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Table 1 Standards used in 'omics public repositories

From: The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again

Technology Type Minimum Information Guidelines Metadata Format Ontology or Controlled Vocabulary Public Repositories
DNA microarraya MIAME [37] MAGE-Tab [44] MGED [45] ArrayExpress [7], GEO [46]
(via ArrayExpressb)
next generation sequencing MIMARKS, MIxS [47] SRA-XML internal to SRA-schema SRA, ENA
mass spectrometry MIAPE [48] PRIDE-XML MS PRIDEc [9]
mass spectrometry, NMR spectroscopy CIMRd ISA-Tab OBI [43], PSI-MS Metabolights [10]
  1. Some examples of formats, data models, terminologies and public repositories for omics experiments
  2. a. Both repositories, ArrayExpress and GEO, were originally designed to store DNA microarray data. While nowadays, they also allow submission of next generation sequencing data, these are done through underlying submissions to ENA (see http://www.ebi.ac.uk/training/online/course/arrayexpress-submitting-data-using-mage-tab/submission-hts-data) and SRA
  3. b. The GEO database does not deal with the MAGE-Tab format, but data from GEO can be accessed in ArrayExpress exposed in MAGE-Tab.
  4. c. PRIDE submission guidelines: http://www.ebi.ac.uk/pride/submissionGuidelines.do
  5. d. CIMR: http://msi-workgroups.sourceforge.net/