{"id":"https://openalex.org/W758685619","doi":null,"title":"The Galaxy Framework as a Unifying Bioinformatics Solution for \u2018omics\u2019 Core Facilities.","display_name":"The Galaxy Framework as a Unifying Bioinformatics Solution for \u2018omics\u2019 Core Facilities.","publication_year":2014,"publication_date":"2014-05-01","ids":{"openalex":"https://openalex.org/W758685619","mag":"758685619"},"language":"en","primary_location":{"id":"pmh:oai:europepmc.org:3134434","doi":null,"is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4162280","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},"volume":null,"type":"article","indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4162280","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","observed_orcids":["https://orcid.org/0000-0002-2590-4765"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"James E. Johnson","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-2590-4765","affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"B Gottschalk","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"B Gottschalk","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028223333","display_name":"Getiria Onsongo","orcid":"https://orcid.org/0000-0001-5305-3251","observed_orcids":["https://orcid.org/0000-0001-5305-3251"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Getiria Onsongo","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0001-5305-3251","affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089121355","display_name":"Sricharan Bandhakavi","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sricharan Bandhakavi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075684030","display_name":"E.P. deJong","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"E.P. deJong","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050908951","display_name":"Joel A. Kooren","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Joel A. Kooren","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004989633","display_name":"T.W. Markowsk","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"T.W. Markowsk","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108488604","display_name":"Lee Ann Higgins","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"L. A. Higgins","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074168289","display_name":"Joel D. Rudney","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Joel Rudney","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017175864","display_name":"Timothy J. Griffin","orcid":"https://orcid.org/0000-0001-6801-2559","observed_orcids":["https://orcid.org/0000-0001-6801-2559"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Timothy J. Griffin","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0001-6801-2559","affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5067118759","display_name":"Pratik Dilip Jagtap","orcid":"https://orcid.org/0000-0003-0984-0973","observed_orcids":["https://orcid.org/0000-0003-0984-0973"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Pratik Jagtap","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0003-0984-0973","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0203356,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"25","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.7993000149726868,"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":0.7993000149726868,"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":0.11320000141859055,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.04879999905824661,"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/multi-omics-integration","display_name":"multi-omics integration","score":0.9010000228881836},{"id":"https://openalex.org/keywords/proteogenomics","display_name":"proteogenomics","score":0.9879999756813049},{"id":"https://openalex.org/keywords/metaproteomics","display_name":"metaproteomics","score":1.0},{"id":"https://openalex.org/keywords/bioinformatics-pipeline","display_name":"bioinformatics pipeline","score":0.7319999933242798},{"id":"https://openalex.org/keywords/proteoforms","display_name":"proteoforms","score":0.6690000295639038},{"id":"https://openalex.org/keywords/salivary-proteomics","display_name":"salivary proteomics","score":0.7889999747276306},{"id":"https://openalex.org/keywords/oral-premalignant-lesions","display_name":"oral potentially malignant disorders","score":0.8960000276565552},{"id":"https://openalex.org/keywords/severe-early-childhood-caries","display_name":"severe early childhood caries","score":0.890999972820282},{"id":"https://openalex.org/keywords/microbial-identification","display_name":"microbial identification","score":0.7269999980926514},{"id":"https://openalex.org/keywords/megan","display_name":"MEGAN","score":0.7789999842643738},{"id":"https://openalex.org/keywords/x-tandem","display_name":"X!Tandem","score":0.6520000100135803}],"concepts":[{"id":"https://openalex.org/C145741570","wikidata":"https://www.wikidata.org/wiki/Q7251534","display_name":"Proteogenomics","level":5,"score":0.9349855184555054},{"id":"https://openalex.org/C199465337","wikidata":"https://www.wikidata.org/wiki/Q6823168","display_name":"Metaproteomics","level":4,"score":0.8511505126953125},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6694678068161011},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6586482524871826},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.6053637266159058},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5733828544616699},