{"id":"https://openalex.org/W3106905956","doi":"https://doi.org/10.1093/database/baaa092","title":"VarStack: a web tool for data retrieval to interpret somatic variants in cancer","display_name":"VarStack: a web tool for data retrieval to interpret somatic variants in cancer","publication_year":2020,"publication_date":"2020-01-01","ids":{"openalex":"https://openalex.org/W3106905956","doi":"https://doi.org/10.1093/database/baaa092","mag":"3106905956","pmid":"https://pubmed.ncbi.nlm.nih.gov/33247936"},"language":"en","primary_location":{"id":"doi:10.1093/database/baaa092","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baaa092","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baaa092/34568837/baaa092.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baaa092/34568837/baaa092.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058288770","display_name":"Morgan Howard","orcid":"https://orcid.org/0000-0002-9213-2929"},"institutions":[{"id":"https://openalex.org/I196272386","display_name":"Providence College","ror":"https://ror.org/00rxpqe74","country_code":"US","type":"education","lineage":["https://openalex.org/I196272386"]},{"id":"https://openalex.org/I2800446032","display_name":"Rhode Island Hospital","ror":"https://ror.org/01aw9fv09","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2800446032","https://openalex.org/I4210151747"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Morgan Howard","raw_affiliation_strings":["Rhode Island Hospital\u2009Department of Pathology, Providence, RI 02903, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Rhode Island Hospital\u2009Department of Pathology, Providence, RI 02903, USA","institution_ids":["https://openalex.org/I2800446032","https://openalex.org/I196272386"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013794967","display_name":"Bruce Kane","orcid":null},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bruce Kane","raw_affiliation_strings":["Computing and Information Services, Brown University, Providence, RI 02912, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computing and Information Services, Brown University, Providence, RI 02912, USA","institution_ids":["https://openalex.org/I27804330"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037014261","display_name":"Mary Lepry","orcid":null},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mary Lepry","raw_affiliation_strings":["Computing and Information Services, Brown University, Providence, RI 02912, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computing and Information Services, Brown University, Providence, RI 02912, USA","institution_ids":["https://openalex.org/I27804330"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070707634","display_name":"Paul Stey","orcid":null},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul Stey","raw_affiliation_strings":["Brown University, Providence, RI, 02906, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Brown University, Providence, RI, 02906, USA","institution_ids":["https://openalex.org/I27804330"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039029228","display_name":"Ashok Ragavendran","orcid":"https://orcid.org/0000-0003-3540-9343"},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ashok Ragavendran","raw_affiliation_strings":["Brown University, Providence, RI, 02906, USA","Center for Computational Biology of Human Disease, Brown University, Providence, RI 02912, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Brown University, Providence, RI, 02906, USA","institution_ids":["https://openalex.org/I27804330"]},{"raw_affiliation_string":"Center for Computational Biology of Human Disease, Brown University, Providence, RI 02912, USA","institution_ids":["https://openalex.org/I27804330"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043436828","display_name":"Ece D. Gamsiz Uzun","orcid":"https://orcid.org/0000-0003-4068-7153"},"institutions":[{"id":"https://openalex.org/I196272386","display_name":"Providence College","ror":"https://ror.org/00rxpqe74","country_code":"US","type":"education","lineage":["https://openalex.org/I196272386"]},{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]},{"id":"https://openalex.org/I2800446032","display_name":"Rhode Island Hospital","ror":"https://ror.org/01aw9fv09","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2800446032","https://openalex.org/I4210151747"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ece D Gamsiz Uzun","raw_affiliation_strings":["Center for Computational Molecular Biology, Brown University, Providence, RI 02906, USA","Department of Pathology and Laboratory Medicine, Brown University Alpert Medical School, Providence, RI 02903, USA","Rhode Island Hospital\u2009Department of Pathology, Providence, RI 02903, USA"],"raw_orcid":"https://orcid.org/0000-0003-4068-7153","affiliations":[{"raw_affiliation_string":"Center for Computational Molecular Biology, Brown University, Providence, RI 02906, USA","institution_ids":["https://openalex.org/I27804330"]},{"raw_affiliation_string":"Department of Pathology and Laboratory Medicine, Brown University Alpert Medical School, Providence, RI 02903, USA","institution_ids":["https://openalex.org/I27804330"]},{"raw_affiliation_string":"Rhode Island Hospital\u2009Department of Pathology, Providence, RI 