{"id":"https://openalex.org/W2025824350","doi":"https://doi.org/10.1109/bibm.2013.6732541","title":"Using silver and semi-gold standard corpora to compare open named entity recognisers","display_name":"Using silver and semi-gold standard corpora to compare open named entity recognisers","publication_year":2013,"publication_date":"2013-12-01","ids":{"openalex":"https://openalex.org/W2025824350","doi":"https://doi.org/10.1109/bibm.2013.6732541","mag":"2025824350"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2013.6732541","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2013.6732541","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 IEEE International Conference on Bioinformatics and Biomedicine","raw_type":"proceedings-article"},"type":"conference-paper","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/A5011041769","display_name":"Tudor Groza","orcid":"https://orcid.org/0000-0003-2267-8333"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Tudor Groza","raw_affiliation_strings":["School of ITEE, The University of Queensland, St. Lucia, QLD, Australia","School of ITEE, University of Queensland, St. Lucia, QLD, Australia#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of ITEE, The University of Queensland, St. Lucia, QLD, Australia","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"School of ITEE, University of Queensland, St. Lucia, QLD, Australia#TAB#","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012061875","display_name":"Anika Oellrich","orcid":null},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Anika Oellrich","raw_affiliation_strings":["Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK","Eur. Bioinf. Inst., Cambridge, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK","institution_ids":["https://openalex.org/I2802476451"]},{"raw_affiliation_string":"Eur. Bioinf. Inst., Cambridge, UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073413742","display_name":"Nigel Collier","orcid":"https://orcid.org/0000-0002-7230-4164"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I184597095","display_name":"National Institute of Informatics","ror":"https://ror.org/04ksd4g47","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I184597095","https://openalex.org/I4210158934"]}],"countries":["GB","JP"],"is_corresponding":false,"raw_author_name":"Nigel Collier","raw_affiliation_strings":["European Bioinformatics Institute, The National Institute of Informatics, Tokyo, Cambridge, Japan","Eur. Bioinf. Inst., Cambridge, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Bioinformatics Institute, The National Institute of Informatics, Tokyo, Cambridge, Japan","institution_ids":["https://openalex.org/I184597095"]},{"raw_affiliation_string":"Eur. Bioinf. Inst., Cambridge, UK","institution_ids":["https://openalex.org/I1303153112"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"481","last_page":"485"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9937999844551086,"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/T10028","display_name":"Topic Modeling","score":0.9908999800682068,"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/gold-standard","display_name":"Gold standard (test)","score":0.7714592218399048},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7606467008590698},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6862117052078247},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.6169698238372803},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.579963207244873},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.5701978802680969},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.49857163429260254},{"id":"https://openalex.org/keywords/extant-taxon","display_name":"Extant taxon","score":0.46948060393333435},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4183761775493622},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.113925039768219},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10016003251075745}],"concepts":[{"id":"https://openalex.org/C40993552","wikidata":"https://www.wikidata.org/wiki/Q514654","display_name":"Gold standard (test)","level":2,"score":0.7714592218399048},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7606467008590698},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6862117052078247},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.6169698238372803},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.579963207244873},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5701978802680969},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.49857163429260254},{"id":"https://openalex.org/C178300618","wikidata":"https://www.wikidata.org/wiki/Q1898509","display_name":"Extant taxon","level":2,"score":0.46948060393333435},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4183761775493622},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.113925039768219},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10016003251075745},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","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/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","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/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/bibm.2013.6732541","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2013.6732541","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 IEEE International Conference on Bioinformatics and Biomedicine","raw_type":"proceedings-article"},{"id":"pmh:oai:espace.library.uq.edu.au:UQ:325232","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402388","display_name":"Queensland's institutional digital repository (The University of Queensland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165143802","host_organization_name":"The University of Queensland","host_organization_lineage":["https://openalex.org/I165143802"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Conference Paper"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W102787101","https://openalex.org/W1550258693","https://openalex.org/W2015079391","https://openalex.org/W2056616115","https://openalex.org/W2086776298","https://openalex.org/W2096777607","https://openalex.org/W2106797966","https://openalex.org/W2124772738","https://openalex.org/W2126276057","https://openalex.org/W2128323588","https://openalex.org/W2139865360","https://openalex.org/W2141869602","https://openalex.org/W2146089916","https://openalex.org/W2159583324","https://openalex.org/W4381594492","https://openalex.org/W6604181502","https://openalex.org/W6632766574","https://openalex.org/W6678739045"],"related_works":["https://openalex.org/W3016239368","https://openalex.org/W2402755139","https://openalex.org/W4378651134","https://openalex.org/W2378211422","https://openalex.org/W4290948148","https://openalex.org/W4249944690","https://openalex.org/W2745001401","https://openalex.org/W4321353415","https://openalex.org/W2353808877","https://openalex.org/W3197991489"],"abstract_inverted_index":{"Ontologies":[0],"have":[1],"become":[2],"a":[3,73,147],"central":[4],"resource":[5],"for":[6],"defining":[7],"biomedical":[8],"concepts":[9],"but":[10,176],"linkage":[11],"to":[12,149],"and":[13,43,61,72,125,144],"from":[14],"textual":[15],"data":[16,55],"is":[17,81],"still":[18],"an":[19,67,159],"unresolved":[20],"technology.":[21],"In":[22],"this":[23],"paper":[24],"we":[25,113],"approach":[26],"the":[27,84,116,123,137,154,163,172,180],"task":[28],"of":[29,57,86,97,165],"concept":[30,88,98],"recognition":[31,99],"in":[32],"text":[33],"by":[34],"comparing":[35],"four":[36],"extant":[37],"systems":[38,50],"(cTAKES,":[39],"NCBO":[40,130],"Annotator,":[41],"BeCAS":[42,143],"Metamap)":[44],"with":[45,171],"default":[46],"parameter":[47],"settings.":[48],"The":[49,109],"are":[51],"compared":[52],"on":[53,83,100,105,115,121,162],"benchmark":[54],"consisting":[56],"2,163":[58],"scientific":[59,106],"abstracts":[60],"906":[62],"clinical":[63,101,126],"trial":[64,102,127],"reports":[65,103],"using":[66],"automatically":[68],"constructed":[69],"\u201csilver\u201d":[70],"standard":[71,76,118,174,182],"random":[74,155],"semi-gold":[75,156],"evaluation":[77,80,157,175],"methodology.":[78],"Furthermore,":[79],"conducted":[82],"basis":[85],"specific":[87],"identifiers.":[89],"Experimental":[90],"results":[91],"show:":[92],"(i)":[93],"Generally":[94],"higher":[95],"levels":[96],"than":[104],"abstracts;":[107],"(ii)":[108],"best":[110],"performing":[111],"system":[112],"observed":[114],"silver":[117,173,181],"was":[119],"cTAKES":[120],"both":[122],"abstract":[124],"corpora,":[128],"however":[129],"Annotator":[131],"performed":[132],"stronger":[133],"when":[134],"considering":[135],"only":[136],"selected":[138],"broad":[139,169],"semantic":[140],"types;":[141],"(iii)":[142],"Metamap":[145],"had":[146],"tendency":[148],"annotate":[150],"coarser-grained":[151],"annotations;":[152],"(iv)":[153],"places":[158],"upper":[160],"bound":[161],"performance":[164],"systems.":[166],"This":[167],"shows":[168],"agreement":[170],"highlights":[177],"areas":[178],"where":[179],"methodology":[183],"might":[184],"be":[185],"improved.":[186]},"counts_by_year":[{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
