Chris Rawlings on Ondex, BBSRC Systems Biology Workshop

BBSRC Systems Biology Grantholder Workshop, University of Nottingham, 16 December 2008.

Introduction (common knowledge): Systems biology projects need data integration. Syntactic and semantic integration must both be considered.

Ondex (http://wwww.ondex.org) is a framework for integrating multi-omics data both syntactically and semantically. Everything in Ondex is presented as a network. It is a domain-independent approach to semantic data integration. Though is currently a data warehouse, a more federated approach is planned. Strongly committed to an open-source and standards approach. Rothamsted: software integraion, releases, infrastructure, outreach. Text mining: NaCTeM (National Centre for Text Mining) – Ananiadou. Workflows, Distribution: U of Manchester (Stevens, Goble). Statistical Methods, Semantic Reasoning comes from Newcastle University (Wipat, Wilkinson, Lord). Integrating Data sources is worked on in a variety of ways: SBML loader (being developed at Newcastle Uni), for example. They're getting taverna-ready, and providing exports in phg, jpg, bmp, and vector formats like eps and graphml. Also allowing exports in Prolog (for CISBIC).

Text Mining work: providing enhanced search, access, and associations in the biological literature, analysis of yeast metabolic reactions (Manchester Uni), association of microorganisms and habitats (Newcastle Uni). Lots of outreach activities.

They've integrated data sources from TAIR and the Poplar resource. In Manchester, they've integrated yeast metabolic models, which is a instance of the general problem of comparing SBML models. In Newcastle, David Lydall is using Ondex to annotate and classify the mutant phenotypes for yeast.

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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