{"id":"https://openalex.org/W2748474343","doi":"https://doi.org/10.1145/3107411.3108198","title":"Novel Unsupervised Named Entity Recognition Used in Text Annotation Tool (OntoMate) At Rat Genome Database","display_name":"Novel Unsupervised Named Entity Recognition Used in Text Annotation Tool (OntoMate) At Rat Genome Database","publication_year":2017,"publication_date":"2017-08-20","ids":{"openalex":"https://openalex.org/W2748474343","doi":"https://doi.org/10.1145/3107411.3108198","mag":"2748474343"},"language":"en","primary_location":{"id":"doi:10.1145/3107411.3108198","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3108198","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5052192895","display_name":"Omid Ghiasvand","orcid":null},"institutions":[{"id":"https://openalex.org/I204308271","display_name":"Medical College of Wisconsin","ror":"https://ror.org/00qqv6244","country_code":"US","type":"education","lineage":["https://openalex.org/I204308271"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Omid Ghiasvand","raw_affiliation_strings":["Medical College of Wisconsin, Milwaukee, WI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medical College of Wisconsin, Milwaukee, WI, USA","institution_ids":["https://openalex.org/I204308271"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031193159","display_name":"Mary Shimoyama","orcid":"https://orcid.org/0000-0003-1176-0796"},"institutions":[{"id":"https://openalex.org/I204308271","display_name":"Medical College of Wisconsin","ror":"https://ror.org/00qqv6244","country_code":"US","type":"education","lineage":["https://openalex.org/I204308271"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mary Shimoyama","raw_affiliation_strings":["Medical College of Wisconsin, Milwaukee, WI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medical College of Wisconsin, Milwaukee, WI, USA","institution_ids":["https://openalex.org/I204308271"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.09029731,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"590","last_page":"590"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9945999979972839,"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":0.9945999979972839,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9532999992370605,"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/T10885","display_name":"Gene expression and cancer classification","score":0.923799991607666,"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":0.7798261046409607},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.6513983607292175},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.584794819355011},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.5812996029853821},{"id":"https://openalex.org/keywords/rank","display_name":"Rank (graph theory)","score":0.5477586984634399},{"id":"https://openalex.org/keywords/gene-annotation","display_name":"Gene Annotation","score":0.49148690700531006},{"id":"https://openalex.org/keywords/relevance","display_name":"Relevance (law)","score":0.46056491136550903},{"id":"https://openalex.org/keywords/ontology-learning","display_name":"Ontology learning","score":0.4446307122707367},{"id":"https://openalex.org/keywords/controlled-vocabulary","display_name":"Controlled vocabulary","score":0.43505141139030457},{"id":"https://openalex.org/keywords/unified-medical-language-system","display_name":"Unified Medical Language System","score":0.4337172508239746},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.43031054735183716},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.38670510053634644},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3483614921569824},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2952670454978943},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.25008130073547363},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.23348203301429749},{"id":"https://openalex.org/keywords/ontology-based-data-integration","display_name":"Ontology-based data integration","score":0.12473377585411072},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10954999923706055}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7798261046409607},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.6513983607292175},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.584794819355011},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.5812996029853821},{"id":"https://openalex.org/C164226766","wikidata":"https://www.wikidata.org/wiki/Q7293202","display_name":"Rank (graph theory)","level":2,"score":0.5477586984634399},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.49148690700531006},{"id":"https://openalex.org/C158154518","wikidata":"https://www.wikidata.org/wiki/Q7310970","display_name":"Relevance (law)","level":2,"score":0.46056491136550903},{"id":"https://openalex.org/C2777002027","wikidata":"https://www.wikidata.org/wiki/Q3620938","display_name":"Ontology learning","level":5,"score":0.4446307122707367},{"id":"https://openalex.org/C110615152","wikidata":"https://www.wikidata.org/wiki/Q1469824","display_name":"Controlled vocabulary","level":2,"score":0.43505141139030457},{"id":"https://openalex.org/C69505689","wikidata":"https://www.wikidata.org/wiki/Q455338","display_name":"Unified Medical Language