Synergistic Standards for Omics Data – An Overview

Susanna-Assunta Sansone / Philippe Rocca-Serra
Afternoon Session, 2 September (11th MGED Meeting, 1-4 September, 2008)

Standards are a means to an end: they are meant to provide an unambiguous representation, description, and communication of data and metadata. They allow interoperability of resources and advance science, and facilitate data integration.

There is a proliferation of standarization efforts, which can be subdivided into three main categories: Syntax (FuGE, ISA_TAB), Content (checklists, e.g. MIAME), and Semantics (OBI). There are both standards developing organizations as well as grass-roots movements. However, what tends to happen is that a particular community is focused on their needs, which can lead to duplication of effort. This is normal, but the natural progression is a shared, integrated standard.

One example of fragmentation is as follows: within the EBI, MGED required submission to ArrayExpress, and HUPO-PSI required the same for PRIDE. However, each had their own interface and toolset, which makes things difficult when you have both types of data – they're not interoperable.

So, how can we move on? There is a growing complexity in the datasets, and a move towards systems biology. We make use of the synergistic integrative standards.

Integrative Content Efforts: The MIBBI project contains the  list of other people trying to define minimum content, and using these aims to ensure orthologous work. Also, the OBO Foundry aims to allow new ontologies to be created in an orthologous way. Also, publishing an open ontology should be analogous to publishing an open-access scientific paper, in many respects.

Integrative Semantics Efforts: OBI.

Integrative Syntactic Efforts: FuGE, ISA-TAB. FuGE is an extensible framework for describing life-science experiments. ISA-TAB is similar to both FuGE and MAGE-TAB. It is a bit like a tabular format of FuGE, and it is an upgrade of MAGE-TAB that works for other omics data types. It is completely backwords-compatible with MAGE-TAB.

The BioInvestigation Index, being developed at the EBI, will use many of these.

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. 🙂

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