SysMO-DB: Sharing and Exchanging SB Data and Models (ISMB DAM SIG 2009)

Kathy Wolstencroft, University of Manchester

91 groups are part of the SysMO consortium. Started in 2008, a year after the other projects. They want to retrofit the data access and modelling platform over the existing resources used by the consortium. Their web interface looks similar to myExperiment. Sharing policies are present: your stuff is private until you say it isn’t. How are the assets exchanged? They’re divided into experimental and bioinformatics processes. In terms of models (and not data), they say SBML is the recommended format. For those who model with SBML, they have integrated with JWS online.

Their data comes from excel spreadsheets (the majority), SABIO-RK, iChiP, MeMo, and others. In order to exchange data, they have the “just enough results model” which lists a minimal amount of information for exchanging results. For each data type, you define a jerm and generate and apply that jerm to your data. Keeping the data at the project sites has challenges: reliability, support, and archiving. Final thoughts: find a solution that fits their current practices; start simple, show benefits, add more; engage with peopel actually doing the work; let the scientists retain control over their data and who can see it; don’t reinvent; help prevent people duplicating work by linking the people as well as the resources.

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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!


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