System","level":2,"score":0.4337172508239746},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.43031054735183716},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.38670510053634644},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3483614921569824},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2952670454978943},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.25008130073547363},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.23348203301429749},{"id":"https://openalex.org/C22550185","wikidata":"https://www.wikidata.org/wiki/Q7095047","display_name":"Ontology-based data integration","level":3,"score":0.12473377585411072},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10954999923706055},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"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/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C50971890","wikidata":"https://www.wikidata.org/wiki/Q7635093","display_name":"Suggested Upper Merged Ontology","level":4,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"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/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3107411.3108198","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3108198","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","score":0.4399999976158142,"display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2509297716","https://openalex.org/W1508778694","https://openalex.org/W138082899","https://openalex.org/W2114373757","https://openalex.org/W2159583324","https://openalex.org/W2059565715","https://openalex.org/W2901823680","https://openalex.org/W2036729745","https://openalex.org/W2010487328","https://openalex.org/W2340589664"],"abstract_inverted_index":{"In":[0,97,115],"model":[1],"organism":[2,81],"databases,":[3],"one":[4],"of":[5,32,173,199,223,321],"the":[6,24,29,53,162,174,194,200,210,237,256,268,278,319],"important":[7],"tasks":[8],"is":[9,241,292],"to":[10,17,93,107,136,155,164,236,273,277,329],"convert":[11],"free":[12],"text":[13],"in":[14,23,193,231,267],"biomedical":[15],"literature":[16,61,291],"a":[18,118,137,166,213,285,306],"structured":[19],"data":[20,63],"format.":[21],"Curators":[22],"Rat":[25],"Genome":[26],"Database":[27],"(RGD),":[28],"primary":[30],"source":[31],"rat":[33],"genomic,":[34],"genetic,":[35],"and":[36,42,50,59,83,90,144,180,219,227,249,259,262,264,287,290,301,311],"physiological":[37],"data,":[38],"spend":[39],"considerable":[40],"time":[41],"effort":[43,110],"curating":[44],"functional":[45,95],"information":[46],"for":[47,62,111],"genes,":[48,76],"QTLs,":[49],"strains":[51],"from":[52,85,171],"literature.":[54],"To":[55],"increase":[56],"curation":[57,245,331],"efficiency":[58],"prioritize":[60],"extraction":[64],"OntoMate":[65],"was":[66,282],"developed":[67],"at":[68],"RGD.":[69],"This":[70,295],"tool":[71,121,240,296],"tags":[72,269,312],"Pubmed":[73],"abstracts":[74,186,250],"with":[75,146,188,197,221,284],"gene":[77,79,176],"names,":[78],"mutations,":[80],"name":[82],"terms":[84,170,202,266],"16":[86],"ontologies/vocabularies,":[87],"including":[88],"synonyms":[89],"aliases,":[91],"used":[92,102],"represent":[94],"information.":[96],"this":[98,116],"project,":[99],"we":[100],"have":[101],"an":[103],"unsupervised":[104],"tagging":[105],"method":[106],"reduce":[108],"human":[109],"creating":[112],"training":[113],"data.":[114],"approach,":[117],"machine":[119],"learning":[120],"based":[122,304],"on":[123,305],"decision":[124],"tree":[125],"classification":[126],"techniques":[127],"has":[128,325],"been":[129],"developed.":[130],"Mentions":[131],"that":[132,215],"are":[133,153,229],"uniquely":[134],"belong":[135],"semantic":[138,147],"type":[139],"play":[140],"positive":[141],"sample":[142],"roles,":[143],"those":[145],"types":[148],"other":[149,181],"than":[150,314],"desired":[151],"group":[152],"assumed":[154],"be":[156,206,252,271],"negative":[157],"samples.":[158],"An":[159],"interface":[160],"allows":[161],"user":[163,211],"create":[165,274],"complex":[167],"query":[168],"incorporating":[169],"any":[172],"ontologies,":[175],"symbols,":[177],"organisms,":[178,217],"dates":[179],"parameters.":[182],"The":[183,239,280],"results":[184],"return":[185],"along":[187,196],"all":[189],"tagged":[190],"parameters":[191],"indicated":[192],"query,":[195],"children":[198],"ontology":[201,265],"chosen.":[203],"Results":[204],"can":[205,251,270],"further":[207],"filtered":[208],"by":[209,234],"through":[212],"panel":[214],"lists":[216],"genes":[218,263],"diseases":[220],"number":[222],"paper":[224],"returned.":[225],"Abstracts":[226],"papers":[228,303],"provided":[230],"rank":[232],"order":[233],"relevance":[235,307],"query.":[238],"fully":[242],"integrated":[243],"into":[244,255],"software":[246],"so":[247],"citations":[248],"automatically":[253],"entered":[254],"RGD":[257,324],"database":[258],"given":[260],"ID":[261],"checked":[272],"annotations":[275],"linked":[276],"paper.":[279],"system":[281],"built":[283],"scalable":[286],"open":[288],"architecture,":[289],"updated":[293],"daily.":[294],"uses":[297],"Solr":[298],"indexing":[299],"technology":[300],"categorizes":[302],"score.":[308],"It":[309],"indexes":[310],"more":[313,327],"27":[315],"million":[316],"abstracts.":[317],"With":[318],"use":[320],"bioNLP":[322],"tools,":[323],"added":[326],"automation":[328],"its":[330],"workflow.":[332]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}