Introduction and update on MGED Standards

Chris Stoeckert
Afternoon Session, 2 September (11th MGED Meeting, 1-4 September, 2008)

How do we tie together the various "silos" of communities and data? There is a real ecosystem of biomedical standards. Not just MGED, but also PSI, MSI, OBO, BIRN, etc. Each community generates its own list of acronyms etc πŸ™‚

We need to bring community standards together into a single, common, integrative standards. MGED is working on MIBBI, FuGE, ISA-TAB, OBI, and MINSEQE. But having standards is only the first step: we need tools to make use of these standards.

MINSEQE is to help prepare for datasets based on UHTS related to research typically done with microarrays. There is crossover with communities primarily concerned with sequence data (e.g. GSC), and existing formats such as SRF. Where should such data get deposited?

Examples of an ultra-high-throughput (UHTS) experiment: chromatin modifications from normal versus disease cells, meta-genomic analysis of a microbial culture. UHTS requires standardization at multiple levels: from sequence reads to interpreting results.

These are just my notes and are not guaranteed to be correct.
Please feel free to let me know about any errors, which are all my
fault and not the fault of the speaker. πŸ™‚

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