5510179400444031},{"id":"https://openalex.org/keywords/vocabulary","display_name":"Vocabulary","score":0.5272257328033447},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5182452201843262},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.41180533170700073},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3847784996032715},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3337048590183258},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1518094539642334},{"id":"https://openalex.org/keywords/linguistics","display_name":"Linguistics","score":0.08575505018234253}],"concepts":[{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.8195654153823853},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7882754802703857},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.6613643169403076},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5877030491828918},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5510179400444031},{"id":"https://openalex.org/C2777601683","wikidata":"https://www.wikidata.org/wiki/Q6499736","display_name":"Vocabulary","level":2,"score":0.5272257328033447},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5182452201843262},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.41180533170700073},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3847784996032715},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3337048590183258},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1518094539642334},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.08575505018234253},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","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/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"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/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":true},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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:10.1093/bioinformatics/btx172","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx172","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/15/2363/25157980/btx172.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"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:28369171","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28369171","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx172","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx172","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/15/2363/25157980/btx172.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"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":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.4399999976158142}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1647671624","https://openalex.org/W1983018376","https://openalex.org/W1992442866","https://openalex.org/W2116983617","https://openalex.org/W2129038679","https://openalex.org/W2142016317","https://openalex.org/W2143902665","https://openalex.org/W2156235098","https://openalex.org/W2169099542","https://openalex.org/W2176996276","https://openalex.org/W2259159222","https://openalex.org/W2296474619","https://openalex.org/W2346452181","https://openalex.org/W2412122516","https://openalex.org/W2414378847","https://openalex.org/W6636915900","https://openalex.org/W6697152374","https://openalex.org/W6704842505","https://openalex.org/W6714946971","https://openalex.org/W6726710110"],"related_works":["https://openalex.org/W3199871245","https://openalex.org/W2953716828","https://openalex.org/W2904857019","https://openalex.org/W2944728705","https://openalex.org/W3011538607","https://openalex.org/W2904022177","https://openalex.org/W2591697403","https://openalex.org/W4321441197","https://openalex.org/W2793132289","https://openalex.org/W2963217253"],"abstract_inverted_index":{"MOTIVATION:":[0],"Disease":[1,198],"named":[2,43,62,119],"entities":[3,21],"play":[4],"a":[5,41,60,77,112],"central":[6],"role":[7],"in":[8,26,56,76],"many":[9],"areas":[10],"of":[11,19,54,83,137],"biomedical":[12,27],"research,":[13],"and":[14,17,58,96,122,149,171,202,234],"automatic":[15],"recognition":[16,45,121],"normalization":[18,64],"such":[20,84],"have":[22],"received":[23],"increasing":[24],"attention":[25],"research":[28],"communities.":[29],"Existing":[30],"methods":[31],"typically":[32],"used":[33,49,68],"pipeline":[34,104,220],"models":[35,85,105],"with":[36,155,163],"two":[37,192],"independent":[38],"phases:":[39],"(i)":[40,87],"disease":[42,61,118,205],"entity":[44,63,120],"(DER)":[46],"system":[47,66],"is":[48,67,89,99],"to":[50,69,74,94,115,143,159,178,218,226],"find":[51],"the":[52,71,125,164,184,194,203],"boundaries":[53],"mentions":[55,72],"text":[57],"(ii)":[59,97],"(DEN)":[65],"connect":[70],"recognized":[73],"concepts":[75],"controlled":[78],"vocabulary.":[79],"The":[80],"main":[81],"problems":[82],"are:":[86],"there":[88],"error":[90],"propagation":[91],"from":[92],"DER":[93],"DEN":[95,98,170],"useful":[100],"for":[101,168],"DER,":[102,172],"but":[103],"cannot":[106],"utilize":[107],"this.":[108],"METHODS:":[109],"We":[110,187],"propose":[111],"transition-based":[113],"model":[114,190],"jointly":[116],"perform":[117],"normalization,":[123],"casting":[124],"output":[126],"construction":[127],"process":[128],"into":[129],"an":[130],"incremental":[131],"state":[132],"transition":[133,138],"process,":[134],"learning":[135,152,156],"sequences":[136],"actions":[139],"globally,":[140],"which":[141,181],"correspond":[142],"joint":[144,169,211],"structural":[145],"outputs.":[146],"Beam":[147],"search":[148],"online":[150],"structured":[151],"are":[153,236],"used,":[154,180],"being":[157],"designed":[158],"guide":[160],"search.":[161],"Compared":[162],"only":[165],"existing":[166],"method":[167,174,223],"our":[173,189,210],"allows":[175],"non-local":[176],"features":[177],"be":[179],"significantly":[182,214],"improves":[183],"accuracies.":[185],"RESULTS:":[186],"evaluate":[188],"on":[191],"corpora:":[193],"BioCreative":[195],"V":[196],"Chemical":[197],"Relation":[199],"(CDR)":[200],"corpus":[201],"NCBI":[204],"corpus.":[206],"Experiments":[207],"show":[208],"that":[209],"framework":[212],"achieves":[213],"higher":[215],"performances":[216],"compared":[217],"competitive":[219],"baselines.":[221],"Our":[222],"compares":[224],"favourably":[225],"other":[227],"state-of-the-art":[228],"approaches.":[229],"AVAILABILITY":[230],"AND":[231],"IMPLEMENTATION:":[232],"Data":[233],"code":[235],"available":[237],"at":[238],"https://github.com/louyinxia/jointRN.":[239],"CONTACT:":[240],"dhji@whu.edu.cn.":[241]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":16},{"year":2020,"cited_by_count":17},{"year":2019,"cited_by_count":14},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":3}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
