{"id":"https://openalex.org/W2549120143","doi":"https://doi.org/10.1039/9781782626732-00289","title":"Using Galaxy for Proteomics","display_name":"Using Galaxy for Proteomics","publication_year":2016,"publication_date":"2016-11-15","ids":{"openalex":"https://openalex.org/W2549120143","doi":"https://doi.org/10.1039/9781782626732-00289","mag":"2549120143"},"language":"en","primary_location":{"id":"doi:10.1039/9781782626732-00289","is_oa":false,"landing_page_url":"https://doi.org/10.1039/9781782626732-00289","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proteome Informatics","raw_type":"book-chapter"},"type":"book-chapter","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088936138","display_name":"Candace Guerrero","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":true,"raw_author_name":"Candace R. Guerrero","raw_affiliation_strings":["Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota 321 Church St SE/6-155 Jackson Hall Minneapolis MN 55455 USA tgriffin@umn.edu"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota 321 Church St SE/6-155 Jackson Hall Minneapolis MN 55455 USA tgriffin@umn.edu","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":["Center for Mass Spectrometry and Proteomics, University of Minnesota 1479 Gortner Avenue, St. Paul MN 55108 USA","Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota 321 Church St SE/6-155 Jackson Hall Minneapolis MN 55455 USA tgriffin@umn.edu"],"affiliations":[{"raw_affiliation_string":"Center for Mass Spectrometry and Proteomics, University of Minnesota 1479 Gortner Avenue, St. Paul MN 55108 USA","institution_ids":["https://openalex.org/I130238516"]},{"raw_affiliation_string":"Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota 321 Church St SE/6-155 Jackson Hall Minneapolis MN 55455 USA tgriffin@umn.edu","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","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 512 Walter Library, 117 Pleasant Street SE Minneapolis MN 55455 USA"],"affiliations":[{"raw_affiliation_string":"Minnesota Supercomputing Institute, University of Minnesota 512 Walter Library, 117 Pleasant Street SE Minneapolis MN 55455 USA","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":["Center for Mass Spectrometry and Proteomics, University of Minnesota 1479 Gortner Avenue, St. Paul MN 55108 USA","Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota 321 Church St SE/6-155 Jackson Hall Minneapolis MN 55455 USA tgriffin@umn.edu"],"affiliations":[{"raw_affiliation_string":"Center for Mass Spectrometry and Proteomics, University of Minnesota 1479 Gortner Avenue, St. Paul MN 55108 USA","institution_ids":["https://openalex.org/I130238516"]},{"raw_affiliation_string":"Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota 321 Church St SE/6-155 Jackson Hall Minneapolis MN 55455 USA tgriffin@umn.edu","institution_ids":["https://openalex.org/I130238516"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5088936138"],"corresponding_institution_ids":["https://openalex.org/I130238516"],"apc_list":null,"apc_paid":null,"fwci":1.7049,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.84196429,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"289","last_page":"320"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9995999932289124,"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":0.9995999932289124,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9977999925613403,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9957000017166138,"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":0.6651754379272461},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.6364420056343079},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.581985354423523},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5805022716522217},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5519178509712219},{"id":"https://openalex.org/keywords/informatics","display_name":"Informatics","score":0.46646296977996826},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.4596102237701416},{"id":"https://openalex.org/keywords/health-informatics-tools","display_name":"Health informatics tools","score":0.4279446005821228},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.15244776010513306},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.1496289074420929},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1364896595478058}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6651754379272461},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.6364420056343079},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.581985354423523},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5805022716522217},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5519178509712219},{"id":"https://openalex.org/C191630685","wikidata":"https://www.wikidata.org/wiki/Q4027615","display_name":"Informatics","level":2,"score":0.46646296977996826},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.4596102237701416},{"id":"https://openalex.org/C167785021","wikidata":"https://www.wikidata.org/wiki/Q5691083","display_name":"Health informatics