{"id":"https://openalex.org/W2794612626","doi":"https://doi.org/10.1093/database/bay014","title":"TransAtlasDB: an integrated database connecting expression data, metadata and variants","display_name":"TransAtlasDB: an integrated database connecting expression data, metadata and variants","publication_year":2018,"publication_date":"2018-01-01","ids":{"openalex":"https://openalex.org/W2794612626","doi":"https://doi.org/10.1093/database/bay014","mag":"2794612626","pmid":"https://pubmed.ncbi.nlm.nih.gov/29688361"},"language":"en","primary_location":{"id":"doi:10.1093/database/bay014","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bay014","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bay014/27438668/bay014.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bay014/27438668/bay014.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074103912","display_name":"Modupeore O. Adetunji","orcid":"https://orcid.org/0000-0001-8870-1052"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Modupeore O Adetunji","raw_affiliation_strings":["Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085190560","display_name":"Susan J. Lamont","orcid":"https://orcid.org/0000-0003-3974-4050"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Susan J Lamont","raw_affiliation_strings":["Department of Animal Science, Iowa State University, Ames, IA 50011-3150, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Animal Science, Iowa State University, Ames, IA 50011-3150, USA","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004246605","display_name":"Carl J. Schmidt","orcid":"https://orcid.org/0000-0002-8386-4781"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carl J Schmidt","raw_affiliation_strings":["Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716, USA","institution_ids":["https://openalex.org/I86501945"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5074103912"],"corresponding_institution_ids":["https://openalex.org/I86501945"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":0.1856,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.5244068,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":96},"biblio":{"volume":"2018","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987000226974487,"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":0.9987000226974487,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9908999800682068,"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/T11247","display_name":"Plant nutrient uptake and metabolism","score":0.9593999981880188,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.796425461769104},{"id":"https://openalex.org/keywords/nosql","display_name":"NoSQL","score":0.651047945022583},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.6492496728897095},{"id":"https://openalex.org/keywords/perl","display_name":"Perl","score":0.5983821153640747},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.592317521572113},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5275632739067078},{"id":"https://openalex.org/keywords/relational-database","display_name":"Relational database","score":0.4560633897781372},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.41223204135894775},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3699348270893097},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.17051580548286438},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.09252926707267761}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.796425461769104},{"id":"https://openalex.org/C2779599972","wikidata":"https://www.wikidata.org/wiki/Q82231","display_name":"NoSQL","level":3,"score":0.651047945022583},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.6492496728897095},{"id":"https://openalex.org/C2777002779","wikidata":"https://www.wikidata.org/wiki/Q42478","display_name":"Perl","level":2,"score":0.5983821153640747},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.592317521572113},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5275632739067078},{"id":"https://openalex.org/C5655090","wikidata":"https://www.wikidata.org/wiki/Q192588","display_name":"Relational database","level":2,"score":0.4560633897781372},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.41223204135894775},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3699348270893097},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.17051580548286438},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.09252926707267761}],"mesh":[{"descriptor_ui":"D001330","descriptor_name":"Electronic Data Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001330","descriptor_name":"Electronic Data Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001330","descriptor_name":"Electronic Data Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/database/bay014","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bay014","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bay014/27438668/bay014.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},{"id":"pmid:29688361","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29688361","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:lib.dr.iastate.edu:ans_pubs-1557","is_oa":true,"landing_page_url":"https://lib.dr.iastate.edu/cgi/viewcontent.cgi?article=1557&context=ans_pubs","pdf_url":"https://lib.dr.iastate.edu/ans_pubs/556","source":{"id":"https://openalex.org/S4377196104","display_name":"Iowa State University Digital Repository (Iowa State University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I173911158","host_organization_name":"Iowa State University","host_organization_lineage":["https://openalex.org/I173911158"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Animal Science Publications","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:5824778","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5824778","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Database (Oxford)","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/bay014","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bay014","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bay014/27438668/bay014.