{"id":"https://openalex.org/W2252382131","doi":"https://doi.org/10.1093/bioinformatics/btv654","title":"Comparison of genetic variants in matched samples using thesaurus annotation","display_name":"Comparison of genetic variants in matched samples using thesaurus annotation","publication_year":2015,"publication_date":"2015-11-05","ids":{"openalex":"https://openalex.org/W2252382131","doi":"https://doi.org/10.1093/bioinformatics/btv654","mag":"2252382131","pmid":"https://pubmed.ncbi.nlm.nih.gov/26545822"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv654","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv654","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/5/657/49017594/bioinformatics_32_5_657.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","license_id":"https://openalex.org/licenses/cc-by","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/32/5/657/49017594/bioinformatics_32_5_657.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058480508","display_name":"Tomasz Konopka","orcid":"https://orcid.org/0000-0003-3042-4712"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I4210106789","display_name":"Ludwig Cancer Research","ror":"https://ror.org/01e473h50","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I4210106789","https://openalex.org/I4210150094"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Tomasz Konopka","raw_affiliation_strings":["Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149","https://openalex.org/I4210106789"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024996152","display_name":"Sebastian Nijman","orcid":"https://orcid.org/0000-0003-0464-6661"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I4210106789","display_name":"Ludwig Cancer Research","ror":"https://ror.org/01e473h50","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I4210106789","https://openalex.org/I4210150094"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Sebastian M.B. Nijman","raw_affiliation_strings":["Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149","https://openalex.org/I4210106789"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5058480508"],"corresponding_institution_ids":["https://openalex.org/I40120149","https://openalex.org/I4210106789"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.4502,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.72358065,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"32","issue":"5","first_page":"657","last_page":"663"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.8281999826431274,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11642","display_name":"Genomics and Rare Diseases","score":0.8281999826431274,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.03739999979734421,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.03720000013709068,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/annotation","display_name":"Annotation","score":0.8370243310928345},{"id":"https://openalex.org/keywords/thesaurus","display_name":"Thesaurus","score":0.7208624482154846},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6120241284370422},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.43374955654144287},{"id":"https://openalex.org/keywords/genetic-variants","display_name":"Genetic variants","score":0.4166754186153412},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40298670530319214},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.378568559885025},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.37727469205856323},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.27294713258743286},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24823808670043945},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.08521619439125061},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07999637722969055}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.8370243310928345},{"id":"https://openalex.org/C2778698081","wikidata":"https://www.wikidata.org/wiki/Q179797","display_name":"Thesaurus","level":2,"score":0.7208624482154846},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6120241284370422},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.43374955654144287},{"id":"https://openalex.org/C2993967602","wikidata":"https://www.wikidata.org/wiki/Q5532932","display_name":"Genetic variants","level":4,"score":0.4166754186153412},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40298670530319214},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.378568559885025},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.37727469205856323},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27294713258743286},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24823808670043945},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.08521619439125061},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07999637722969055}],"mesh":[{"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":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","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":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","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":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btv654","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv654","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/5/657/49017594/bioinformatics_32_5_657.