Inadequacies of the major data repositories to serve as access points to genomics data have resulted in numerous fragmented projects providing access to data from a single dataset [ 6, 7], a set of thematically related datasets [ 8- 10], or the results of genomics data analyses [ 11- 15].
For example, Minimum Information About a Microarray Experiment (MIAME) in conjunction with the Microarray and Gene Expression Data (MGED) ontology has become the standard for describing microarray experiments in the major data repositories, including Gene Expression Omnibus (GEO), ArrayExpress (AE), Short-Read Archive (SRA) and the National Center for Biotechnology Information (NCBI) (6).
The major oceanographic data repository is the National Institute of Water and Atmospheric Research (NIWA), which is involved in several Census of Marine Life field projects and is the location of the Southwestern Pacific Regional OBIS Node NIWAA is also data manager and custodian for fisheries research data owned by the Ministry of Fisheries.
An important adjunct to routine QC annotation would be the ability, in major public data repositories, to flag and explain the exceptional cases for which QC scores should not be taken at face value.
To illustrate this we investigated the availability of GLY-related datasets in Gene Expression Omnibus (GEO [ 8, 9]) as an example of a major gene expression data repository and we readily made two observations.
Data are available at the University of Bristol data repository, data.bris, at https://doi.org/10.5523/bris.org/10.5523/brisznygvh0s02.org/10.5523/bris
The RNA-seq data were deposited in the Gene Expression Omnibus (NCBI) data repository under accession number GSE84125.
Have these data files been deposited in the most appropriate available data repository?
New York, for instance, is spending $32.1 million over several years to build a state data repository system.
"Well, if you're asking is it data repository or information-hierarchy domain?" he said.
