{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,6]],"date-time":"2026-08-06T16:36:21Z","timestamp":1786034181768,"version":"3.56.0"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"1","funder":[{"DOI":"10.13039\/100006108","name":"National Center for Advancing Translational Sciences","doi-asserted-by":"publisher","award":["ZIC TR000410-03"],"award-info":[{"award-number":["ZIC TR000410-03"]}],"id":[{"id":"10.13039\/100006108","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Functional interpretation of high-throughput metabolomic and transcriptomic results is a crucial step in generating insight from experimental data. However, pathway and functional information for genes and metabolites are distributed among many siloed resources, limiting the scope of analyses that rely on a single knowledge source.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>RaMP-DB 2.0 is a web interface, relational database, API and R package designed for straightforward and comprehensive functional interpretation of metabolomic and multi-omic data. RaMP-DB 2.0 has been upgraded with an expanded breadth and depth of functional and chemical annotations (ClassyFire, LIPID MAPS, SMILES, InChIs, etc.), with new data types related to metabolites and lipids incorporated. To streamline entity resolution across multiple source databases, we have implemented a new semi-automated process, thereby lessening the burden of harmonization and supporting more frequent updates. The associated RaMP-DB 2.0 R package now supports queries on pathways, common reactions (e.g. metabolite-enzyme relationship), chemical functional ontologies, chemical classes and chemical structures, as well as enrichment analyses on pathways (multi-omic) and chemical classes. Lastly, the RaMP-DB web interface has been completely redesigned using the Angular framework.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The code used to build all components of RaMP-DB 2.0 are freely available on GitHub at https:\/\/github.com\/ncats\/ramp-db, https:\/\/github.com\/ncats\/RaMP-Client\/ and https:\/\/github.com\/ncats\/RaMP-Backend. The RaMP-DB web application can be accessed at https:\/\/rampdb.nih.gov\/.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac726","type":"journal-article","created":{"date-parts":[[2022,11,14]],"date-time":"2022-11-14T08:19:09Z","timestamp":1668413949000},"source":"Crossref","is-referenced-by-count":64,"title":["RaMP-DB 2.0: a renovated knowledgebase for deriving biological and chemical insight from metabolites, proteins, and genes"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8093-6463","authenticated-orcid":false,"given":"John","family":"Braisted","sequence":"first","affiliation":[{"name":"Division of Preclinical Innovation, National Center for Advancing Translational Sciences , Rockville, MD 20850, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6373-9545","authenticated-orcid":false,"given":"Andrew","family":"Patt","sequence":"additional","affiliation":[{"name":"Division of Preclinical Innovation, National Center for Advancing Translational Sciences , Rockville, MD 20850, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cole","family":"Tindall","sequence":"additional","affiliation":[{"name":"Division of Preclinical Innovation, National Center for Advancing Translational Sciences , Rockville, MD 20850, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9987-3738","authenticated-orcid":false,"given":"Timothy","family":"Sheils","sequence":"additional","affiliation":[{"name":"Division of Preclinical Innovation, National Center for Advancing Translational Sciences , Rockville, MD 20850, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jorge","family":"Neyra","sequence":"additional","affiliation":[{"name":"Somatus , McLean, VA 22102, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6720-5348","authenticated-orcid":false,"given":"Kyle","family":"Spencer","sequence":"additional","affiliation":[{"name":"Division of Preclinical Innovation, National Center for Advancing Translational Sciences , Rockville, MD 20850, USA"},{"name":"Department of Biomedical Informatics, The Ohio State University , Columbus, OH 43210, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1809-4458","authenticated-orcid":false,"given":"Tara","family":"Eicher","sequence":"additional","affiliation":[{"name":"Division of Preclinical Innovation, National Center for Advancing Translational Sciences , Rockville, MD 20850, USA"},{"name":"Department of Computer Science and Engineering, The Ohio State University , Columbus OH 43210, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4491-8107","authenticated-orcid":false,"given":"Ewy A","family":"Math\u00e9","sequence":"additional","affiliation":[{"name":"Division of Preclinical Innovation, National Center for Advancing Translational Sciences , Rockville, MD 20850, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,11,14]]},"reference":[{"key":"2023010805381678500_btac726-B2","doi-asserted-by":"crossref","first-page":"8623","DOI":"10.3390\/ijms21228623","article-title":"Large-scale plasma analysis revealed new mechanisms and molecules associated with the host response to SARS-CoV-2","volume":"21","author":"Barberis","year":"2020","journal-title":"IJMS"},{"key":"2023010805381678500_btac726-B4","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. 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