{"id":"https://openalex.org/W3040000993","doi":"https://doi.org/10.1093/bioinformatics/btaa591","title":"Epiviz File Server: Query, transform and interactively explore data from indexed genomic files","display_name":"Epiviz File Server: Query, transform and interactively explore data from indexed genomic files","publication_year":2020,"publication_date":"2020-06-27","ids":{"openalex":"https://openalex.org/W3040000993","doi":"https://doi.org/10.1093/bioinformatics/btaa591","mag":"3040000993"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa591","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa591","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/18/4682/34560181/btaa591.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"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/18/4682/34560181/btaa591.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083494889","display_name":"Jayaram Kancherla","orcid":"https://orcid.org/0000-0001-5855-5031"},"institutions":[{"id":"https://openalex.org/I143663144","display_name":"Research Institute for Advanced Computer Science","ror":"https://ror.org/022qmyy53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1329765538","https://openalex.org/I143663144"]},{"id":"https://openalex.org/I4210148697","display_name":"Institute of Bioinformatics","ror":"https://ror.org/04hqfvm50","country_code":"IN","type":"nonprofit","lineage":["https://openalex.org/I4210148697"]},{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["IN","US"],"is_corresponding":false,"raw_author_name":"Jayaram Kancherla","raw_affiliation_strings":["Center for Bioinformatics and Computational Biology","Department of Computer Science, University of Maryland , College Park, MD 20742, USA","Institute for Advanced Computer Studies"],"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology","institution_ids":["https://openalex.org/I4210148697"]},{"raw_affiliation_string":"Department of Computer Science, University of Maryland , College Park, MD 20742, USA","institution_ids":["https://openalex.org/I66946132"]},{"raw_affiliation_string":"Institute for Advanced Computer Studies","institution_ids":["https://openalex.org/I143663144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101407131","display_name":"Yifan Yang","orcid":"https://orcid.org/0000-0003-0947-5603"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yifan Yang","raw_affiliation_strings":["Department of Computer Science, University of Maryland , College Park, MD 20742, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Maryland , College Park, MD 20742, USA","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075735784","display_name":"Hyeyun Chae","orcid":null},"institutions":[{"id":"https://openalex.org/I118020396","display_name":"Swarthmore College","ror":"https://ror.org/012dg8a96","country_code":"US","type":"education","lineage":["https://openalex.org/I118020396"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hyeyun Chae","raw_affiliation_strings":["Biology and Computer Science, Swarthmore College , Swarthmore, PA 19081, USA"],"affiliations":[{"raw_affiliation_string":"Biology and Computer Science, Swarthmore College , Swarthmore, PA 19081, USA","institution_ids":["https://openalex.org/I118020396"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048253009","display_name":"H\u00e9ctor Corrada Bravo","orcid":"https://orcid.org/0000-0002-1255-4444"},"institutions":[{"id":"https://openalex.org/I143663144","display_name":"Research Institute for Advanced Computer Science","ror":"https://ror.org/022qmyy53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1329765538","https://openalex.org/I143663144"]},{"id":"https://openalex.org/I4210148697","display_name":"Institute of Bioinformatics","ror":"https://ror.org/04hqfvm50","country_code":"IN","type":"nonprofit","lineage":["https://openalex.org/I4210148697"]},{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["IN","US"],"is_corresponding":true,"raw_author_name":"Hector Corrada Bravo","raw_affiliation_strings":["Center for Bioinformatics and Computational Biology","Department of Computer Science, University of Maryland , College Park, MD 20742, USA","Institute for Advanced Computer Studies"],"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology","institution_ids":["https://openalex.org/I4210148697"]},{"raw_affiliation_string":"Department of Computer Science, University of Maryland , College Park, MD 20742, USA","institution_ids":["https://openalex.org/I66946132"]},{"raw_affiliation_string":"Institute for Advanced Computer Studies","institution_ids":["https://openalex.org/I143663144"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5048253009"],"corresponding_institution_ids":["https://openalex.org/I143663144","https://openalex.org/I4210148697","https://openalex.org/I66946132"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.1701,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.77731401,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"36","issue":"18","first_page":"4682","last_page":"4690"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9915000200271606,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9915000200271606,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9757999777793884,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9650999903678894,"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/computer-science","display_name":"Computer science","score":0.7983474731445312},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4362521171569824},{"id":"https://openalex.org/keywords/data-file","display_name":"Data