{"id":"https://openalex.org/W2147796343","doi":"https://doi.org/10.1093/bioinformatics/btg445","title":"HIVbase: a PC/Windows-based software offering storage and querying power for locally held HIV-1 genetic, experimental and clinical data","display_name":"HIVbase: a PC/Windows-based software offering storage and querying power for locally held HIV-1 genetic, experimental and clinical data","publication_year":2004,"publication_date":"2004-01-22","ids":{"openalex":"https://openalex.org/W2147796343","doi":"https://doi.org/10.1093/bioinformatics/btg445","mag":"2147796343","pmid":"https://pubmed.ncbi.nlm.nih.gov/14960476"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btg445","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg445","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/3/436/48905083/bioinformatics_20_3_436.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/20/3/436/48905083/bioinformatics_20_3_436.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024152947","display_name":"Susanna L. Lamers","orcid":"https://orcid.org/0000-0002-8163-5571"},"institutions":[{"id":"https://openalex.org/I1330063522","display_name":"Johnson & Johnson (United States)","ror":"https://ror.org/03qd7mz70","country_code":"US","type":"company","lineage":["https://openalex.org/I1330063522"]},{"id":"https://openalex.org/I2800069191","display_name":"St. Augustine College","ror":"https://ror.org/059ap3j92","country_code":"US","type":"education","lineage":["https://openalex.org/I2800069191"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Susanna Lamers","raw_affiliation_strings":["Gene Johnson Inc., St Augustine, FL, USA","Gene Johnson Inc., St Augustine, FL, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Gene Johnson Inc., St Augustine, FL, USA","institution_ids":["https://openalex.org/I1330063522","https://openalex.org/I2800069191"]},{"raw_affiliation_string":"Gene Johnson Inc., St Augustine, FL, USA#TAB#","institution_ids":["https://openalex.org/I1330063522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029188858","display_name":"Scott Beason","orcid":null},"institutions":[{"id":"https://openalex.org/I1330063522","display_name":"Johnson & Johnson (United States)","ror":"https://ror.org/03qd7mz70","country_code":"US","type":"company","lineage":["https://openalex.org/I1330063522"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Scott Beason","raw_affiliation_strings":["Gene Johnson Inc., St Augustine, FL, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Gene Johnson Inc., St Augustine, FL, USA#TAB#","institution_ids":["https://openalex.org/I1330063522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015278212","display_name":"Luke Dunlap","orcid":null},"institutions":[{"id":"https://openalex.org/I1330063522","display_name":"Johnson & Johnson (United States)","ror":"https://ror.org/03qd7mz70","country_code":"US","type":"company","lineage":["https://openalex.org/I1330063522"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Luke Dunlap","raw_affiliation_strings":["Gene Johnson Inc., St Augustine, FL, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Gene Johnson Inc., St Augustine, FL, USA#TAB#","institution_ids":["https://openalex.org/I1330063522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000070381","display_name":"Robert Compton","orcid":null},"institutions":[{"id":"https://openalex.org/I1330063522","display_name":"Johnson & Johnson (United States)","ror":"https://ror.org/03qd7mz70","country_code":"US","type":"company","lineage":["https://openalex.org/I1330063522"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert Compton","raw_affiliation_strings":["Gene Johnson Inc., St Augustine, FL, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Gene Johnson Inc., St Augustine, FL, USA#TAB#","institution_ids":["https://openalex.org/I1330063522"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030387965","display_name":"Marco Salemi","orcid":"https://orcid.org/0000-0003-0136-2102"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marco Salemi","raw_affiliation_strings":["Department of Ecology and Evolutionary Biology, University of California at Irvine, Irvine, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Ecology and Evolutionary Biology, University of California at Irvine, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5024152947"],"corresponding_institution_ids":["https://openalex.org/I1330063522","https://openalex.org/I2800069191"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.6812,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.66771597,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"20","issue":"3","first_page":"436","last_page":"438"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.23770000040531158,"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":0.23770000040531158,"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/T10112","display_name":"HIV Research and Treatment","score":0.20730000734329224,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10526","display_name":"HIV/AIDS drug development and treatment","score":0.1843000054359436,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7531347274780273},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6805562973022461},{"id":"https://openalex.org/keywords/human-immunodeficiency-virus","display_name":"Human immunodeficiency virus (HIV)","score":0.621778666973114},{"id":"https://openalex.org/keywords/raw-data","display_name":"Raw data","score":0.601524293422699},{"id":"https://openalex.org/keywords/software-package","display_name":"Software