{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,8]],"date-time":"2026-02-08T17:00:48Z","timestamp":1770570048774,"version":"3.49.0"},"reference-count":15,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2024,1,19]],"date-time":"2024-01-19T00:00:00Z","timestamp":1705622400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"US National Science Foundation","doi-asserted-by":"publisher","award":["NSF2109898"],"award-info":[{"award-number":["NSF2109898"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"US National Science Foundation","doi-asserted-by":"publisher","award":["R01AI160719"],"award-info":[{"award-number":["R01AI160719"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Institute of Allergy and Infectious Diseases of the National Institutes of Health","award":["NSF2109898"],"award-info":[{"award-number":["NSF2109898"]}]},{"name":"National Institute of Allergy and Infectious Diseases of the National Institutes of Health","award":["R01AI160719"],"award-info":[{"award-number":["R01AI160719"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Metabolites"],"abstract":"<jats:p>The Omics Dashboard is a software tool for interactive exploration and analysis of metabolomics, transcriptomics, proteomics, and multi-omics datasets. Organized as a hierarchy of cellular systems, the Dashboard at its highest level contains graphical panels for the full range of cellular systems, including biosynthesis, energy metabolism, and response to stimulus. Thus, the Dashboard top level surveys the state of the cell across a broad range of key systems in a single screen. Each Dashboard panel contains a series of X\u2013Y plots depicting the aggregated omics data values relevant to different subsystems of that panel, e.g., subsystems within the biosynthesis panel include amino acid biosynthesis, carbohydrate biosynthesis and cofactor biosynthesis. Users can interactively drill down to focus in on successively lower-level subsystems of interest. In this article, we present for the first time the metabolomics analysis capabilities of the Omics Dashboard, along with significant new extensions to better accommodate metabolomics datasets, enable analysis and visualization of multi-omics datasets, and provide new data-filtering options.<\/jats:p>","DOI":"10.3390\/metabo14010065","type":"journal-article","created":{"date-parts":[[2024,1,19]],"date-time":"2024-01-19T05:46:44Z","timestamp":1705643204000},"page":"65","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["The Omics Dashboard for Interactive Exploration of Metabolomics and Multi-Omics Data"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5763-8935","authenticated-orcid":false,"given":"Suzanne","family":"Paley","sequence":"first","affiliation":[{"name":"Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5876-6418","authenticated-orcid":false,"given":"Peter D.","family":"Karp","sequence":"additional","affiliation":[{"name":"Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,1,19]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Paley, S.M., Parker, K., Spaulding, A., Tomb, J., O\u2019Maille, P., and Karp, P.D. (2017). The Omics Dashboard for Interactive Exploration of Gene-Expression Data. Nucleic Acids Res., Available online: https:\/\/academic.oup.com\/nar\/article\/45\/21\/12113\/4508872.","DOI":"10.1093\/nar\/gkx910"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1085","DOI":"10.1093\/bib\/bbx085","article-title":"The BioCyc collection of microbial genomes and metabolic pathways","volume":"20","author":"Karp","year":"2017","journal-title":"Brief. Bioinform."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1093\/bib\/bbz104","article-title":"Pathway Tools Version 23.0 Update: Software for Pathway\/Genome Informatics and Systems Biology","volume":"22","author":"Karp","year":"2019","journal-title":"Brief. Bioinform."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"291","DOI":"10.3390\/metabo5020291","article-title":"Computational Metabolomics Operations at BioCyc.org","volume":"5","author":"Karp","year":"2015","journal-title":"Metabolites"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Midford, P., Latendresse, M., O\u2019Maille, P., and Karp, P.D. (2019). Using Pathway Covering to Explore Connections among Metabolites. 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Available online: https:\/\/biocyc.org\/download.shtml."}],"container-title":["Metabolites"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2218-1989\/14\/1\/65\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T13:45:52Z","timestamp":1760103952000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2218-1989\/14\/1\/65"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,1,19]]},"references-count":15,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,1]]}},"alternative-id":["metabo14010065"],"URL":"https:\/\/doi.org\/10.3390\/metabo14010065","relation":{},"ISSN":["2218-1989"],"issn-type":[{"value":"2218-1989","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,1,19]]}}}