{"id":"https://openalex.org/W2161403045","doi":"https://doi.org/10.1093/bioinformatics/btq164","title":"The Genomedata format for storing large-scale functional genomics data","display_name":"The Genomedata format for storing large-scale functional genomics data","publication_year":2010,"publication_date":"2010-04-29","ids":{"openalex":"https://openalex.org/W2161403045","doi":"https://doi.org/10.1093/bioinformatics/btq164","mag":"2161403045","pmid":"https://pubmed.ncbi.nlm.nih.gov/20435580"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btq164","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq164","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/11/1458/48850910/bioinformatics_26_11_1458.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/26/11/1458/48850910/bioinformatics_26_11_1458.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5043633648","display_name":"Michael M. Hoffman","orcid":"https://orcid.org/0000-0002-4517-1562"},"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":"Michael M. Hoffman","raw_affiliation_strings":["1 Department of Genome Sciences, University of Washington, PO Box 355065, Seattle, WA 98195-5065 and 2 Department of Computer Science and Engineering, University of Washington, PO Box 352350, Seattle, WA 98195-2350, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Genome Sciences, University of Washington, PO Box 355065, Seattle, WA 98195-5065 and 2 Department of Computer Science and Engineering, University of Washington, PO Box 352350, Seattle, WA 98195-2350, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087171516","display_name":"Orion J. Buske","orcid":"https://orcid.org/0000-0002-9064-092X"},"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":"Orion J. Buske","raw_affiliation_strings":["1 Department of Genome Sciences, University of Washington, PO Box 355065, Seattle, WA 98195-5065 and 2 Department of Computer Science and Engineering, University of Washington, PO Box 352350, Seattle, WA 98195-2350, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Genome Sciences, University of Washington, PO Box 355065, Seattle, WA 98195-5065 and 2 Department of Computer Science and Engineering, University of Washington, PO Box 352350, Seattle, WA 98195-2350, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057375933","display_name":"William Stafford Noble","orcid":"https://orcid.org/0000-0001-7283-4715"},"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":"William Stafford Noble","raw_affiliation_strings":["1 Department of Genome Sciences, University of Washington, PO Box 355065, Seattle, WA 98195-5065 and 2 Department of Computer Science and Engineering, University of Washington, PO Box 352350, Seattle, WA 98195-2350, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Genome Sciences, University of Washington, PO Box 355065, Seattle, WA 98195-5065 and 2 Department of Computer Science and Engineering, University of Washington, PO Box 352350, Seattle, WA 98195-2350, USA","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5043633648"],"corresponding_institution_ids":["https://openalex.org/I201448701"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.8132,"has_fulltext":true,"cited_by_count":23,"citation_normalized_percentile":{"value":0.72587669,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"26","issue":"11","first_page":"1458","last_page":"1459"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991999864578247,"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":0.9991999864578247,"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":0.9983999729156494,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9941999912261963,"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/python","display_name":"Python (programming language)","score":0.8712841868400574},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8164469599723816},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.7490224838256836},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.5821811556816101},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.48140859603881836},{"id":"https://openalex.org/keywords/data-format","display_name":"Data format","score":0.4282105267047882},{"id":"https://openalex.org/keywords/file-format","display_name":"File format","score":0.4251956641674042},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.39015766978263855},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.373481422662735},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3563213348388672},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35039448738098145},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.14619922637939453}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8712841868400574},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8164469599723816},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.7490224838256836},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.5821811556816101},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.48140859603881836},{"id":"https://openalex.org/C2985331491","wikidata":"https://www.wikidata.org/wiki/Q5227298","display_name":"Data format","level":2,"score":0.4282105267047882},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.4251956641674042},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.39015766978263855},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.373481422662735},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3563213348388672},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35039448738098145},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.14619922637939453}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":"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":"D030541","descriptor_name":"Databases, Genetic","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":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btq164","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq164","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/11/1458/48850910/bioinformatics_26_11_1458.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:20435580","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20435580","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:pubmedcentral.nih.gov:2872006","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2872006","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"doi:10.25504/fairsharing.lkgrmr","is_oa":true,"landing_page_url":"https://doi.org/10.25504/fairsharing.lkgrmr","pdf_url":null,"source":{"id":"https://openalex.org/S7407053452","display_name":"FAIRsharing.org","issn_l":null,"issn":[],"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":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"dataset"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btq164","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq164","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/11/1458/48850910/bioinformatics_26_11_1458.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.41999998688697815}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2161403045.pdf","grobid_xml":"https://content.openalex.org/works/W2161403045.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W149722931","https://openalex.org/W1820394219","https://openalex.org/W2001798854","https://openalex.org/W2108234281","https://openalex.org/W2127640118","https://openalex.org/W2140600399","https://openalex.org/W2161403045","https://openalex.org/W2164813466","https://openalex.org/W2171111703","https://openalex.org/W2918025614"],"related_works":["https://openalex.org/W2546377002","https://openalex.org/W4226320247","https://openalex.org/W4287789247","https://openalex.org/W3021400038","https://openalex.org/W4221162707","https://openalex.org/W4225687299","https://openalex.org/W3169119567","https://openalex.org/W4366457864","https://openalex.org/W2999281421","https://openalex.org/W2273140517"],"abstract_inverted_index":{"SUMMARY:":[0],"We":[1,37,48],"present":[2],"a":[3,16,32,63],"format":[4,19,55],"for":[5],"efficient":[6],"storage":[7],"of":[8,11,26,28],"multiple":[9],"tracks":[10],"numeric":[12],"data":[13,44,52],"anchored":[14],"to":[15,24,42],"genome.":[17],"The":[18],"allows":[20],"fast":[21],"random":[22],"access":[23],"hundreds":[25],"gigabytes":[27],"data,":[29],"while":[30],"retaining":[31],"small":[33],"disk":[34],"space":[35],"footprint.":[36],"have":[38],"also":[39],"developed":[40],"utilities":[41],"load":[43],"into":[45],"this":[46,54],"format.":[47],"show":[49],"that":[50],"retrieving":[51],"from":[53],"is":[56],"more":[57],"than":[58,62],"2900":[59],"times":[60],"faster":[61],"naive":[64],"approach":[65],"using":[66],"wiggle":[67],"files.":[68],"AVAILABILITY":[69],"AND":[70],"IMPLEMENTATION:":[71],"Reference":[72],"implementation":[73],"in":[74],"Python":[75],"and":[76],"C":[77],"components":[78],"available":[79],"at":[80],"http://noble.gs.washington.edu/proj/genomedata/":[81],"under":[82],"the":[83],"GNU":[84],"General":[85],"Public":[86],"License.":[87]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2014,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-04-28T14:05:53.105641","created_date":"2016-06-24T00:00:00"}