package","score":0.5024943351745605},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.402299702167511},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.370843768119812},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32936033606529236},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.32388633489608765},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.17854079604148865},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16931921243667603}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7531347274780273},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6805562973022461},{"id":"https://openalex.org/C3013748606","wikidata":"https://www.wikidata.org/wiki/Q15787","display_name":"Human immunodeficiency virus (HIV)","level":2,"score":0.621778666973114},{"id":"https://openalex.org/C132964779","wikidata":"https://www.wikidata.org/wiki/Q2110223","display_name":"Raw data","level":2,"score":0.601524293422699},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.5024943351745605},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.402299702167511},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.370843768119812},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32936033606529236},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.32388633489608765},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.17854079604148865},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16931921243667603},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006678","descriptor_name":"HIV","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006678","descriptor_name":"HIV","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006678","descriptor_name":"HIV","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008838","descriptor_name":"Microcomputers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008838","descriptor_name":"Microcomputers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008838","descriptor_name":"Microcomputers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":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":"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":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btg445","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg445","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/3/436/48905083/bioinformatics_20_3_436.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:14960476","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/14960476","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btg445","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg445","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/3/436/48905083/bioinformatics_20_3_436.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":[{"score":0.6600000262260437,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G1807778955","display_name":null,"funder_award_id":"R01-HD32259","funder_id":"https://openalex.org/F4320337611","funder_display_name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development"},{"id":"https://openalex.org/G7184814062","display_name":null,"funder_award_id":"AI47723","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G7957440222","display_name":null,"funder_award_id":"R43 AI56904-01","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"},{"id":"https://openalex.org/F4320337611","display_name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","ror":"https://ror.org/04byxyr05"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":4,"referenced_works":["https://openalex.org/W325121155","https://openalex.org/W1966406643","https://openalex.org/W2041469490","https://openalex.org/W2395808804"],"related_works":["https://openalex.org/W4252510819","https://openalex.org/W3012838233","https://openalex.org/W2363876787","https://openalex.org/W2903803878","https://openalex.org/W2149263892","https://openalex.org/W2354111411","https://openalex.org/W4235496431","https://openalex.org/W2155302041","https://openalex.org/W1990412843","https://openalex.org/W3042945901"],"abstract_inverted_index":{"BACKGROUND:":[0],"Human":[1],"immunodeficiency":[2],"virus":[3],"(HIV)":[4],"research":[5],"involves":[6],"ongoing,":[7],"repetitious":[8,109],"sequencing":[9],"of":[10,18,27,75,91,104,122,134],"the":[11,15,25,70,101,113,132],"HIV":[12,120],"genome":[13],"and":[14,61,73,85,118,141],"massive":[16],"accumulation":[17],"associated":[19],"investigational":[20],"data.":[21,78,93],"As":[22],"a":[23,63],"result,":[24],"storage":[26],"annotated":[28],"DNA":[29],"and/or":[30],"protein":[31,128],"sequences,":[32,129],"as":[33,35],"well":[34],"information":[36,47],"retrieval,":[37],"have":[38,112],"become":[39],"increasingly":[40],"difficult":[41],"tasks,":[42],"with":[43],"scientists":[44],"extracting":[45],"less":[46],"from":[48,124],"their":[49,76],"collected":[50],"data":[51,135],"than":[52],"they":[53],"should.":[54],"OBJECTIVES:":[55],"Our":[56],"objective":[57],"was":[58],"to":[59,66,115],"design":[60],"develop":[62],"software":[64,95],"package":[65],"aid":[67],"researchers":[68],"in":[69,136],"storage,":[71],"analysis":[72],"exploration":[74],"HIV-associated":[77],"RESULTS:":[79],"HIVbase":[80],"contains":[81,96],"familiar,":[82],"easy-to-use":[83],"interfaces":[84],"functionality":[86],"for":[87,100,131,142],"integrating":[88],"many":[89],"types":[90],"disparate":[92],"The":[94],"tools":[97],"that":[98],"allow":[99,130],"mass":[102],"import":[103],"raw":[105],"genetic":[106],"data,":[107],"eliminate":[108],"sequence":[110],"translations,":[111],"ability":[114],"identify":[116],"automatically":[117],"store":[119],"regions":[121],"interest":[123],"nucleic":[125],"acid":[126],"or":[127],"export":[133],"commonly":[137],"used":[138],"analysis-ready":[139],"formats,":[140],"unique":[143],"querying":[144],"approaches.":[145]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
