{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,4]],"date-time":"2026-07-04T08:11:10Z","timestamp":1783152670653,"version":"3.54.6"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2020,5,6]],"date-time":"2020-05-06T00:00:00Z","timestamp":1588723200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100013060","name":"EMBL","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100013060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2017YFC0908404"],"award-info":[{"award-number":["2017YFC0908404"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2017YFC0908405"],"award-info":[{"award-number":["2017YFC0908405"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"BBSRC","doi-asserted-by":"publisher","award":["BB\/N022432\/1"],"award-info":[{"award-number":["BB\/N022432\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["208391\/Z\/17\/Z"],"award-info":[{"award-number":["208391\/Z\/17\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"name":"EPIC-XS","award":["823839"],"award-info":[{"award-number":["823839"]}]},{"DOI":"10.13039\/501100000780","name":"European Union","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The Omics Discovery Index is an open source platform that can be used to access, discover and disseminate omics datasets. OmicsDI integrates proteomics, genomics, metabolomics, models and transcriptomics datasets. Using an efficient indexing system, OmicsDI integrates different biological entities including genes, transcripts, proteins, metabolites and the corresponding publications from PubMed. In addition, it implements a group of pipelines to estimate the impact of each dataset by tracing the number of citations, reanalysis and biological entities reported by each dataset. Here, we present the OmicsDI REST interface (www.omicsdi.org\/ws\/) to enable programmatic access to any dataset in OmicsDI or all the datasets for a specific provider (database). Clients can perform queries on the API using different metadata information such as sample details (species, tissues, etc), instrumentation (mass spectrometer, sequencer), keywords and other provided annotations. In addition, we present two different libraries in R and Python to facilitate the development of tools that can programmatically interact with the OmicsDI REST interface.<\/jats:p>","DOI":"10.1093\/nar\/gkaa326","type":"journal-article","created":{"date-parts":[[2020,4,21]],"date-time":"2020-04-21T15:09:19Z","timestamp":1587481759000},"page":"W380-W384","source":"Crossref","is-referenced-by-count":7,"title":["The omics discovery REST interface"],"prefix":"10.1093","volume":"48","author":[{"given":"Gaurhari","family":"Dass","sequence":"first","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manh-Tu","family":"Vu","sequence":"first","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pan","family":"Xu","sequence":"first","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences Beijing, 102206\u00a0Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9201-7840","authenticated-orcid":false,"given":"Enrique","family":"Audain","sequence":"first","affiliation":[{"name":"Department of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marc-Phillip","family":"Hitz","sequence":"first","affiliation":[{"name":"Department of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bj\u00f6rn\u00a0A","family":"Gr\u00fcning","sequence":"first","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-K\u00f6hler-Allee 106, 79110 Freiburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8479-0262","authenticated-orcid":false,"given":"Henning","family":"Hermjakob","sequence":"first","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, UK"},{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences Beijing, 102206\u00a0Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6579-6941","authenticated-orcid":false,"given":"Yasset","family":"Perez-Riverol","sequence":"first","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,5,6]]},"reference":[{"key":"2020062614040974500_B1","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1038\/nbt.3790","article-title":"Discovering and linking public omics data sets using the Omics Discovery Index","volume":"35","author":"Perez-Riverol","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"2020062614040974500_B2","doi-asserted-by":"crossref","first-page":"e0189875","DOI":"10.1371\/journal.pone.0189875","article-title":"Accurate and fast feature selection workflow for high-dimensional omics data","volume":"12","author":"Perez-Riverol","year":"2017","journal-title":"PLoS One"},{"key":"2020062614040974500_B3","doi-asserted-by":"crossref","first-page":"286","DOI":"10.1093\/bib\/bbw114","article-title":"Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences","volume":"19","author":"Manzoni","year":"2018","journal-title":"Brief. Bioinform."},{"key":"2020062614040974500_B4","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1126\/science.1180598","article-title":"Megascience. 'Omics data sharing","volume":"326","author":"Field","year":"2009","journal-title":"Science"},{"key":"2020062614040974500_B5","doi-asserted-by":"crossref","first-page":"3512","DOI":"10.1038\/s41467-019-11461-w","article-title":"Quantifying the impact of public omics data","volume":"10","author":"Perez-Riverol","year":"2019","journal-title":"Nat. Commun."},{"key":"2020062614040974500_B6","doi-asserted-by":"crossref","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR Guiding Principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci Data"},{"key":"2020062614040974500_B7","doi-asserted-by":"crossref","first-page":"816","DOI":"10.1038\/ng.3864","article-title":"Finding useful data across multiple biomedical data repositories using DataMed","volume":"49","author":"Ohno-Machado","year":"2017","journal-title":"Nat. Genet."},{"key":"2020062614040974500_B8","doi-asserted-by":"crossref","first-page":"bbz055","DOI":"10.1093\/bib\/bbz055","article-title":"MENDA: a comprehensive curated resource of metabolic characterization in depression","volume":"3","author":"Pu","year":"2019","journal-title":"Brief. Bioinform."},{"key":"2020062614040974500_B9","doi-asserted-by":"crossref","first-page":"D442","DOI":"10.1093\/nar\/gky1106","article-title":"The PRIDE database and related tools and resources in 2019: improving support for quantification data","volume":"47","author":"Perez-Riverol","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020062614040974500_B10","doi-asserted-by":"crossref","first-page":"828","DOI":"10.1038\/nbt.3597","article-title":"Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking","volume":"34","author":"Wang","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"2020062614040974500_B11","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1038\/nm.4089","article-title":"Facilitating a culture of responsible and effective sharing of cancer genome data","volume":"22","author":"Siu","year":"2016","journal-title":"Nat. Med."},{"key":"2020062614040974500_B12","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1016\/j.atg.2014.09.011","article-title":"To share or not to share is the question","volume":"3","author":"Chalmers","year":"2014","journal-title":"Appl Transl Genom"},{"key":"2020062614040974500_B13","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1038\/s41587-019-0046-x","article-title":"Federated discovery and sharing of genomic data using Beacons","volume":"37","author":"Fiume","year":"2019","journal-title":"Nat. Biotechnol."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/48\/W1\/W380\/33432982\/gkaa326.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/48\/W1\/W380\/33432982\/gkaa326.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,6,27]],"date-time":"2020-06-27T02:25:54Z","timestamp":1593224754000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/48\/W1\/W380\/5831190"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,5,6]]},"references-count":13,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2020,5,6]]},"published-print":{"date-parts":[[2020,7,2]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkaa326","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.02.10.939967","asserted-by":"object"}]},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,7,2]]},"published":{"date-parts":[[2020,5,6]]}}}