{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,31]],"date-time":"2026-07-31T20:39:27Z","timestamp":1785530367843,"version":"3.56.0"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2018,9,4]],"date-time":"2018-09-04T00:00:00Z","timestamp":1536019200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100005010","name":"Italian Association for Cancer Research","doi-asserted-by":"publisher","award":["IG17185"],"award-info":[{"award-number":["IG17185"]}],"id":[{"id":"10.13039\/501100005010","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Metabolomics is an emerging \u2018omics\u2019 science involving the characterization of metabolites and metabolism in biological systems. Few bioinformatic tools have been developed for the visualization, exploration and analysis of metabolomic data within the context of metabolic pathways: some of them became rapidly obsolete and are no longer supported, others are based on a single database. A systematic collection of existing annotations has the potential of considerably boosting the investigation and contextualization of metabolomic measurements.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We have released a major update of our Bioconductor package graphite which explicitly tracks small molecules within pathway topologies and their interactions with proteins. The package gathers the information stored in eight major databases, oriented both at genes and at metabolites, across 14 different species. Depending on user preferences, all pathways can be retrieved as gene-only, gene metabolite or metabolite-only networks.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The new graphite version (1.24) is available on Bioconductor.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty719","type":"journal-article","created":{"date-parts":[[2018,9,3]],"date-time":"2018-09-03T12:44:09Z","timestamp":1535978649000},"page":"1258-1260","source":"Crossref","is-referenced-by-count":36,"title":["<i>meta<\/i>Graphite\u2013a new layer of pathway annotation to get metabolite networks"],"prefix":"10.1093","volume":"35","author":[{"given":"Gabriele","family":"Sales","sequence":"first","affiliation":[{"name":"Department of Biology, University of Padova, Padova, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Enrica","family":"Calura","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Padova, Padova, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4792-9047","authenticated-orcid":false,"given":"Chiara","family":"Romualdi","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Padova, Padova, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,9,4]]},"reference":[{"key":"2023013107271782800_bty719-B1","doi-asserted-by":"crossref","first-page":"W132","DOI":"10.1093\/nar\/gkq312","article-title":"Metexplore: a web server to link metabolomic experiments and genome-scale metabolic networks","volume":"38","author":"Cottret","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2023013107271782800_bty719-B2","doi-asserted-by":"crossref","first-page":"1537","DOI":"10.1101\/gr.6202607","article-title":"A systems biology approach for pathway level analysis","volume":"17","author":"Draghici","year":"2007","journal-title":"Genome Res"},{"key":"2023013107271782800_bty719-B3","doi-asserted-by":"crossref","first-page":"e19","DOI":"10.1093\/nar\/gks866","article-title":"Along signal paths: an empirical gene set approach exploiting pathway topology","volume":"41","author":"Martini","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023013107271782800_bty719-B4","doi-asserted-by":"crossref","first-page":"121.","DOI":"10.1186\/1752-0509-4-121","article-title":"Gene set analysis exploiting the topology of a pathway","volume":"4","author":"Massa","year":"2010","journal-title":"BMC Syst. Biol"},{"key":"2023013107271782800_bty719-B5","doi-asserted-by":"crossref","first-page":"278.","DOI":"10.3389\/fphys.2013.00278","article-title":"Methods and approaches in the topology-based analysis of biological pathways","volume":"4","author":"Mitrea","year":"2013","journal-title":"Front. Physiol"},{"key":"2023013107271782800_bty719-B6","doi-asserted-by":"crossref","first-page":"893","DOI":"10.1093\/bioinformatics\/btt612","article-title":"Metabonetworks, an interactive matlab-based toolbox for creating, customizing and exploring sub-networks from Kegg","volume":"30","author":"Posma","year":"2014","journal-title":"Bioinformatics"},{"key":"2023013107271782800_bty719-B7","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1093\/bioinformatics\/btw697","article-title":"Metabosignal: a network-based approach for topological analysis of metabotype regulation via metabolic and signaling pathways","volume":"33","author":"Rodriguez-Martinez","year":"2017","journal-title":"Bioinformatics"},{"key":"2023013107271782800_bty719-B8","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1186\/1471-2105-13-20","article-title":"Graphite\u2013a bioconductor package to convert pathway topology to gene network","volume":"13","author":"Sales","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"2023013107271782800_bty719-B9","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1093\/bioinformatics\/btn577","article-title":"A novel signaling pathway impact analysis","volume":"25","author":"Tarca","year":"2009","journal-title":"Bioinformatics"},{"key":"2023013107271782800_bty719-B10","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1172\/JCI71180","article-title":"Myc-driven accumulation of 2-hydroxyglutarate is associated with breast cancer prognosis","volume":"124","author":"Terunuma","year":"2014","journal-title":"J. Clin. Investig"},{"key":"2023013107271782800_bty719-B11","doi-asserted-by":"crossref","first-page":"473.","DOI":"10.1038\/nrd.2016.32","article-title":"Emerging applications of metabolomics in drug discovery and precision medicine","volume":"15","author":"Wishart","year":"2016","journal-title":"Nat. Rev. Drug Discov"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/7\/1258\/48967487\/bioinformatics_35_7_1258.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/7\/1258\/48967487\/bioinformatics_35_7_1258.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,4]],"date-time":"2023-09-04T20:50:56Z","timestamp":1693860656000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/7\/1258\/5090451"}},"subtitle":[],"editor":[{"given":"Janet","family":"Kelso","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,9,4]]},"references-count":11,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2019,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty719","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,4,1]]},"published":{"date-parts":[[2018,9,4]]}}}