Kinetic Data for Reaction Mechanism Steps in SABIO-RK (BioSysBio 2009)

Ulrike Wittig
EML Research GmbH, Germany

SABIO-RK stores information biochemical reactions and enzyme kinetics. Reactions are mainly from KEGG and from literature. Kinetic information comes only from the literature. You can access SABIO-RK both via a user interface and via web services. She then took us through a tour of the website and how to get information from SABIO-RK. They don't just store the overall reaction, but also the intermediate steps.

Other sources for reaction mechanisms. MACiE, which stores qualitative information based on the 3d crystal structure of the enzyme. Literature also has it, but not in a standardized way. That's why SABIO-RK is so helpful. The new data model for SABIO-RK has extra features to store the intermediate steps. How does the information get into the db? She then explained how information from a paper gets into the database. SABIO-RK now contains more detailled information about the mechanisms of reactions and the intermediate steps. In the future there will be a search function for the mechanism, and there will be the ability to export in formats like SBML (SBML currently cannot handle the hierarchy of reactions used in mechanisms). Reaction mechanisms can be used for the representation of signalling reactions (e.g. protein-ligand binding), and this will be implemented in future.

Personal Comments: A very nice tour and explanation of how to use SABIO-RK. It's good to see a data model in a talk, too.

Tuesday Session 2
http://friendfeed.com/rooms/biosysbio
http://conferences.theiet.org/biosysbio

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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