{"id":"https://openalex.org/W2109487646","doi":"https://doi.org/10.1093/bioinformatics/btr042","title":"GeneTUKit: a software for document-level gene normalization","display_name":"GeneTUKit: a software for document-level gene normalization","publication_year":2011,"publication_date":"2011-02-08","ids":{"openalex":"https://openalex.org/W2109487646","doi":"https://doi.org/10.1093/bioinformatics/btr042","mag":"2109487646","pmid":"https://pubmed.ncbi.nlm.nih.gov/21303863"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr042","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr042","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/7/1032/48867306/bioinformatics_27_7_1032.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/27/7/1032/48867306/bioinformatics_27_7_1032.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044042138","display_name":"Minlie Huang","orcid":"https://orcid.org/0000-0001-7111-1849"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Minlie Huang","raw_affiliation_strings":["Department of Computer Science and Technology, Tsinghua University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112605601","display_name":"Jingchen Liu","orcid":"https://orcid.org/0000-0002-4937-2601"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jingchen Liu","raw_affiliation_strings":["Department of Computer Science and Technology, Tsinghua University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100452969","display_name":"Xiaoyan Zhu","orcid":"https://orcid.org/0000-0001-9616-9289"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoyan Zhu","raw_affiliation_strings":["Department of Computer Science and Technology, Tsinghua University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5044042138"],"corresponding_institution_ids":["https://openalex.org/I99065089"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":4.8525,"has_fulltext":true,"cited_by_count":73,"citation_normalized_percentile":{"value":0.96159454,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"27","issue":"7","first_page":"1032","last_page":"1033"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.998199999332428,"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":0.998199999332428,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.00019999999494757503,"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":0.00019999999494757503,"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":0.7922230958938599},{"id":"https://openalex.org/keywords/normalization","display_name":"Normalization (sociology)","score":0.7165712118148804},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6488664746284485},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6454601883888245},{"id":"https://openalex.org/keywords/gene-nomenclature","display_name":"Gene nomenclature","score":0.5493979454040527},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.5481432676315308},{"id":"https://openalex.org/keywords/ambiguity","display_name":"Ambiguity","score":0.5398601293563843},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4943816661834717},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.46682044863700867},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.46216604113578796},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.36304396390914917},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3243338465690613},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1313241422176361},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11209112405776978},{"id":"https://openalex.org/keywords/taxonomy","display_name":"Taxonomy (biology)","score":0.06292775273323059}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7922230958938599},{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.7165712118148804},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6488664746284485},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6454601883888245},{"id":"https://openalex.org/C62177273","wikidata":"https://www.wikidata.org/wiki/Q5531556","display_name":"Gene nomenclature","level":4,"score":0.5493979454040527},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.5481432676315308},{"id":"https://openalex.org/C2780522230","wikidata":"https://www.wikidata.org/wiki/Q1140419","display_name":"Ambiguity","level":2,"score":0.5398601293563843},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4943816661834717},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.46682044863700867},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.46216604113578796},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.36304396390914917},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3243338465690613},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1313241422176361},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11209112405776978},{"id":"https://openalex.org/C58642233","wikidata":"https://www.wikidata.org/wiki/Q8269924","display_name":"Taxonomy (biology)","level":2,"score":0.06292775273323059},{"id":"https://openalex.org/C514705636","wikidata":"https://www.wikidata.org/wiki/Q863247","display_name":"Nomenclature","level":3,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"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/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","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},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012016","descriptor_name":"Reference Values","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012016","descriptor_name":"Reference Values","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012016","descriptor_name":"Reference Values","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btr042","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr042","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/7/1032/48867306/bioinformatics_27_7_1032.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21303863","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21303863","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:europepmc.org:2075335","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3065680","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btr042","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr042","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/7/1032/48867306/bioinformatics_27_7_1032.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/8","score":0.7400000095367432,"display_name":"Decent work and economic growth"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2109487646.pdf","grobid_xml":"https://content.openalex.org/works/W2109487646.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1991154713","https://openalex.org/W2101265630","https://openalex.org/W2108862644","https://openalex.org/W2123439964","https://openalex.org/W2129113459","https://openalex.org/W2129267433","https://openalex.org/W2141869602","https://openalex.org/W2146954401","https://openalex.org/W2154142897","https://openalex.org/W2161653775","https://openalex.org/W2169918010","https://openalex.org/W2172016350","https://openalex.org/W6648116614"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2353179089","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2923538289","https://openalex.org/W1922686488","https://openalex.org/W2127546476","https://openalex.org/W2116418175"],"abstract_inverted_index":{"MOTIVATION:":[0],"Linking":[1],"gene":[2,26,64,77],"mentions":[3,78],"in":[4,97,116],"an":[5],"article":[6],"to":[7,21,50],"entries":[8],"of":[9,25,55,91,118],"biological":[10,17],"databases":[11],"can":[12,88],"facilitate":[13,51],"indexing":[14],"and":[15,43,79,114,121],"querying":[16],"literature":[18],"greatly.":[19],"Due":[20],"the":[22,52,83,100,108,125],"high":[23,56],"ambiguity":[24],"names,":[27],"this":[28,36],"task":[29,37,53],"is":[30,38,54,135],"particularly":[31],"challenging.":[32],"Manual":[33],"annotation":[34],"for":[35,67],"cost":[39],"expensive,":[40],"time":[41],"consuming":[42],"labor":[44],"intensive.":[45],"Therefore,":[46],"providing":[47],"assistive":[48],"tools":[49],"value.":[57],"RESULTS:":[58],"We":[59],"developed":[60],"GeneTUKit,":[61],"a":[62],"document-level":[63],"normalization":[65],"software":[66,71,134],"full-text":[68,85,127],"articles.":[69,129],"This":[70],"employs":[72],"both":[73],"local":[74],"context":[75,81],"surrounding":[76],"global":[80],"from":[82],"whole":[84],"document.":[86],"It":[87],"normalize":[89],"genes":[90],"different":[92],"species":[93],"simultaneously.":[94],"When":[95],"participating":[96],"BioCreAtIvE":[98],"III,":[99],"system":[101,109],"obtained":[102],"good":[103],"results":[104],"among":[105],"37":[106],"runs:":[107],"was":[110],"ranked":[111],"first,":[112],"fourth":[113],"seventh":[115],"terms":[117],"TAP-20,":[119],"TAP-10":[120],"TAP-5,":[122],"respectively":[123],"on":[124],"507":[126],"test":[128],"AVAILABILITY":[130],"AND":[131],"IMPLEMENTATION:":[132],"The":[133],"available":[136],"at":[137],"http://www.qanswers.net/GeneTUKit/.":[138]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":8},{"year":2014,"cited_by_count":8},{"year":2013,"cited_by_count":15},{"year":2012,"cited_by_count":8}],"updated_date":"2026-07-13T07:31:44.756512","created_date":"2025-10-10T00:00:00"}
