{"id":"https://openalex.org/W2132091595","doi":"https://doi.org/10.1093/bioinformatics/btv376","title":"GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications","display_name":"GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications","publication_year":2015,"publication_date":"2015-06-20","ids":{"openalex":"https://openalex.org/W2132091595","doi":"https://doi.org/10.1093/bioinformatics/btv376","mag":"2132091595","pmid":"https://pubmed.ncbi.nlm.nih.gov/26093150"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv376","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv376","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/20/3348/49035872/bioinformatics_31_20_3348.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":"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://academic.oup.com/bioinformatics/article-pdf/31/20/3348/49035872/bioinformatics_31_20_3348.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5050640673","display_name":"Matthew R. Laird","orcid":"https://orcid.org/0000-0003-0967-3175"},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Matthew R. Laird","raw_affiliation_strings":["1 Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6 and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6 and","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061354858","display_name":"Morgan G. I. Langille","orcid":"https://orcid.org/0000-0002-6604-3009"},"institutions":[{"id":"https://openalex.org/I129902397","display_name":"Dalhousie University","ror":"https://ror.org/01e6qks80","country_code":"CA","type":"education","lineage":["https://openalex.org/I129902397"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Morgan G.I. Langille","raw_affiliation_strings":["2 Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada","institution_ids":["https://openalex.org/I129902397"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050197558","display_name":"Fiona S. L. Brinkman","orcid":"https://orcid.org/0000-0002-0584-4099"},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Fiona S.L. Brinkman","raw_affiliation_strings":["1 Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6 and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6 and","institution_ids":["https://openalex.org/I18014758"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5050197558"],"corresponding_institution_ids":["https://openalex.org/I18014758"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.7736,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.84860606,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"31","issue":"20","first_page":"3348","last_page":"3349"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.23510000109672546,"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":0.23510000109672546,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.15410000085830688,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.06589999794960022,"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/visualization","display_name":"Visualization","score":0.7830345630645752},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7692487239837646},{"id":"https://openalex.org/keywords/json","display_name":"JSON","score":0.7315911054611206},{"id":"https://openalex.org/keywords/javascript","display_name":"JavaScript","score":0.681716799736023},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6810364723205566},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.6135156154632568},{"id":"https://openalex.org/keywords/scalable-vector-graphics","display_name":"Scalable Vector Graphics","score":0.5892404913902283},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.5098020434379578},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.5057313442230225},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.4407673180103302},{"id":"https://openalex.org/keywords/interactive-visualization","display_name":"Interactive visualization","score":0.4311804473400116},{"id":"https://openalex.org/keywords/genome-browser","display_name":"Genome browser","score":0.4278579652309418},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4114048182964325},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.33455461263656616},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.2610390782356262},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.20999842882156372},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1612023413181305}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7830345630645752},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7692487239837646},{"id":"https://openalex.org/C2780416260","wikidata":"https://www.wikidata.org/wiki/Q2063","display_name":"JSON","level":2,"score":0.7315911054611206},{"id":"https://openalex.org/C544833334","wikidata":"https://www.wikidata.org/wiki/Q2005","display_name":"JavaScript","level":2,"score":0.681716799736023},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6810364723205566},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.6135156154632568},{"id":"https://openalex.org/C202629362","wikidata":"https://www.wikidata.org/wiki/Q2078","display_name":"Scalable Vector