02903, USA","institution_ids":["https://openalex.org/I2800446032","https://openalex.org/I196272386"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5043436828"],"corresponding_institution_ids":["https://openalex.org/I196272386","https://openalex.org/I27804330","https://openalex.org/I2800446032"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":0.1606,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.45493721,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"2020","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9991000294685364,"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"}},"topics":[{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9991000294685364,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.9919999837875366,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9890999794006348,"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/information-retrieval","display_name":"Information retrieval","score":0.6007543802261353},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5701319575309753},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.5452050566673279},{"id":"https://openalex.org/keywords/somatic-cell","display_name":"Somatic cell","score":0.5370179414749146},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.32821792364120483},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24634119868278503},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13293322920799255}],"concepts":[{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.6007543802261353},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5701319575309753},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.5452050566673279},{"id":"https://openalex.org/C134305767","wikidata":"https://www.wikidata.org/wiki/Q725508","display_name":"Somatic cell","level":3,"score":0.5370179414749146},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.32821792364120483},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24634119868278503},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13293322920799255},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/database/baaa092","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baaa092","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baaa092/34568837/baaa092.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},{"id":"pmid:33247936","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33247936","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7698661","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7698661","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Database (Oxford)","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/baaa092","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baaa092","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baaa092/34568837/baaa092.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4760462093","display_name":null,"funder_award_id":"P20 GM109035","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W2096525273","https://openalex.org/W2114843025","https://openalex.org/W2137297899","https://openalex.org/W2149441684","https://openalex.org/W2174602966","https://openalex.org/W2583911935","https://openalex.org/W2614443510","https://openalex.org/W2898789672","https://openalex.org/W2986925253","https://openalex.org/W3029661147","https://openalex.org/W4248735723","https://openalex.org/W6758451182","https://openalex.org/W6770216092"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2060908277","https://openalex.org/W2358668433","https://openalex.org/W2048083752","https://openalex.org/W4396701345","https://openalex.org/W2376932109"],"abstract_inverted_index":{"Advances":[0],"in":[1,70,95,132,137,150,168,221],"tumor":[2],"genome":[3],"sequencing":[4],"created":[5],"an":[6,56,158,180,222],"urgent":[7],"need":[8],"for":[9],"bioinformatics":[10],"tools":[11],"to":[12,33,39,92,104,134,139,215],"support":[13],"the":[14,17,21,65,83,93,99,146,155,164,170,184,187,190,216],"interpretation":[15],"of":[16,20,67,98,129,176],"clinical":[18],"significance":[19],"variants":[22,177],"detected.":[23],"VarStack":[24,44,161,201,207,227],"is":[25,30,228],"a":[26,31,96,112,115,127,174],"web":[27],"tool":[28],"which":[29,169],"base":[32],"retrieve":[34],"somatic":[35,212],"variant":[36,113,213],"data":[37,46,63,84,185,194],"relating":[38],"cancer":[40],"from":[41,47,64,85,145,186,218],"existing":[42],"databases.":[43,188],"incorporates":[45],"several":[48],"publicly":[49],"available":[50,230],"databases":[51,87,147,220],"and":[52,77,88,120,178,193,224],"presents":[53],"them":[54,90],"with":[55,114,183],"easy-to-navigate":[57],"user":[58,94,171,217],"interface.":[59],"It":[60,81],"currently":[61],"supports":[62],"Catalogue":[66],"Somatic":[68],"Mutations":[69],"Cancer,":[71],"gnomAD,":[72],"cBioPortal,":[73],"ClinVar,":[74],"OncoKB,":[75],"CiViC":[76],"UCSC":[78],"Genome":[79],"Browser.":[80],"retrieves":[82],"these":[86],"returns":[89],"back":[91],"fraction":[97],"time":[100,209],"it":[101],"would":[102],"take":[103],"manually":[105],"navigate":[106],"each":[107],"site":[108],"independently.":[109],"Users":[110,152],"submit":[111,173],"gene":[116],"symbol,":[117],"peptide":[118],"change":[119],"coding":[121],"sequence":[122],"change.":[123],"They":[124],"may":[125],"select":[126],"variety":[128],"tumor-specific":[130],"studies":[131],"cBioPortal":[133],"search":[135,166,192],"through":[136],"addition":[138],"their":[140,203],"original":[141],"query.":[142],"The":[143],"results":[144,156],"are":[148],"presented":[149],"tabs.":[151],"can":[153,172,198],"export":[154],"as":[157],"Excel":[159,181],"file.":[160],"also":[162],"has":[163],"batch":[165,191],"feature":[167],"list":[175],"download":[179,195],"file":[182],"With":[189],"options,":[196],"users":[197],"easily":[199],"incorporate":[200],"into":[202],"workflow":[204],"or":[205],"tools.":[206],"saves":[208],"by":[210],"providing":[211],"information":[214],"multiple":[219],"easy-to-export":[223],"interpretable":[225],"format.":[226],"freely":[229],"under":[231],"https://varstack.brown.edu.":[232]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
