Enzymes and EC mappings
From GO Public
- Chris Mungall (software guru at Berkeley)
- Rebecca Foulger (GO editor at EBI)
- Rafael Alcántara ? (software engineer at Intenz, EBI)
Aims and Issues
The GO editors are having trouble keeping up with the EC updates, now that the Enzyme Commission are doing larger and more regular updates to their EC entries. We need a more automated system to keep up with new enzymes and updates to existing enzymes.
Ways To Proceed
Jane has been in touch with Paula de Matos (just left ChEBI), who suggested that we use IntEnz as a pipeline initially for EC numbers and in the longer term use Rhea reactions for this. When Rafael Alcántara (Rafa, a software engineer at Intenz) is back, we can discuss how to best use the internal IntEnz-UniProt pipeline.
In the Rhea project the curators from the SIB are currently working on several aspects, including improving the coverage of known reactions, as well as improving the handling and representation of reactions including polymers and macromolecules, in collaboration with colleagues from ChEBI. The main focus at the current time is really improving the coverage of Rhea (chemically balanced reactions), with a view to promoting its use as a resource for metabolic network reconstruction (e.g. Microme, MetaNetX projects) and as a source of reaction descriptions for UniProt.
Rhea can be used as a source for automation of some of the GO--ChEBI cross-products. It confers the benefit of a more sophisticated representation of chemical roles in reactions than just "input" and "output".
However, it might be more efficient if GO just outsources the whole reaction hierarchy to Rhea, and gets everything from Rhea - text definitions, logical definitions, synonyms etc. The GO editors would give Rhea a block of GO IDs and new reaction term requests would go via Rhea. Either way, we would get the ec2go links via go2rhea and rhea2ec
Current SOPs for handling enzyme updates and new terms
Amelia's Guidelines for New Enzyme Requests
S.O.P for multi-step enzyme reactions