Graphics","level":2,"score":0.5892404913902283},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.5098020434379578},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.5057313442230225},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.4407673180103302},{"id":"https://openalex.org/C64073096","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Interactive visualization","level":3,"score":0.4311804473400116},{"id":"https://openalex.org/C2781148417","wikidata":"https://www.wikidata.org/wiki/Q5533486","display_name":"Genome browser","level":5,"score":0.4278579652309418},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4114048182964325},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.33455461263656616},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.2610390782356262},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.20999842882156372},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1612023413181305},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","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":"D044404","descriptor_name":"Genomic Islands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044404","descriptor_name":"Genomic Islands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044404","descriptor_name":"Genomic Islands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btv376","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv376","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/20/3348/49035872/bioinformatics_31_20_3348.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":"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:26093150","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26093150","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:europepmc.org:3576058","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4595901","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:31/20/3348","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/20/3348","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv376","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv376","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/20/3348/49035872/bioinformatics_31_20_3348.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":"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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320310787","display_name":"Genome Canada","ror":"https://ror.org/029s29983"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":9,"referenced_works":["https://openalex.org/W1967779392","https://openalex.org/W2119892487","https://openalex.org/W2139627484","https://openalex.org/W2145477956","https://openalex.org/W2158804744","https://openalex.org/W2160219419","https://openalex.org/W2163262659","https://openalex.org/W2167155938","https://openalex.org/W2170382524"],"related_works":["https://openalex.org/W4250821095","https://openalex.org/W4301217393","https://openalex.org/W2267058868","https://openalex.org/W2922064259","https://openalex.org/W2742949799","https://openalex.org/W2799210984","https://openalex.org/W3163912985","https://openalex.org/W2505408505","https://openalex.org/W2268687088","https://openalex.org/W2121832590"],"abstract_inverted_index":{"MOTIVATION:":[0],"A":[1],"simple":[2],"static":[3],"image":[4],"of":[5,54,154],"genomes":[6],"and":[7],"associated":[8],"metadata":[9],"is":[10,31,121,163],"very":[11],"limiting,":[12],"as":[13],"researchers":[14,74],"expect":[15],"rich,":[16],"interactive":[17],"tools":[18],"similar":[19],"to":[20,49,75,101,131,146],"the":[21,26,41,51,81,88,125,166],"web":[22,70],"applications":[23],"found":[24],"in":[25,38,90,99,107,115,124,157],"post-Web":[27],"2.0":[28],"world.":[29],"GenomeD3Plot":[30,44,72,96,120,162],"a":[32,46,59],"light":[33],"weight":[34],"visualization":[35,53,89,106,153],"library":[36],"written":[37],"javascript":[39],"using":[40,58],"D3":[42],"library.":[43],"provides":[45],"rich":[47],"API":[48],"allow":[50],"rapid":[52],"complex":[55],"genomic":[56,134,155],"data":[57,156],"convenient":[60],"standards":[61],"based":[62],"JSON":[63],"configuration":[64],"file.":[65],"When":[66],"integrated":[67],"into":[68],"existing":[69],"services":[71],"allows":[73],"interact":[76],"with":[77,136],"data,":[78],"dynamically":[79],"alter":[80],"view,":[82],"or":[83,86,109,117],"even":[84],"resize":[85],"reposition":[87],"their":[91],"browser":[92],"window.":[93],"In":[94],"addition":[95],"has":[97],"built":[98],"functionality":[100],"export":[102],"any":[103],"resulting":[104],"genome":[105,138],"PNG":[108],"SVG":[110],"format":[111],"for":[112,151],"easy":[113],"inclusion":[114],"manuscripts":[116],"presentations.":[118],"RESULTS:":[119],"being":[122],"utilized":[123],"recently":[126],"released":[127],"Islandviewer":[128],"3":[129],"(www.pathogenomics.sfu.ca/islandviewer/)":[130],"visualize":[132],"predicted":[133],"islands":[135],"other":[137],"annotation":[139],"data.":[140],"However,":[141],"its":[142],"features":[143],"enable":[144],"it":[145],"be":[147],"more":[148],"widely":[149],"applicable":[150],"dynamic":[152],"general.":[158],"AVAILABILITY":[159],"AND":[160],"IMPLEMENTATION:":[161],"licensed":[164],"under":[165],"GNU-GPL":[167],"v3":[168],"at":[169],"https://github.com/brinkmanlab/GenomeD3Plot/.":[170],"CONTACT:":[171],"brinkman@sfu.ca.":[172]},"counts_by_year":[{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":1}],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2025-10-10T00:00:00"}
