{"id":"https://openalex.org/W3204089263","doi":"https://doi.org/10.12688/f1000research.16450.1","title":"Improve your Galaxy text life: The Query Tabular Tool","display_name":"Improve your Galaxy text life: The Query Tabular Tool","publication_year":2018,"publication_date":"2018-10-05","ids":{"openalex":"https://openalex.org/W3204089263","doi":"https://doi.org/10.12688/f1000research.16450.1","mag":"3204089263"},"language":"en","primary_location":{"id":"doi:10.12688/f1000research.16450.1","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.16450.1","pdf_url":"https://f1000research.com/articles/7-1604/v1/pdf","source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357"],"host_organization_lineage_names":["Faculty of 1000"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"F1000Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://f1000research.com/articles/7-1604/v1/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042203635","display_name":"James E. Johnson","orcid":"https://orcid.org/0000-0002-2590-4765"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James E. Johnson","raw_affiliation_strings":["Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, 55455"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, 55455","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055499257","display_name":"Praveen Kumar","orcid":"https://orcid.org/0000-0002-7818-671X"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]},{"id":"https://openalex.org/I4210120349","display_name":"University of Minnesota Rochester","ror":"https://ror.org/02rh4fw73","country_code":"US","type":"education","lineage":["https://openalex.org/I4210120349"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Praveen Kumar","raw_affiliation_strings":["Bioinformatics and Computational Biology Program, University of Minnesota-Rochester, Rochester, MN, 55904","Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics and Computational Biology Program, University of Minnesota-Rochester, Rochester, MN, 55904","institution_ids":["https://openalex.org/I4210120349"]},{"raw_affiliation_string":"Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032999165","display_name":"Caleb Easterly","orcid":"https://orcid.org/0000-0001-7853-377X"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Caleb Easterly","raw_affiliation_strings":["Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455"],"raw_orcid":"https://orcid.org/0000-0001-7853-377X","affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029334492","display_name":"Mark Esler","orcid":null},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark Esler","raw_affiliation_strings":["Department of Horticulture, University of Minnesota, St. Paul, MN, 55108"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Horticulture, University of Minnesota, St. Paul, MN, 55108","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082971131","display_name":"Subina Mehta","orcid":"https://orcid.org/0000-0001-9818-0537"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Subina Mehta","raw_affiliation_strings":["Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027307091","display_name":"Arthur C. Eschenlauer","orcid":"https://orcid.org/0000-0002-2882-0508"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arthur C. Eschenlauer","raw_affiliation_strings":["Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455","Department of Horticulture, University of Minnesota, St. Paul, MN, 55108"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455","institution_ids":["https://openalex.org/I130238516"]},{"raw_affiliation_string":"Department of Horticulture, University of Minnesota, St. Paul, MN, 55108","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041592939","display_name":"Adrian D. Hegeman","orcid":"https://orcid.org/0000-0003-1008-6066"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adrian D. Hegeman","raw_affiliation_strings":["Department of Horticulture, University of Minnesota, St. Paul, MN, 55108"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Horticulture, University of Minnesota, St. Paul, MN, 55108","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067118759","display_name":"Pratik Jagtap","orcid":"https://orcid.org/0000-0003-0984-0973"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pratik D. Jagtap","raw_affiliation_strings":["Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455"],"raw_orcid":"https://orcid.org/0000-0003-0984-0973","affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017175864","display_name":"Timothy J. Griffin","orcid":"https://orcid.org/0000-0001-6801-2559"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Timothy  J. Griffin","raw_affiliation_strings":["Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455"],"raw_orcid":"https://orcid.org/0000-0001-6801-2559","affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455","institution_ids":["https://openalex.org/I130238516"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1350,"currency":"USD","value_usd":1350},"apc_paid":{"value":1350,"currency":"USD","value_usd":1350},"fwci":0.1159,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.43295129,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"7","issue":null,"first_page":"1604","last_page":"1604"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9972000122070312,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9972000122070312,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9972000122070312,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9965000152587891,"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/workflow","display_name":"Workflow","score":0.8221921920776367},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7995040416717529},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6515038013458252},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6390937566757202},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.541987955570221},{"id":"https://openalex.org/keywords/usability","display_name":"Usability","score":0.4587751626968384},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4356543719768524},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.37426215410232544},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3512057065963745},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3394383490085602},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.31950777769088745},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.19545036554336548},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.16910147666931152}