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

BMC Bioinformatics

Table 1 Standards used in 'omics public repositories

Technology Type	Minimum Information Guidelines	Metadata Format	Ontology or Controlled Vocabulary	Public Repositories
DNA microarray^a	MIAME [37]	MAGE-Tab [44]	MGED [45]	ArrayExpress [7], GEO [46] (via ArrayExpress^b)
next generation sequencing	MIMARKS, MIxS [47]	SRA-XML	internal to SRA-schema	SRA, ENA
mass spectrometry	MIAPE [48]	PRIDE-XML	MS	PRIDE^c [9]
mass spectrometry, NMR spectroscopy	CIMR^d	ISA-Tab	OBI [43], PSI-MS	Metabolights [10]

Some examples of formats, data models, terminologies and public repositories for omics experiments
^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
^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.
^c. PRIDE submission guidelines: http://www.ebi.ac.uk/pride/submissionGuidelines.do
^d. CIMR: http://msi-workgroups.sourceforge.net/

ISSN: 1471-2105