{"id":"https://openalex.org/W2132917398","doi":"https://doi.org/10.1093/bioinformatics/btg476","title":"Java-based application framework for visualization of gene regulatory region annotations","display_name":"Java-based application framework for visualization of gene regulatory region annotations","publication_year":2004,"publication_date":"2004-01-29","ids":{"openalex":"https://openalex.org/W2132917398","doi":"https://doi.org/10.1093/bioinformatics/btg476","mag":"2132917398","pmid":"https://pubmed.ncbi.nlm.nih.gov/14751988"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btg476","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg476","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":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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001836351","display_name":"Hao Sun","orcid":"https://orcid.org/0000-0002-5547-9501"},"institutions":[{"id":"https://openalex.org/I4210145812","display_name":"Cancer Genetics (United States)","ror":"https://ror.org/05feyya22","country_code":"US","type":"company","lineage":["https://openalex.org/I4210145812"]},{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hao Sun","raw_affiliation_strings":["Human Cancer Genetics Program, Comprehensive Cancer Center, Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, 420 W 12th Avenue, TMRF 524, Columbus, OH 43210, USA","Human Cancer Genetics Program, Comprehensive Cancer Center, Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, 420 W 12th Avenue, TMRF 524, Columbus, OH ...#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Human Cancer Genetics Program, Comprehensive Cancer Center, Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, 420 W 12th Avenue, TMRF 524, Columbus, OH 43210, USA","institution_ids":["https://openalex.org/I4210145812"]},{"raw_affiliation_string":"Human Cancer Genetics Program, Comprehensive Cancer Center, Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, 420 W 12th Avenue, TMRF 524, Columbus, OH ...#TAB#","institution_ids":["https://openalex.org/I4210145812","https://openalex.org/I52357470"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017429478","display_name":"Ramana V. Davuluri","orcid":"https://orcid.org/0000-0002-7053-1064"},"institutions":[{"id":"https://openalex.org/I4210145812","display_name":"Cancer Genetics (United States)","ror":"https://ror.org/05feyya22","country_code":"US","type":"company","lineage":["https://openalex.org/I4210145812"]},{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ramana V. Davuluri","raw_affiliation_strings":["Human Cancer Genetics Program, Comprehensive Cancer Center, Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, 420 W 12th Avenue, TMRF 524, Columbus, OH ...#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Human Cancer Genetics Program, Comprehensive Cancer Center, Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, 420 W 12th Avenue, TMRF 524, Columbus, OH ...#TAB#","institution_ids":["https://openalex.org/I4210145812","https://openalex.org/I52357470"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.0777,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.75239426,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"20","issue":"5","first_page":"727","last_page":"734"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.5753999948501587,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.5753999948501587,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.04769999906420708,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.04280000180006027,"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/java","display_name":"Java","score":0.7683314681053162},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.7408827543258667},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6468594074249268},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.5864881277084351},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5711615085601807},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5617173314094543},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.5483957529067993},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.520867109298706},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4702519178390503},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.42418092489242554},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.41037917137145996},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3784027695655823},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3573441207408905},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2948629856109619},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.2862006425857544},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.24259915947914124},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24003255367279053},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.23651641607284546},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16464337706565857},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.07794564962387085}],"concepts":[{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.7683314681053162},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7408827543258667},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6468594074249268},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.5864881277084351},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5711615085601807},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5617173314094543},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.5483957529067993},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.520867109298706},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4702519178390503},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.42418092489242554},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.41037917137145996},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3784027695655823},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3573441207408905},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2948629856109619},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.2862006425857544},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.24259915947914124},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24003255367279053},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.23651641607284546},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16464337706565857},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.07794564962387085}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","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":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","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":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D019146","descriptor_name":"Hypermedia","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019146","descriptor_name":"Hypermedia","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019146","descriptor_name":"Hypermedia","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":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/btg476","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg476","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:14751988","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/14751988","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":null,"sustainable_development_goals":[{"display_name":"Partnerships for the goals","score":0.46000000834465027,"id":"https://metadata.un.org/sdg/17"},{"display_name":"Industry, innovation and infrastructure","score":0.4000000059604645,"id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1499728294","https://openalex.org/W1504178245","https://openalex.org/W1992102171","https://openalex.org/W2004818131","https://openalex.org/W2070884496","https://openalex.org/W2083105784","https://openalex.org/W2091106901","https://openalex.org/W2096525273","https://openalex.org/W2113745578","https://openalex.org/W2115621351","https://openalex.org/W2120615294","https://openalex.org/W2128016314","https://openalex.org/W2130919037","https://openalex.org/W2131581981","https://openalex.org/W2134515324","https://openalex.org/W2145477956","https://openalex.org/W2150934173","https://openalex.org/W2151464048","https://openalex.org/W2152089378","https://openalex.org/W2163506270","https://openalex.org/W2164085656","https://openalex.org/W2168783124","https://openalex.org/W2168909179"],"related_works":["https://openalex.org/W2528467228","https://openalex.org/W270927586","https://openalex.org/W1575927706","https://openalex.org/W4224120179","https://openalex.org/W2796515132","https://openalex.org/W1962482270","https://openalex.org/W283806354","https://openalex.org/W2373899618","https://openalex.org/W2892158704","https://openalex.org/W2132917398"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,99],"genome":[2,14,52,57],"sequences":[3],"of":[4,22,26,68,71,102,105,131],"several":[5],"organisms":[6],"are":[7,113],"either":[8],"complete,":[9],"or":[10],"being":[11],"sequenced.":[12],"Each":[13],"needs":[15],"to":[16,49,89],"be":[17,43,159],"integrated":[18],"with":[19],"various":[20,51],"types":[21],"annotations,":[23],"e.g.":[24],"locations":[25],"genes,":[27],"promoters":[28],"and":[29,74,108,116,124,155],"other":[30],"functional":[31],"elements":[32],"such":[33],"as":[34,62],"transcriptional":[35],"regulatory":[36,93],"elements.":[37],"A":[38],"robust":[39],"application":[40,64],"framework":[41,65,84],"will":[42],"useful":[44],"for":[45,85,118,129],"developing":[46,86],"web-based":[47,87,140],"applications":[48,88],"visualize":[50],"annotations.":[53],"RESULTS:":[54],"We":[55,126],"developed":[56],"data":[58,72,122],"visualization":[59,130],"toolkit":[60],"(GDVTK)":[61],"an":[63],"that":[66,112],"consists":[67,104],"a":[69,82,139],"set":[70],"structures":[73],"core":[75],"classes,":[76],"using":[77],"Java":[78,110],"technology.":[79],"GDVTK":[80,103,128,145],"is":[81,146],"sound":[83],"present":[90],"the":[91,162],"gene":[92],"region":[94],"annotations":[95,133],"in":[96,120,134],"visual":[97],"form.":[98],"current":[100],"version":[101],"eight":[106],"packages":[107],"38":[109],"classes":[111],"portable,":[114],"reusable":[115],"extensible":[117],"plugging":[119],"new":[121],"sources":[123],"models.":[125],"implemented":[127],"promoter":[132],"Mammalian":[135],"Promoter":[136],"Database":[137],"(MPromDb),":[138],"gene-regulatory":[141],"information":[142],"server.":[143],"AVAILABILITY:":[144],"available":[147],"under":[148],"GNU":[149],"general":[150],"public":[151],"license.":[152],"Source":[153],"code":[154],"software":[156],"documentation":[157],"can":[158],"found":[160],"at":[161],"URL":[163],"http://bioinformatics.med.ohio-state.edu/GDVTK.":[164]},"counts_by_year":[{"year":2015,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
