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Standards and infrastructure for managing experimental metadata (ISMB DAM SIG 2009)

Philippe Rocca-Serra, EBI

Metagenomics and metatranscriptomics experiments are growing in size and complexity. Gilbert et al PLoS One, 2008 is one example. There are many different domains of science, and the all share some common problems. Consistent reporting of the experimental metadata along with the resulting data has a positive and long-lasting impact on the value of collective scientific outputs. To help solve these problems, many communities have developed reporting standards covering minimal information to be reported about an experiment type (MIBBI).

At the EBI, there are separate submission systems for proteomics data, transcriptomics data, sequence data etc. This is frustrating for the researcher who may have all of this information in one experiment. Therefore, BII is being developed to simplify the submission process. More generally, work is underway to promote synergies among standards initiatives. The common efforts include: MIBBI for scope, FuGE and ISA-TAB for syntax, and OBO foundry ontologies and terminologies for semantics. There is a MIBBI talk later this week at ISMB by Chris Taylor.

There are a number of components that are part of the ISA infrastructure (for more information, see http://isatab.sf.net): The isacreator configurator allows you to set metadata fields and allowed values; isacreator itself is used to describe and upload the experimental metadata (ontologies are accessed in real time via the ontology lookup services and BioPortal, and groups of samples are colour coded); isacreator has a nice visualisation of the various group types that gives you an overview of size and relative importance to other groups.

My thoughts: Firstly, you should know that I contributed to both the FuGE projects and the ISA-TAB projects, and helped develop the ISA-TAB specification. Therefore, I have an interest in this. Moving on… Overall, it really looks like isacreator is coming along nicely from its early incarnations. It looks nice, which is very important for user uptake. It also is compatible with FuGE (though development is still ongoing to increase compatibility, I think).

FriendFeed discussion: http://ff.im/4vcW5

Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else’s. I’m happy to correct any errors you may spot – just let me know!