tools","level":3,"score":0.4279446005821228},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.15244776010513306},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.1496289074420929},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1364896595478058},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"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/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1039/9781782626732-00289","is_oa":false,"landing_page_url":"https://doi.org/10.1039/9781782626732-00289","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proteome Informatics","raw_type":"book-chapter"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":58,"referenced_works":["https://openalex.org/W320946909","https://openalex.org/W1568341953","https://openalex.org/W1874606962","https://openalex.org/W1968063944","https://openalex.org/W1973095624","https://openalex.org/W1975224781","https://openalex.org/W1982429513","https://openalex.org/W1991694145","https://openalex.org/W1994978698","https://openalex.org/W1996692127","https://openalex.org/W2006886495","https://openalex.org/W2008117982","https://openalex.org/W2009460670","https://openalex.org/W2018126724","https://openalex.org/W2019126169","https://openalex.org/W2019158910","https://openalex.org/W2021341670","https://openalex.org/W2024954384","https://openalex.org/W2026433130","https://openalex.org/W2027974246","https://openalex.org/W2029849110","https://openalex.org/W2030498712","https://openalex.org/W2032964150","https://openalex.org/W2040151959","https://openalex.org/W2041399050","https://openalex.org/W2045117578","https://openalex.org/W2049468030","https://openalex.org/W2058060770","https://openalex.org/W2087610532","https://openalex.org/W2098494636","https://openalex.org/W2101607266","https://openalex.org/W2105805940","https://openalex.org/W2106074866","https://openalex.org/W2110017950","https://openalex.org/W2110768797","https://openalex.org/W2114401611","https://openalex.org/W2115511842","https://openalex.org/W2115646700","https://openalex.org/W2122064342","https://openalex.org/W2123324242","https://openalex.org/W2126362155","https://openalex.org/W2126647821","https://openalex.org/W2130706354","https://openalex.org/W2136482257","https://openalex.org/W2139561888","https://openalex.org/W2149039878","https://openalex.org/W2149309843","https://openalex.org/W2153132589","https://openalex.org/W2164522178","https://openalex.org/W2167403730","https://openalex.org/W2173626314","https://openalex.org/W2214731401","https://openalex.org/W2223675028","https://openalex.org/W2292856761","https://openalex.org/W2320466996","https://openalex.org/W2324909991","https://openalex.org/W2461798152","https://openalex.org/W4233550359"],"related_works":["https://openalex.org/W4294281692","https://openalex.org/W2320705913","https://openalex.org/W2086112825","https://openalex.org/W2901387949","https://openalex.org/W150760603","https://openalex.org/W2808516408","https://openalex.org/W2463183163","https://openalex.org/W2000729083","https://openalex.org/W2049468030","https://openalex.org/W2109118345"],"abstract_inverted_index":{"The":[0,73],"area":[1],"of":[2,27,62,70,85,144],"informatics":[3],"for":[4,24,76,82,112,150,173],"mass":[5],"spectrometry":[6],"(MS)-based":[7],"proteomics":[8,114,153,162],"data":[9,58,100,154,177,183],"has":[10],"steadily":[11],"grown":[12],"over":[13],"the":[14,137,145],"last":[15],"two":[16],"decades.":[17],"Numerous,":[18],"effective":[19],"software":[20,50,111,129],"programs":[21],"now":[22,105],"exist":[23],"various":[25],"aspects":[26],"proteomic":[28,90],"informatics.":[29,91,157],"However,":[30],"many":[31,84],"researchers":[32,103],"still":[33],"have":[34],"difficulties":[35,41],"in":[36,89,148,164],"using":[37],"these":[38,86],"software.":[39,72],"These":[40],"arise":[42],"from":[43],"problems":[44],"with":[45,56,169],"running":[46],"and":[47,60,66,123,126,134,156,175],"integrating":[48],"disparate":[49],"programs,":[51],"scalability":[52],"issues":[53,88],"when":[54],"dealing":[55],"large":[57],"volumes,":[59],"lack":[61],"ability":[63],"to":[64,97,107,109,121,179],"share":[65],"reproduce":[67],"workflows":[68],"comprised":[69],"different":[71],"Galaxy":[74,108,122,149,165],"framework":[75],"bioinformatics":[77],"provides":[78],"an":[79,119],"attractive":[80],"option":[81],"solving":[83],"current":[87],"Originally":[92],"developed":[93],"as":[94],"a":[95],"workbench":[96],"enable":[98,180],"genomic":[99,174],"analysis,":[101],"numerous":[102],"are":[104,131],"turning":[106],"implement":[110],"MS-based":[113,152],"applications.":[115,185],"Here,":[116],"we":[117,159],"provide":[118],"introduction":[120],"its":[124],"features,":[125],"describe":[127,142,160],"how":[128,161],"tools":[130,147,163,172],"deployed,":[132],"published":[133],"shared":[135],"via":[136],"scalable":[138],"framework.":[139],"We":[140],"also":[141],"some":[143],"existing":[146,171],"basic":[151],"analysis":[155,178,184],"Finally,":[158],"can":[166],"be":[167],"combined":[168],"other":[170],"transcriptomic":[176],"powerful":[181],"multi-omic":[182]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}