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8221921920776367},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7995040416717529},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6515038013458252},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6390937566757202},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.541987955570221},{"id":"https://openalex.org/C170130773","wikidata":"https://www.wikidata.org/wiki/Q216378","display_name":"Usability","level":2,"score":0.4587751626968384},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4356543719768524},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.37426215410232544},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3512057065963745},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3394383490085602},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.31950777769088745},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.19545036554336548},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.16910147666931152}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.12688/f1000research.16450.1","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.16450.1","pdf_url":"https://f1000research.com/articles/7-1604/v1/pdf","source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357"],"host_organization_lineage_names":["Faculty of 1000"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"F1000Research","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:403fc11e965244a3a743aeaef8ae3bd7","is_oa":true,"landing_page_url":"https://doaj.org/article/403fc11e965244a3a743aeaef8ae3bd7","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"F1000Research, Vol 7 (2018)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.12688/f1000research.16450.1","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.16450.1","pdf_url":"https://f1000research.com/articles/7-1604/v1/pdf","source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357"],"host_organization_lineage_names":["Faculty of 1000"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"F1000Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3459972501","display_name":"ABI Development: A unified Galaxy-based platform for multi-omic data analysis and informatics","funder_award_id":"1458524","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8898499613","display_name":"A Galaxy\u2010based multi\u2010omic informatics hub for cancer researchers","funder_award_id":"5u24ca199347-04","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309636","display_name":"University of Minnesota","ror":"https://ror.org/03grvy078"},{"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/W3204089263.pdf","grobid_xml":"https://content.openalex.org/works/W3204089263.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1967961065","https://openalex.org/W1991694145","https://openalex.org/W2026433130","https://openalex.org/W2040151959","https://openalex.org/W2167403730","https://openalex.org/W2214731401","https://openalex.org/W2277322264","https://openalex.org/W2567711320","https://openalex.org/W2735452220","https://openalex.org/W2766678440","https://openalex.org/W2787737694","https://openalex.org/W2917207851","https://openalex.org/W2952157594"],"related_works":["https://openalex.org/W2429057255","https://openalex.org/W2187546663","https://openalex.org/W148745890","https://openalex.org/W4389670110","https://openalex.org/W2611942503","https://openalex.org/W4315621326","https://openalex.org/W2899790217","https://openalex.org/W2598865957","https://openalex.org/W1576092969","https://openalex.org/W2524154428"],"abstract_inverted_index":{"<ns4:p>Galaxy":[0],"provides":[1],"an":[2,82,197],"accessible":[3],"platform":[4,233],"where":[5],"multi-step":[6,213],"data":[7],"analysis":[8],"workflows":[9,27,195,240],"integrating":[10],"disparate":[11],"software":[12,34,69],"can":[13,115,154,173],"be":[14,58,117,155,175],"run,":[15],"even":[16,178],"by":[17],"researchers":[18,97],"with":[19,66,167],"limited":[20],"programming":[21],"expertise.":[22],"Applications":[23],"of":[24,128,212,230],"such":[25,111,182],"sophisticated":[26,122,180,239],"are":[28,49,64,79,110],"many,":[29],"including":[30],"those":[31],"which":[32,56,63,142],"integrate":[33],"from":[35,148],"different":[36],"\u2018omic":[37],"domains":[38],"(e.g.":[39],"genomics,":[40],"proteomics,":[41],"metabolomics).":[42],"In":[43,102],"these":[44],"complex":[45,84],"workflows,":[46],"intermediate":[47],"outputs":[48,165],"often":[50],"generated":[51,147],"as":[52,183,196],"tabular":[53,149,164,245],"text":[54,76,108,242],"files,":[55],"must":[57],"transformed":[59,161],"into":[60],"customized":[61,163],"formats":[62],"compatible":[65,166],"the":[67,72,88,126,137,202,210,231],"next":[68],"tools":[70],"in":[71],"pipeline.":[73],"Consequently,":[74],"many":[75],"manipulation":[77,109,243],"steps":[78,124],"added":[80],"to":[81,106,159,235],"already":[83],"workflow,":[85],"overly":[86],"complicating":[87],"process":[89],"and":[90,157,162,185,187,208,220,237],"decreasing":[91],"usability,":[92],"especially":[93],"for":[94,177,228],"non-expert":[95],"bench":[96],"focused":[98],"on":[99,244],"obtaining":[100],"results.":[101],"some":[103],"cases,":[104],"limitations":[105],"existing":[107],"that":[112],"desired":[113],"analyses":[114],"only":[116],"carried":[118],"out":[119],"using":[120],"highly":[121],"processing":[123,169],"beyond":[125],"reach":[127],"most":[129],"users.":[130],"As":[131],"a":[132,144],"solution,":[133],"we":[134,199],"have":[135],"developed":[136],"Query":[138,203],"Tabular":[139,204],"Galaxy":[140,232],"tool,":[141],"leverages":[143],"SQLite":[145],"database":[146,153],"input":[150],"data.":[151],"This":[152,222],"queried":[156],"manipulated":[158],"produce":[160],"downstream":[168],"steps.":[170],"Regular":[171],"expressions":[172],"also":[174],"utilized":[176],"more":[179],"manipulations,":[181],"find":[184,225],"replace":[186],"other":[188],"filtering":[189],"actions.":[190],"Using":[191],"several":[192],"Galaxy-based":[193],"multi-omic":[194],"example,":[198],"demonstrate":[200],"how":[201],"tool":[205,223],"dramatically":[206],"streamlines":[207],"simplifies":[209],"creation":[211],"analyses,":[214],"efficiently":[215],"enabling":[216],"complicated":[217],"textual":[218],"manipulations":[219],"processing.":[221],"should":[224],"broad":[226],"utility":[227],"users":[229],"seeking":[234],"develop":[236],"use":[238],"involving":[241],"outputs.</ns4:p>":[246]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":1}],"updated_date":"2026-08-06T08:24:18.245995","created_date":"2021-10-11T00:00:00"}
