{"id":"https://openalex.org/W4210567745","doi":"https://doi.org/10.1093/bioinformatics/btac042","title":"StructuralVariantAnnotation: a R/Bioconductor foundation for a caller-agnostic structural variant software ecosystem","display_name":"StructuralVariantAnnotation: a R/Bioconductor foundation for a caller-agnostic structural variant software ecosystem","publication_year":2022,"publication_date":"2022-01-28","ids":{"openalex":"https://openalex.org/W4210567745","doi":"https://doi.org/10.1093/bioinformatics/btac042","pmid":"https://pubmed.ncbi.nlm.nih.gov/35134827"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac042","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac042","pdf_url":null,"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://doi.org/10.1093/bioinformatics/btac042","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056298672","display_name":"Daniel Cameron","orcid":"https://orcid.org/0000-0002-0951-7116"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Daniel L Cameron","raw_affiliation_strings":["Department of Medical Biology, University of Melbourne , Parkville, VIC 3052, Australia","The Walter and Eliza Hall Institute of Medical Research , Parkville, VIC 3052, Australia"],"raw_orcid":"https://orcid.org/0000-0002-0951-7116","affiliations":[{"raw_affiliation_string":"Department of Medical Biology, University of Melbourne , Parkville, VIC 3052, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"The Walter and Eliza Hall Institute of Medical Research , Parkville, VIC 3052, Australia","institution_ids":["https://openalex.org/I196021976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003063782","display_name":"Ruining Dong","orcid":"https://orcid.org/0000-0003-1433-0484"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Ruining Dong","raw_affiliation_strings":["Department of Medical Biology, University of Melbourne , Parkville, VIC 3052, Australia","The Walter and Eliza Hall Institute of Medical Research , Parkville, VIC 3052, Australia"],"raw_orcid":"https://orcid.org/0000-0003-1433-0484","affiliations":[{"raw_affiliation_string":"Department of Medical Biology, University of Melbourne , Parkville, VIC 3052, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"The Walter and Eliza Hall Institute of Medical Research , Parkville, VIC 3052, Australia","institution_ids":["https://openalex.org/I196021976"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054939935","display_name":"Anthony T. Papenfuss","orcid":"https://orcid.org/0000-0002-1102-8506"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]},{"id":"https://openalex.org/I2800555584","display_name":"Peter MacCallum Cancer Centre","ror":"https://ror.org/02a8bt934","country_code":"AU","type":"healthcare","lineage":["https://openalex.org/I2800555584"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Anthony T Papenfuss","raw_affiliation_strings":["Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre , East Melbourne, VIC 3002, Australia","Department of Medical Biology, University of Melbourne , Parkville, VIC 3052, Australia","Sir Peter MacCallum Department of Oncology, University of Melbourne , Melbourne, VIC 3010, Australia","The Walter and Eliza Hall Institute of Medical Research , Parkville, VIC 3052, Australia"],"raw_orcid":"https://orcid.org/0000-0002-1102-8506","affiliations":[{"raw_affiliation_string":"Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre , East Melbourne, VIC 3002, Australia","institution_ids":["https://openalex.org/I2800555584"]},{"raw_affiliation_string":"Department of Medical Biology, University of Melbourne , Parkville, VIC 3052, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Sir Peter MacCallum Department of Oncology, University of Melbourne , Melbourne, VIC 3010, Australia","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I2800555584"]},{"raw_affiliation_string":"The Walter and Eliza Hall Institute of Medical Research , Parkville, VIC 3052, Australia","institution_ids":["https://openalex.org/I196021976"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5054939935","https://openalex.org/A5056298672"],"corresponding_institution_ids":["https://openalex.org/I165779595","https://openalex.org/I196021976","https://openalex.org/I2800555584"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.7835,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.66949183,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"38","issue":"7","first_page":"2046","last_page":"2048"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.5738000273704529,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.5738000273704529,"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/T10260","display_name":"Software Engineering Research","score":0.09369999915361404,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"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/T11642","display_name":"Genomics and Rare Diseases","score":0.08910000324249268,"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/bioconductor","display_name":"Bioconductor","score":0.990218460559845},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7209787368774414},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.529512882232666},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5215299129486084},{"id":"https://openalex.org/keywords/downstream","display_name":"Downstream (manufacturing)","score":0.41992971301078796},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.41569364070892334},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3462761640548706},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.24565380811691284},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22355446219444275},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19570019841194153},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11365938186645508}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.990218460559845},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7209787368774414},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.529512882232666},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5215299129486084},{"id":"https://openalex.org/C2776207758","wikidata":"https://www.wikidata.org/wiki/Q5303302","display_name":"Downstream (manufacturing)","level":2,"score":0.41992971301078796},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.41569364070892334},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3462761640548706},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.24565380811691284},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22355446219444275},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19570019841194153},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11365938186645508},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac042","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac042","pdf_url":null,"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:35134827","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35134827","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:pubmedcentral.nih.gov:8963309","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8963309","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac042","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac042","pdf_url":null,"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":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.4699999988079071}],"awards":[{"id":"https://openalex.org/G816890712","display_name":"Advancing the state-of-the-art in genomic rearrangement detection in cancer","funder_award_id":"1188098","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320332014","display_name":"Lorenzo and Pamela Galli Charitable Trust","ror":null},{"id":"https://openalex.org/F4320334705","display_name":"National Health and Medical Research Council","ror":"https://ror.org/011kf5r70"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W1980099549","https://openalex.org/W2131478115","https://openalex.org/W2136939537","https://openalex.org/W2149992227","https://openalex.org/W2407798683","https://openalex.org/W2963186762","https://openalex.org/W3034581902","https://openalex.org/W3091245808","https://openalex.org/W3109802858","https://openalex.org/W3160770927","https://openalex.org/W3195118166","https://openalex.org/W4220843895","https://openalex.org/W4232061444","https://openalex.org/W4301603101","https://openalex.org/W6786483106"],"related_works":["https://openalex.org/W43224192","https://openalex.org/W2469206883","https://openalex.org/W1892467659","https://openalex.org/W1529400504","https://openalex.org/W90653389","https://openalex.org/W2998403542","https://openalex.org/W2808586768","https://openalex.org/W2136939537","https://openalex.org/W1965530278","https://openalex.org/W2079027948"],"abstract_inverted_index":{"SUMMARY:":[0],"StructuralVariantAnnotation":[1,78,108,120],"is":[2,109],"an":[3],"R/Bioconductor":[4,86],"package":[5],"that":[6,74],"provides":[7,79],"a":[8,41,85,133],"framework":[9],"for":[10,47,84,115],"decoupling":[11],"downstream":[12,76],"analysis":[13],"of":[14,32,63,88],"structural":[15,89],"variant":[16,20,90],"breakpoints":[17,58],"from":[18,28],"upstream":[19],"calling":[21],"methods.":[22],"It":[23,54,128],"standardizes":[24],"the":[25,33,50,80,118],"representational":[26],"format":[27],"BEDPE,":[29],"or":[30],"any":[31],"three":[34],"different":[35],"notations":[36],"supported":[37],"by":[38,49],"VCF":[39],"into":[40],"breakpoint":[42],"GRanges":[43],"data":[44],"structure":[45],"suitable":[46],"use":[48],"wider":[51],"Bioconductor":[52,119],"ecosystem.":[53],"handles":[55],"both":[56,99],"transitive":[57],"and":[59,93,101,113],"duplication/insertion":[60],"notational":[61],"differences":[62],"identical":[64],"variants-both":[65],"common":[66],"scenarios":[67],"when":[68],"comparing":[69],"short/long":[70],"read-based":[71],"call":[72],"sets":[73],"confound":[75],"analysis.":[77],"caller-agnostic":[81],"foundation":[82],"needed":[83],"ecosystem":[87],"annotation,":[91],"classification":[92],"interpretation":[94],"tools":[95],"able":[96],"to":[97],"handle":[98],"simple":[100],"complex":[102],"genomic":[103],"rearrangements.":[104],"AVAILABILITY":[105],"AND":[106],"IMPLEMENTATION:":[107],"implemented":[110],"in":[111],"R":[112],"available":[114],"download":[116],"as":[117],"package.":[121],"Details":[122],"can":[123],"be":[124],"found":[125],"at":[126],"https://www.bioconductor.org/packages/release/bioc/html/StructuralVariantAnnotation.html.":[127],"has":[129],"been":[130],"released":[131],"under":[132],"GPL":[134],"license.":[135]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
