{"id":"https://openalex.org/W2889411505","doi":"https://doi.org/10.1093/bioinformatics/bty712","title":"ISDB: a database toolkit for storing and analyzing viral integration site data","display_name":"ISDB: a database toolkit for storing and analyzing viral integration site data","publication_year":2018,"publication_date":"2018-08-23","ids":{"openalex":"https://openalex.org/W2889411505","doi":"https://doi.org/10.1093/bioinformatics/bty712","mag":"2889411505","pmid":"https://pubmed.ncbi.nlm.nih.gov/30165425"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty712","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty712","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/6/1073/48967442/bioinformatics_35_6_1073.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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/6/1073/48967442/bioinformatics_35_6_1073.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056706723","display_name":"Thomas R. Sibley","orcid":"https://orcid.org/0000-0001-5269-2297"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Thomas R Sibley","raw_affiliation_strings":["Department of Microbiology, Global Health, and Medicine, University of Washington, Seattle, WA, USA"],"raw_orcid":"https://orcid.org/0000-0001-5269-2297","affiliations":[{"raw_affiliation_string":"Department of Microbiology, Global Health, and Medicine, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054423004","display_name":"Evan J Silberman","orcid":"https://orcid.org/0000-0002-3888-6877"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Evan J Silberman","raw_affiliation_strings":["Department of Microbiology, Global Health, and Medicine, University of Washington, Seattle, WA, USA"],"raw_orcid":"https://orcid.org/0000-0002-3888-6877","affiliations":[{"raw_affiliation_string":"Department of Microbiology, Global Health, and Medicine, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028336562","display_name":"James I. Mullins","orcid":"https://orcid.org/0000-0002-4461-8158"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James I Mullins","raw_affiliation_strings":["Department of Microbiology, Global Health, and Medicine, University of Washington, Seattle, WA, USA","Departments of Laboratory Medicine, Global Health, and Medicine, University of Washington, Seattle, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology, Global Health, and Medicine, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Departments of Laboratory Medicine, Global Health, and Medicine, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5054423004","https://openalex.org/A5056706723"],"corresponding_institution_ids":["https://openalex.org/I201448701"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.691,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.71886572,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"35","issue":"6","first_page":"1073","last_page":"1075"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.3140999972820282,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.3140999972820282,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11581","display_name":"Viral Infections and Outbreaks Research","score":0.033900000154972076,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11243","display_name":"Respiratory viral infections research","score":0.03220000118017197,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7776791453361511},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.6202414035797119},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.6126541495323181},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.5431387424468994},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5149944424629211},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5017940998077393},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.499056339263916},{"id":"https://openalex.org/keywords/relational-database","display_name":"Relational database","score":0.49043533205986023},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.48739129304885864},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4429287314414978},{"id":"https://openalex.org/keywords/data-source","display_name":"Data source","score":0.4389582872390747},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.43087077140808105},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4171910285949707}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7776791453361511},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.6202414035797119},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.6126541495323181},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.5431387424468994},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5149944424629211},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5017940998077393},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.499056339263916},{"id":"https://openalex.org/C5655090","wikidata":"https://www.wikidata.org/wiki/Q192588","display_name":"Relational database","level":2,"score":0.49043533205986023},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.48739129304885864},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4429287314414978},{"id":"https://openalex.org/C2983685735","wikidata":"https://www.wikidata.org/wiki/Q5227355","display_name":"Data source","level":2,"score":0.4389582872390747},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.43087077140808105},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4171910285949707},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"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":[{"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":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016662","descriptor_name":"Virus Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016662","descriptor_name":"Virus Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016662","descriptor_name":"Virus Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016662","descriptor_name":"Virus Integration","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":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty712","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty712","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/6/1073/48967442/bioinformatics_35_6_1073.