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26545822","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26545822","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:3767186","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4795618","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"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/5/657","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/5/657","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:ora.ox.ac.uk:uuid:a0654df9-6f6e-457a-9aa9-c781fa708016","is_oa":true,"landing_page_url":"https://ora.ox.ac.uk/objects/uuid:a0654df9-6f6e-457a-9aa9-c781fa708016","pdf_url":null,"source":{"id":"https://openalex.org/S4306402636","display_name":"Oxford University Research Archive (ORA) (University of Oxford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40120149","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/I40120149"],"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":"Symplectic Elements at Oxford","raw_type":"Journal article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv654","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv654","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/5/657/49017594/bioinformatics_32_5_657.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3207356259","display_name":null,"funder_award_id":"2007\u20132013","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G393177772","display_name":null,"funder_award_id":"FP7 2007-2013","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5702163051","display_name":null,"funder_award_id":"FP7/2007","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2252382131.pdf","grobid_xml":"https://content.openalex.org/works/W2252382131.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W1565378970","https://openalex.org/W2020331089","https://openalex.org/W2025707469","https://openalex.org/W2046137036","https://openalex.org/W2059386911","https://openalex.org/W2060965924","https://openalex.org/W2099377894","https://openalex.org/W2103441770","https://openalex.org/W2108234281","https://openalex.org/W2118151336","https://openalex.org/W2119412782","https://openalex.org/W2138601221","https://openalex.org/W2139838486","https://openalex.org/W2141663748","https://openalex.org/W2146290346","https://openalex.org/W2148811088","https://openalex.org/W2151794156","https://openalex.org/W2152049417","https://openalex.org/W2155943701","https://openalex.org/W2168440186","https://openalex.org/W2170551349","https://openalex.org/W2171543154","https://openalex.org/W2582743722","https://openalex.org/W2949138186"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W2625833328","https://openalex.org/W1533177136","https://openalex.org/W4380994516","https://openalex.org/W2556260348"],"abstract_inverted_index":{"MOTIVATION:":[0],"Calling":[1],"changes":[2,79],"in":[3,12,22,33,80,137,149,152,173],"DNA,":[4],"e.g.":[5],"as":[6,41,161],"a":[7,42,62],"result":[8],"of":[9,16,25,128,133],"somatic":[10],"events":[11,105],"cancer,":[13],"requires":[14],"analysis":[15,121,132],"multiple":[17,56],"matched":[18,83,88],"sequenced":[19],"samples.":[20,84],"Events":[21],"low-mappability":[23],"regions":[24],"the":[26,94,126,129],"human":[27],"genome":[28],"are":[29,187],"difficult":[30],"to":[31,60,76],"encode":[32],"variant":[34,120],"call":[35],"files":[36],"and":[37,70,100,114,160],"have":[38],"been":[39],"under-reported":[40],"result.":[43],"However,":[44],"they":[45],"can":[46,96],"be":[47],"described":[48],"accurately":[49],"through":[50],"thesaurus":[51,74,145],"annotation-a":[52],"technique":[53,95],"that":[54,93],"links":[55],"genomic":[57],"loci":[58],"together":[59],"explicate":[61],"single":[63],"variant.":[64],"RESULTS:":[65],"We":[66,123],"here":[67],"describe":[68],"software":[69],"benchmarks":[71,86],"for":[72,131],"using":[73],"annotation":[75,146],"detect":[77],"point":[78],"DNA":[81],"from":[82],"In":[85],"on":[87,155,164,178],"normal/tumor":[89],"samples":[90],"we":[91],"show":[92],"recover":[97],"between":[98],"five":[99],"ten":[101],"percent":[102],"more":[103],"true":[104],"than":[106],"conventional":[107],"approaches,":[108],"while":[109],"strictly":[110],"limiting":[111],"false":[112],"discovery":[113],"being":[115],"fully":[116],"consistent":[117],"with":[118],"popular":[119],"workflows.":[122],"also":[124],"demonstrate":[125],"utility":[127],"approach":[130],"de":[134],"novo":[135],"mutations":[136],"parents/child":[138],"families.":[139],"AVAILABILITY":[140],"AND":[141],"IMPLEMENTATION:":[142],"Software":[143],"performing":[144],"is":[147,171],"implemented":[148,172],"java;":[150],"available":[151,177,188],"source":[153],"code":[154],"github":[156,179],"at":[157,166,180,189],"GeneticThesaurus":[158],"(https://github.com/tkonopka/GeneticThesaurus)":[159],"an":[162,174],"executable":[163],"sourceforge":[165],"geneticthesaurus":[167],"(https://sourceforge.net/projects/geneticthesaurus).":[168],"Mutation":[169],"calling":[170],"R":[175],"package":[176],"RGeneticThesaurus":[181],"(https://github.com/tkonopka/RGeneticThesaurus).":[182],"SUPPLEMENTARY":[183],"INFORMATION:":[184],"Supplementary":[185],"data":[186],"Bioinformatics":[190],"online.":[191],"CONTACT:":[192],"tomasz.konopka@ludwig.ox.ac.uk.":[193]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":2}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
