{"id":"https://openalex.org/W3093319215","doi":"https://doi.org/10.21105/joss.02410","title":"Viime: Visualization and Integration of Metabolomics Experiments","display_name":"Viime: Visualization and Integration of Metabolomics Experiments","publication_year":2020,"publication_date":"2020-10-18","ids":{"openalex":"https://openalex.org/W3093319215","doi":"https://doi.org/10.21105/joss.02410","mag":"3093319215","pmid":"https://pubmed.ncbi.nlm.nih.gov/33768193"},"language":"en","primary_location":{"id":"doi:10.21105/joss.02410","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.02410","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.02410.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Open Source Software","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://joss.theoj.org/papers/10.21105/joss.02410.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065271047","display_name":"Roni Choudhury","orcid":"https://orcid.org/0000-0003-3898-4626"},"institutions":[{"id":"https://openalex.org/I74786994","display_name":"Kitware (United States)","ror":"https://ror.org/02s2acn37","country_code":"US","type":"company","lineage":["https://openalex.org/I74786994"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Roni Choudhury","raw_affiliation_strings":["Kitware Inc","[Kitware Inc.]"],"affiliations":[{"raw_affiliation_string":"Kitware Inc","institution_ids":["https://openalex.org/I74786994"]},{"raw_affiliation_string":"[Kitware Inc.]","institution_ids":["https://openalex.org/I74786994"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053501305","display_name":"Jon Beezley","orcid":null},"institutions":[{"id":"https://openalex.org/I74786994","display_name":"Kitware (United States)","ror":"https://ror.org/02s2acn37","country_code":"US","type":"company","lineage":["https://openalex.org/I74786994"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jon Beezley","raw_affiliation_strings":["Kitware Inc","[Kitware Inc.]"],"affiliations":[{"raw_affiliation_string":"Kitware Inc","institution_ids":["https://openalex.org/I74786994"]},{"raw_affiliation_string":"[Kitware Inc.]","institution_ids":["https://openalex.org/I74786994"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028928232","display_name":"Brandon Davis","orcid":null},"institutions":[{"id":"https://openalex.org/I74786994","display_name":"Kitware (United States)","ror":"https://ror.org/02s2acn37","country_code":"US","type":"company","lineage":["https://openalex.org/I74786994"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brandon Davis","raw_affiliation_strings":["Kitware Inc","[Kitware Inc.]"],"affiliations":[{"raw_affiliation_string":"Kitware Inc","institution_ids":["https://openalex.org/I74786994"]},{"raw_affiliation_string":"[Kitware Inc.]","institution_ids":["https://openalex.org/I74786994"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077332313","display_name":"Jared Tomeck","orcid":null},"institutions":[{"id":"https://openalex.org/I74786994","display_name":"Kitware (United States)","ror":"https://ror.org/02s2acn37","country_code":"US","type":"company","lineage":["https://openalex.org/I74786994"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jared Tomeck","raw_affiliation_strings":["Kitware Inc","[Kitware Inc.]"],"affiliations":[{"raw_affiliation_string":"Kitware Inc","institution_ids":["https://openalex.org/I74786994"]},{"raw_affiliation_string":"[Kitware Inc.]","institution_ids":["https://openalex.org/I74786994"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078536303","display_name":"Samuel Gratzl","orcid":"https://orcid.org/0000-0002-3712-8660"},"institutions":[{"id":"https://openalex.org/I74786994","display_name":"Kitware (United States)","ror":"https://ror.org/02s2acn37","country_code":"US","type":"company","lineage":["https://openalex.org/I74786994"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Samuel Gratzl","raw_affiliation_strings":["Kitware Inc","[Kitware Inc.]"],"affiliations":[{"raw_affiliation_string":"Kitware Inc","institution_ids":["https://openalex.org/I74786994"]},{"raw_affiliation_string":"[Kitware Inc.]","institution_ids":["https://openalex.org/I74786994"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002938718","display_name":"Lilian Golzarri\u2010Arroyo","orcid":"https://orcid.org/0000-0002-1221-6701"},"institutions":[{"id":"https://openalex.org/I592451","display_name":"Indiana University","ror":"https://ror.org/01kg8sb98","country_code":"US","type":"education","lineage":["https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lilian Golzarri-Arroyo","raw_affiliation_strings":["Department of Epidemiology and Biostatistics, Indiana University School of Public Health","Department of Epidemiology and Biostatistics, Indiana University School of Public Health,"],"affiliations":[{"raw_affiliation_string":"Department of Epidemiology and Biostatistics, Indiana University School of Public Health","institution_ids":["https://openalex.org/I592451"]},{"raw_affiliation_string":"Department of Epidemiology and Biostatistics, Indiana University School of Public Health,","institution_ids":["https://openalex.org/I592451"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102019383","display_name":"Jun Wan","orcid":"https://orcid.org/0000-0001-9286-6562"},"institutions":[{"id":"https://openalex.org/I4394709130","display_name":"Indiana University School of Medicine","ror":"https://ror.org/02ets8c94","country_code":null,"type":"education","lineage":["https://openalex.org/I4394709130","https://openalex.org/I592451"]},{"id":"https://openalex.org/I592451","display_name":"Indiana