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5469061732292175},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46397170424461365},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.4430544078350067},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3282209038734436},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.24951136112213135},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23008516430854797},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.15772241353988647},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.1410621702671051},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:europepmc.org:3134434","doi":null,"is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4162280","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:4162280","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4162280","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,"listed_in":[],"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":"J Biomol Tech","raw_type":"Text"},{"id":"mag:758685619","doi":null,"is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC4162280","pdf_url":null,"source":{"id":"https://openalex.org/S2755344187","display_name":"Journal of Biomolecular Techniques JBT","issn_l":"1524-0215","issn":["1524-0215","1943-4731"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","jufo-1","medline","norway-1"],"host_organization":"https://openalex.org/P4360969280","host_organization_name":"Association of Biomolecular Resource Facilities","host_organization_lineage":["https://openalex.org/P4360969280"],"host_organization_lineage_names":["Association of Biomolecular Resource Facilities"],"type":"journal"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":"Journal of Biomolecular Techniques JBT","raw_type":null}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:4162280","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4162280","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,"listed_in":[],"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":"J Biomol Tech","raw_type":"Text"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Integration":[0,14],"of":[1,15,23,34,45,55,75,101,182,189,256,261],"different":[2],"omics":[3],"data":[4,47],"(genomic,":[5],"transcriptomic,":[6],"proteomic)":[7],"reveals":[8],"novel":[9,190,199],"discoveries":[10],"into":[11],"biological":[12],"systems.":[13],"these":[16,78],"datasets":[17,114,220],"is":[18],"challenging":[19],"however,":[20],"involving":[21],"use":[22,33,170,255],"multiple":[24],"disparate":[25,36],"software":[26,37,86,174],"in":[27,38,66,171,177,186,201,216,264],"a":[28,39,48,106,285],"sequential":[29,40],"manner.":[30,270],"However,":[31],"the":[32,43,53,73,99,102,202,238,254,279],"multiple,":[35],"manner":[41],"makes":[42],"integration":[44],"multi-omic":[46,64,262],"serious":[49],"challenge.":[50],"We":[51,70,93,252],"describe":[52],"extension":[54],"Galaxy":[56,76,103,178,257,282],"for":[57,77,85,109,115,141,161,169,227,242,258,281,289],"mass":[58],"spectrometric-based":[59],"proteomics":[60,163],"software,":[61],"enabling":[62],"advanced":[63],"applications":[65],"proteogenomics":[67,116,228],"and":[68,121,127,132,152,157,160,167,206,218,231,268,273],"metaproteomics.":[69],"will":[71,94],"demonstrate":[72,253,278],"benefits":[74,100],"analyses,":[79],"as":[80,82,105,145],"well":[81],"its":[83],"value":[84],"developers":[87],"seeking":[88],"to":[89,213,283],"publish":[90],"new":[91],"software.":[92,223],"also":[95,249],"share":[96],"insights":[97],"on":[98],"framework":[104,247,277],"bioinformatics":[107,287],"solution":[108,288],"proteomic/metabolomic":[110],"core":[111,291],"facilities.":[112,292],"Multiple":[113],"research":[117,129],"(3D-fractionated":[118],"salivary":[119,203],"dataset":[120,131,204,208],"oral":[122],"pre-malignant":[123],"lesion":[124],"(OPML)":[125],"dataset)":[126],"metaproteomics":[128],"(OPML":[130],"Severe":[133],"Early":[134],"Childhood":[135],"Caries":[136],"(SECC)":[137],"dataset).":[138],"Software":[139],"required":[140],"analytical":[142,183],"steps":[143],"such":[144],"peaklist":[146],"generation,":[147],"database":[148,154],"generation":[149],"(RNA-Seq":[150],"derived":[151],"others),":[153],"search":[155],"(ProteinPilot":[156],"X!":[158],"tandem)":[159],"quantitative":[162],"were":[164],"deployed,":[165],"tested":[166],"optimized":[168],"workflows.":[172],"The":[173],"are":[175,235,248],"shared":[176],"toolshed":[179],"(http://toolshed.g2.bx.psu.edu/).":[180],"Usage":[181],"workflows":[184,226],"resulted":[185],"reliable":[187],"identification":[188,215],"proteoforms":[191,200],"(proteogenomics)":[192],"or":[193],"microorganisms":[194],"(metaproteomics).":[195],"Proteogenomics":[196],"analysis":[197,211,229,233,260],"identified":[198],"(51)":[205],"OPML":[207,217],"(38).":[209],"Metaproteomics":[210],"led":[212],"microbial":[214],"SECC":[219],"using":[221,275],"MEGAN":[222],"As":[224],"examples,":[225],"(http://z.umn.edu/pg140)":[230],"metaproteomic":[232],"(http://z.umn.edu/mp65)":[234],"available":[236,250],"at":[237],"usegalaxyp.org":[239],"website.":[240],"Tutorials":[241],"workflow":[243],"usage":[244],"within":[245],"Galaxy-P":[246],"(http://z.umn.edu/ppingp).":[251],"integrated":[259],"data,":[263],"an":[265],"accessible,":[266],"transparent":[267],"reproducible":[269],"Our":[271],"results":[272],"experiences":[274],"this":[276],"potential":[280],"be":[284],"unifying":[286],"\u2018omics":[290]},"counts_by_year":[],"updated_date":"2026-09-29T14:09:16.559479","created_date":"2025-10-10T00:00:00"}