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G218590244","display_name":null,"funder_award_id":"2011-67003-30228","funder_id":"https://openalex.org/F4320306114","funder_display_name":"U.S. Department of Agriculture"},{"id":"https://openalex.org/G2464809234","display_name":null,"funder_award_id":"2011-67003-30228","funder_id":"https://openalex.org/F4320332299","funder_display_name":"National Institute of Food and Agriculture"}],"funders":[{"id":"https://openalex.org/F4320306114","display_name":"U.S. Department of Agriculture","ror":"https://ror.org/01na82s61"},{"id":"https://openalex.org/F4320332299","display_name":"National Institute of Food and Agriculture","ror":"https://ror.org/05qx3fv49"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2794612626.pdf","grobid_xml":"https://content.openalex.org/works/W2794612626.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W1964733653","https://openalex.org/W1984068087","https://openalex.org/W1993023683","https://openalex.org/W2000252568","https://openalex.org/W2006595462","https://openalex.org/W2036272952","https://openalex.org/W2049620107","https://openalex.org/W2061537056","https://openalex.org/W2097065948","https://openalex.org/W2098832713","https://openalex.org/W2100305481","https://openalex.org/W2102278945","https://openalex.org/W2104005232","https://openalex.org/W2104570606","https://openalex.org/W2108234281","https://openalex.org/W2114104545","https://openalex.org/W2117131162","https://openalex.org/W2119180969","https://openalex.org/W2134526812","https://openalex.org/W2138207763","https://openalex.org/W2140729960","https://openalex.org/W2140980002","https://openalex.org/W2149992227","https://openalex.org/W2150131459","https://openalex.org/W2152060958","https://openalex.org/W2161106528","https://openalex.org/W2179438025","https://openalex.org/W2186043241","https://openalex.org/W2236822143","https://openalex.org/W2277403280","https://openalex.org/W2310622210","https://openalex.org/W2323326409","https://openalex.org/W2405688533","https://openalex.org/W2510875395","https://openalex.org/W2558411436","https://openalex.org/W2566508671","https://openalex.org/W2592811885","https://openalex.org/W2746479894","https://openalex.org/W2950949680","https://openalex.org/W2951188966","https://openalex.org/W6677769943","https://openalex.org/W6683688573","https://openalex.org/W6694876089","https://openalex.org/W7075633510"],"related_works":["https://openalex.org/W1577304934","https://openalex.org/W3153191738","https://openalex.org/W2771285273","https://openalex.org/W60511584","https://openalex.org/W2396673829","https://openalex.org/W2089312862","https://openalex.org/W2957025774","https://openalex.org/W4388191824","https://openalex.org/W2547548876","https://openalex.org/W4385834214"],"abstract_inverted_index":{"High-throughput":[0],"transcriptome":[1],"sequencing":[2],"(RNAseq)":[3],"is":[4,193],"the":[5,128,135,150,154,167,176,187,222],"universally":[6],"applied":[7],"method":[8],"for":[9,94,221],"target-free":[10],"transcript":[11,107],"identification":[12],"and":[13,28,56,66,74,91,96,101,121,144,172,203,234],"gene":[14,124,231],"expression":[15,108,232],"quantification,":[16],"generating":[17],"huge":[18],"amounts":[19,178],"of":[20,24,88,103,131,134,138,147,169,175,179],"data.":[21],"The":[22,190],"constraint":[23],"accessing":[25],"such":[26,49],"data":[27,64,70,98,129,139,156,170,180,199,226],"interpreting":[29],"results":[30,225],"can":[31,71],"be":[32,72,205],"a":[33,62,79,85],"major":[34],"impediment":[35],"in":[36,160],"postulating":[37],"suitable":[38],"hypothesis,":[39],"thus":[40],"an":[41,218],"innovative":[42],"storage":[43,53,65,133,171],"solution":[44],"that":[45,165],"addresses":[46],"these":[47],"limitations,":[48],"as":[50,113,115,119,217],"hard":[51],"disk":[52],"requirements,":[54],"efficiency":[55],"reproducibility":[57],"are":[58],"paramount.":[59],"By":[60],"offering":[61],"uniform":[63],"retrieval":[67],"mechanism,":[68],"various":[69],"compared":[73],"easily":[75],"investigated.":[76],"We":[77],"present":[78],"sophisticated":[80],"system,":[81],"TransAtlasDB,":[82],"which":[83],"incorporates":[84],"hybrid":[86],"architecture":[87],"both":[89],"relational":[90],"NoSQL":[92],"databases":[93],"fast":[95],"efficient":[97],"storage,":[99],"processing":[100],"querying":[102],"large":[104,136,223],"datasets":[105],"from":[106,141,182,200,229],"analysis":[109,143,184],"with":[110,149,162],"corresponding":[111],"metadata,":[112],"well":[114],"gene-associated":[116],"variants":[117],"(such":[118],"SNPs)":[120],"their":[122],"predicted":[123],"effects.":[125],"TransAtlasDB":[126,213],"provides":[127],"model":[130],"accurate":[132],"amount":[137],"derived":[140,228],"RNAseq":[142,183,230],"also":[145],"methods":[146],"interacting":[148],"database,":[151],"either":[152],"via":[153],"command-line":[155],"management":[157],"workflows,":[158],"written":[159],"Perl,":[161],"useful":[163],"functionalities":[164],"simplifies":[166],"complexity":[168],"possibly":[173],"manipulation":[174],"massive":[177],"generated":[181],"or":[185],"through":[186],"web":[188],"interface.":[189],"database":[191],"application":[192],"currently":[194],"modeled":[195],"to":[196,207,215],"handle":[197],"analyses":[198],"agricultural":[201],"species,":[202],"will":[204],"expanded":[206],"include":[208],"more":[209],"species":[210],"groups.":[211],"Overall":[212],"aims":[214],"serve":[216],"accessible":[219],"repository":[220],"complex":[224],"files":[227],"profiling":[233],"variant":[235],"analysis.":[236]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2020,"cited_by_count":2}],"updated_date":"2026-05-16T08:24:45.110214","created_date":"2025-10-10T00:00:00"}