University","ror":"https://ror.org/01kg8sb98","country_code":"US","type":"education","lineage":["https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jun Wan","raw_affiliation_strings":["Center for Computational Biology and Bioinformatics, Indiana University School of Medicine","Department of BioHealth Informatics, Indiana University School of Informatics and Computing","Department of Medical and Molecular Genetics, Indiana University School of Medicine"],"affiliations":[{"raw_affiliation_string":"Center for Computational Biology and Bioinformatics, Indiana University School of Medicine","institution_ids":["https://openalex.org/I592451","https://openalex.org/I4394709130"]},{"raw_affiliation_string":"Department of BioHealth Informatics, Indiana University School of Informatics and Computing","institution_ids":["https://openalex.org/I592451"]},{"raw_affiliation_string":"Department of Medical and Molecular Genetics, Indiana University School of Medicine","institution_ids":["https://openalex.org/I592451","https://openalex.org/I4394709130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023366064","display_name":"Daniel Raftery","orcid":"https://orcid.org/0000-0003-2467-8118"},"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":"Daniel Raftery","raw_affiliation_strings":["Department of Anesthesiology and Pain Medicine, University of Washington","Department of Anesthesiology & Pain Medicine, University of Washington"],"affiliations":[{"raw_affiliation_string":"Department of Anesthesiology and Pain Medicine, University of Washington","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Anesthesiology & Pain Medicine, University of Washington","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009390444","display_name":"Jeff Baumes","orcid":null},"institutions":[{"id":"https://openalex.org/I74786994","display_name":"Kitware (United States)","ror":"https://ror.org/02s2acn37","country_code":"US","type":"company","lineage":["https://openalex.org/I74786994"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeff Baumes","raw_affiliation_strings":["Kitware Inc","[Kitware Inc.]"],"affiliations":[{"raw_affiliation_string":"Kitware Inc","institution_ids":["https://openalex.org/I74786994"]},{"raw_affiliation_string":"[Kitware Inc.]","institution_ids":["https://openalex.org/I74786994"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020644903","display_name":"Thomas M. O\u2019Connell","orcid":"https://orcid.org/0000-0003-4342-9539"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Thomas O\u2019Connell","raw_affiliation_strings":["Department of Otolaryngology-Head & Neck Surgery, Indiana University School of Medicine"],"affiliations":[{"raw_affiliation_string":"Department of Otolaryngology-Head & Neck Surgery, Indiana University School of Medicine","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5065271047"],"corresponding_institution_ids":["https://openalex.org/I74786994"],"apc_list":null,"apc_paid":null,"fwci":0.836,"has_fulltext":true,"cited_by_count":24,"citation_normalized_percentile":{"value":0.71966365,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"5","issue":"54","first_page":"2410","last_page":"2410"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9998999834060669,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9998999834060669,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9218000173568726,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9156000018119812,"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/metabolomics","display_name":"Metabolomics","score":0.7166620492935181},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6876142024993896},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4577535390853882},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.34019291400909424},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3257354497909546},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28474634885787964},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.22345268726348877},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.1401299238204956}],"concepts":[{"id":"https://openalex.org/C21565614","wikidata":"https://www.wikidata.org/wiki/Q12149006","display_name":"Metabolomics","level":2,"score":0.7166620492935181},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6876142024993896},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4577535390853882},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34019291400909424},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3257354497909546},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28474634885787964},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.22345268726348877},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.1401299238204956}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.21105/joss.02410","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.02410","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.02410.