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30165425","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30165425","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":"Journal Article"},{"id":"pmh:oai:europepmc.org:6006080","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6419909","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty712","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty712","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/6/1073/48967442/bioinformatics_35_6_1073.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.41999998688697815},{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.4099999964237213}],"awards":[{"id":"https://openalex.org/G1449530341","display_name":null,"funder_award_id":"R01AI111806","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G2111551601","display_name":"Mechanisms of Formation and Persistence of Active HIV Reservoirs","funder_award_id":"5r01ai111806-05","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2213881162","display_name":null,"funder_award_id":"P30 AI027757","funder_id":"https://openalex.org/F4320332582","funder_display_name":"Center for AIDS Research, University of Washington"},{"id":"https://openalex.org/G264376115","display_name":"University of Washington/Fred Hutch Center for AIDS Research","funder_award_id":"3p30ai027757-36s2","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G378552126","display_name":null,"funder_award_id":"P30 AI 027757","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G3985073149","display_name":null,"funder_award_id":"AI 027757","funder_id":"https://openalex.org/F4320332582","funder_display_name":"Center for AIDS Research, University of Washington"},{"id":"https://openalex.org/G5877261959","display_name":null,"funder_award_id":"R33 AI122361","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G6625095162","display_name":null,"funder_award_id":"P30 AI027757","funder_id":"https://openalex.org/F4320310094","funder_display_name":"University of Washington"},{"id":"https://openalex.org/G6887152030","display_name":"Ex Vivo Detection and Analysis of Non-inducible Latent HIV","funder_award_id":"5r33ai122361-05","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7791962275","display_name":null,"funder_award_id":"AI027757","funder_id":"https://openalex.org/F4320310094","funder_display_name":"University of Washington"},{"id":"https://openalex.org/G894949382","display_name":null,"funder_award_id":"R21 AI122361","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320310094","display_name":"University of Washington","ror":"https://ror.org/00cvxb145"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332582","display_name":"Center for AIDS Research, University of Washington","ror":"https://ror.org/00cvxb145"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2889411505.pdf","grobid_xml":"https://content.openalex.org/works/W2889411505.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W2008301697","https://openalex.org/W2049709740","https://openalex.org/W2064416623","https://openalex.org/W2114261042","https://openalex.org/W2114538357","https://openalex.org/W2125638681","https://openalex.org/W2131200208","https://openalex.org/W2139205741","https://openalex.org/W2139809565","https://openalex.org/W2151397621","https://openalex.org/W2151937780","https://openalex.org/W2171804472","https://openalex.org/W2280129875","https://openalex.org/W2473738987","https://openalex.org/W2510799396"],"related_works":["https://openalex.org/W2036021480","https://openalex.org/W2546377002","https://openalex.org/W4285209474","https://openalex.org/W2046541848","https://openalex.org/W22571951","https://openalex.org/W4309247532","https://openalex.org/W4384009753","https://openalex.org/W2791776396","https://openalex.org/W4286531993","https://openalex.org/W2964820744"],"abstract_inverted_index":{"SUMMARY:":[0],"We":[1],"introduce":[2],"ISDB,":[3,24],"a":[4,28,76],"set":[5,34],"of":[6,14,17,35,56,103],"software":[7],"tools":[8],"for":[9,90,113],"the":[10,80,99,126],"creation":[11],"and":[12,41,49,67,95,110],"administration":[13],"relational":[15],"databases":[16,86],"viral":[18],"integration":[19],"site":[20],"(IS)":[21],"data.":[22,44],"Using":[23],"investigators":[25],"can":[26],"curate":[27],"private":[29,85],"database":[30,65],"from":[31,131],"any":[32],"heterogeneous":[33],"data":[36,47,68,136],"sources,":[37],"including":[38],"previously-published":[39],"datasets":[40],"internal,":[42],"work-in-progress":[43],"To":[45],"make":[46],"visible":[48],"accessible":[50],"to":[51,75,82],"collaborators":[52],"with":[53],"varying":[54],"degrees":[55],"computational":[57],"expertise,":[58],"ISDB":[59,88,114],"automatically":[60],"generates":[61],"web":[62],"sites":[63],"describing":[64],"contents":[66],"exports":[69],"in":[70,92,98],"several":[71],"common":[72],"formats.":[73],"Compared":[74],"public":[77],"depository":[78],"database,":[79],"ability":[81],"build":[83],"local,":[84],"makes":[87],"suitable":[89],"use":[91],"testing":[93],"hypotheses":[94],"developing":[96],"analyses":[97],"long":[100],"pre-publication":[101],"phase":[102],"most":[104],"research.":[105],"AVAILABILITY":[106],"AND":[107],"IMPLEMENTATION:":[108],"Installation":[109],"usage":[111],"documentation":[112],"are":[115,137],"provided":[116],"on":[117],"our":[118],"website":[119],"https://mullinslab.microbiol.washington.edu/isdb/.":[120],"Source":[121],"code":[122],"is":[123],"available":[124,138],"under":[125],"open":[127],"source":[128],"MIT":[129],"license":[130],"https://github.com/MullinsLab/ISDB.":[132],"SUPPLEMENTARY":[133],"INFORMATION:":[134],"Supplementary":[135],"at":[139],"Bioinformatics":[140],"online.":[141]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