file","score":0.41329675912857056},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4000418782234192},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.35515326261520386},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.33682361245155334}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7983474731445312},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4362521171569824},{"id":"https://openalex.org/C171730128","wikidata":"https://www.wikidata.org/wiki/Q5227290","display_name":"Data file","level":2,"score":0.41329675912857056},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4000418782234192},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.35515326261520386},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.33682361245155334}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btaa591","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa591","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/18/4682/34560181/btaa591.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":"pmh:oai:pubmedcentral.nih.gov:7695125","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7695125","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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/btaa591","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa591","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/18/4682/34560181/btaa591.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":[{"id":"https://openalex.org/G12248359","display_name":null,"funder_award_id":"R01GM114267","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3611247453","display_name":null,"funder_award_id":"R01GM","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G841434665","display_name":null,"funder_award_id":"R24MH114815","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3040000993.pdf","grobid_xml":"https://content.openalex.org/works/W3040000993.grobid-xml"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W1973094248","https://openalex.org/W1993202658","https://openalex.org/W2017550851","https://openalex.org/W2021341670","https://openalex.org/W2039564969","https://openalex.org/W2084160423","https://openalex.org/W2097464861","https://openalex.org/W2103207352","https://openalex.org/W2105114815","https://openalex.org/W2112029506","https://openalex.org/W2126958666","https://openalex.org/W2128016314","https://openalex.org/W2129785061","https://openalex.org/W2142386149","https://openalex.org/W2146292423","https://openalex.org/W2158485828","https://openalex.org/W2334656801","https://openalex.org/W2336957559","https://openalex.org/W2342249984","https://openalex.org/W2527672088","https://openalex.org/W2619713135","https://openalex.org/W2767826728","https://openalex.org/W2800392236","https://openalex.org/W2884983930","https://openalex.org/W2888425844","https://openalex.org/W2911473673","https://openalex.org/W2917207851","https://openalex.org/W2951194089","https://openalex.org/W2964844385","https://openalex.org/W6703928569","https://openalex.org/W6758473961","https://openalex.org/W6888003116","https://openalex.org/W6944153807"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2418291489","https://openalex.org/W2068121105","https://openalex.org/W3096519538","https://openalex.org/W2744747300","https://openalex.org/W4241166160","https://openalex.org/W2384826897","https://openalex.org/W2003932708","https://openalex.org/W117643398","https://openalex.org/W1997466117"],"abstract_inverted_index":{"Abstract":[0],"Motivation":[1],"Genomic":[2],"data":[3,27,37,45,60,77,84],"repositories":[4,41],"like":[5],"The":[6,79,157],"Cancer":[7],"Genome":[8],"Atlas,":[9],"Encyclopedia":[10],"of":[11,25,36,103,109],"DNA":[12],"Elements,":[13],"Bioconductor\u2019s":[14],"AnnotationHub":[15],"and":[16,86,91,94,126,142,150],"ExperimentHub":[17],"etc.,":[18],"provide":[19],"public":[20],"access":[21],"to":[22,42,99,130],"large":[23],"amounts":[24],"genomic":[26,69],"as":[28],"flat":[29],"files.":[30],"Researchers":[31],"often":[32],"download":[33],"a":[34,52,132],"subset":[35],"files":[38],"from":[39,88,136],"these":[40],"perform":[43],"exploratory":[44],"analysis.":[46],"We":[47,112],"developed":[48],"Epiviz":[49,129,144],"File":[50,80,115,145,161],"Server,":[51],"Python":[53],"library":[54,82,163],"that":[55],"implements":[56],"an":[57,96],"in":[58,117],"situ":[59],"query":[61],"system":[62],"for":[63,73,159],"local":[64],"or":[65,107],"remotely":[66],"hosted":[67],"indexed":[68],"files,":[70],"not":[71],"only":[72],"visualization":[74,90],"but":[75],"also":[76],"transformation.":[78],"Server":[81,116,146,162],"decouples":[83],"retrieval":[85],"transformation":[87],"specific":[89],"analysis":[92],"tools":[93],"provides":[95],"abstract":[97],"interface":[98],"define":[100],"computations":[101],"independent":[102],"the":[104,110,114,137,160],"location,":[105],"format":[106],"structure":[108],"file.":[111],"demonstrate":[113],"two":[118],"use":[119],"cases:":[120],"(i)":[121],"integration":[122],"with":[123],"Galaxy":[124],"workflows":[125],"(ii)":[127],"using":[128],"create":[131],"custom":[133],"genome":[134],"browser":[135],"Epigenome":[138],"Roadmap":[139],"dataset.":[140],"Availability":[141],"implementation":[143],"is":[147,151,164],"open":[148],"source":[149],"available":[152,165],"on":[153],"GitHub":[154],"at":[155,166],"http://github.com/epiviz/epivizFileServer.":[156],"documentation":[158],"http://epivizfileserver.rtfd.io.":[167]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