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Open Source Software","raw_type":"journal-article"},{"id":"pmid:33768193","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33768193","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":"Journal of open source software","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7990241","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7990241","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":"J Open Source Softw","raw_type":"Text"},{"id":"pmh:oai:scholarworks.indianapolis.iu.edu:1805/29605","is_oa":false,"landing_page_url":"https://hdl.handle.net/1805/29605","pdf_url":null,"source":{"id":"https://openalex.org/S4306400987","display_name":"IUScholarWorks (Indiana University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I592451","host_organization_name":"Indiana University","host_organization_lineage":["https://openalex.org/I592451"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PMC","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.21105/joss.02410","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.02410","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.02410.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Open Source Software","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3068674048","display_name":null,"funder_award_id":"12018","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320306085","display_name":"U.S. Department of Health and Human Services","ror":"https://ror.org/033jnv181"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3093319215.pdf","grobid_xml":"https://content.openalex.org/works/W3093319215.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W1989299822","https://openalex.org/W2043451976","https://openalex.org/W2080046774","https://openalex.org/W2094013107","https://openalex.org/W2095701006","https://openalex.org/W2108222459","https://openalex.org/W2124911115","https://openalex.org/W2149309843","https://openalex.org/W2149917889","https://openalex.org/W2277322264","https://openalex.org/W2295182096","https://openalex.org/W2337859889","https://openalex.org/W2513955315","https://openalex.org/W2743576058","https://openalex.org/W2999240762"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W4283390424","https://openalex.org/W2137270828","https://openalex.org/W1976072307","https://openalex.org/W4205440119","https://openalex.org/W1561393703","https://openalex.org/W4292104203","https://openalex.org/W2040768604","https://openalex.org/W2071288609"],"abstract_inverted_index":{"Metabolomics":[0,269],"involves":[1],"the":[2,25,36,40,65,90,103,158,166,171,189,196,208,213,220,231,245,250],"comprehensive":[3,62],"measurement":[4],"of":[5,35,39,64,98,124,160,169,177,191,205,212,222,252,268,286],"metabolites":[6,140,259],"from":[7,146,233,281],"a":[8,30,60,122],"biological":[9,20,33],"system.":[10],"The":[11,48,67,93,284],"resulting":[12],"metabolite":[13,91,162],"profiles":[14],"are":[15,72,83],"influenced":[16],"by":[17],"genetics,":[18],"lifestyle,":[19],"stresses,":[21],"disease,":[22],"diet":[23],"and":[24,27,77,210,227,256,266,291],"environment":[26],"therefore":[28],"provides":[29],"more":[31,136,201],"holistic":[32],"readout":[34],"pathological":[37],"condition":[38],"organism":[41],"(Beger":[42],"et":[43],"al.,":[44],"2016;":[45],"Wishart,":[46],"2016).":[47],"challenge":[49,94],"for":[50,95,181,288],"metabolomics":[51,279],"is":[52,101,271,293],"that":[53,102],"no":[54],"single":[55],"analytical":[56],"platform":[57],"can":[58,153,173,199,236],"provide":[59,155],"truly":[61],"coverage":[63],"metabolome.":[66],"most":[68],"commonly":[69],"used":[70],"platforms":[71,235],"based":[73],"on":[74,261],"mass-spectrometry":[75],"(MS)":[76],"nuclear":[78],"magnetic":[79],"resonance":[80],"(NMR).":[81],"Investigators":[82],"increasingly":[84],"using":[85],"both":[86],"methods":[87],"to":[88,148,243,277],"increase":[89],"coverage.":[92],"this":[96],"type":[97],"multi-platform":[99],"approach":[100],"data":[104,117,156,187,214,223,232,280,289],"structure":[105],"may":[106,118,215],"be":[107,119,174,200,237],"very":[108],"different":[109,262],"in":[110,142,157,188,295],"these":[111],"two":[112],"platforms.":[113,218,263,283],"For":[114],"example,":[115],"NMR":[116],"reported":[120,141],"as":[121],"list":[123],"spectral":[125],"features,":[126],"e.g.,":[127],"bins":[128],"or":[129,135],"peaks":[130],"with":[131,138],"arbitrary":[132,192],"intensity":[133],"units":[134,144,194],"directly":[137],"named":[139],"concentration":[143],"ranging":[145],"micromolar":[147],"millimolar.":[149],"Some":[150],"MS":[151,184],"approaches":[152,185],"also":[154],"form":[159,190],"identified":[161],"concentrations,":[163],"but":[164],"given":[165],"superior":[167],"sensitivity":[168],"MS,":[170],"concentrations":[172],"several":[175],"orders":[176,204],"magnitude":[178,226],"lower":[179],"than":[180,202],"NMR.":[182],"Other":[183],"yield":[186],"response":[193],"where":[195],"dynamic":[197,228],"range":[198],"6":[203],"magnitude.":[206],"Importantly,":[207],"variability":[209],"reproducibility":[211],"differ":[216],"across":[217],"Given":[219],"diversity":[221],"structures":[224],"(i.e.,":[225],"range)":[229],"integrating":[230],"multiple":[234,282],"challenging.":[238],"This":[239],"often":[240],"leads":[241],"investigators":[242],"analyze":[244],"datasets":[246],"separately,":[247],"which":[248],"prevents":[249],"observation":[251],"potentially":[253],"interesting":[254],"relationships":[255],"correlations":[257],"between":[258],"detected":[260],"Viime":[264,287],"(VIsualization":[265],"Integration":[267],"Experiments)":[270],"an":[272],"open-source,":[273],"web-based":[274],"application":[275],"designed":[276],"integrate":[278],"workflow":[285],"integration":[290],"visualization":[292],"shown":[294],"Figure":[296],"1.":[297]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
