RHEA and EC mappings

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Cross-references for enzyme reactions

Whenever possible, GO uses Rhea for the definitions of reactions.


Note that those cross-references should only be applied to MF terms.


Other mappings for Molecular Functions

Database cross-references used in GO
Ontology Database Sample dbxref
Function Enzyme Commission EC:3.5.1.6
Transport Protein Database TC:2.A.29.10.1
University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) UM-BBD_enzymeID:e0310
MetaCyc metabolic pathway database MetaCyc:XXXX-RXN
Process MetaCyc metabolic pathway database MetaCyc:2ASDEG-PWY
University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) UM-BBD_pathwayID:dcb
Component None

SOP to update GO terms mapped to obsolete ECs

https://docs.google.com/document/d/1YZeKpDjSecKu7P7IQsOzcdnxRDWSUYqoyyCBhvHvU3g/edit

Background on RHEA

(this text needs to be reviewed) In the RHEA is a project from the SIB Swiss Institute of Bioinformatics aiming to improve the coverage of known reactions and 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.

Integration plan GO & RHEA

At some point in the future, we will use the Rhea xrefs to automatically populate definitions and to classify reactions based on reaction participants. In addition, we will use Rhea as the source of information for EC cross-reference when the RHEA xref is available.

Plan of Action (2012/2013)

Plan for setting up a pipeline for automatically incorporating curated catalytic reactions from Rhea into GO MF. 1 and 2 can happen simultaneously.

  1. Map existing GO catalytic activity terms to Rhea. Will require some text-ming/matching etc. and lots of manual review. Add Rhea xrefs to GO. Submit missing reactions to Rhea.
    Considerations:
    • grouping classes won't go into Rhea - will need be handled separately. How do we make axioms for these?
    • do Rhea want to incorporate our reactions?
    • intern to do this?
    Inputs
  2. Design pattern for catalytic reaction xps. Create xps, review and add to GO.
    Considerations:
    • bi-directionality of the reactions won't work in OWL. Did we have a solution to this?
  3. add missing reactions from Rhea to GO. Not sure if we'll want to add all, but certainly everything with an EC. Rhea is available as BioPax, so we will need to convert to OWL and add reactions names, figure out where they fit in the hierarchy.
    Considerations:
    • on what basis we will auto-classify - use EC mechanism as a grouping?
    • naming classes from Rhea - use KEGG?
  4. Set up a pipeline for importing new reactions from Rhea to GO (upon Rhea release?):
    • pull out new reactions from Rhea
    • convert BioPax to OWL
    • use reasoner to place new classes in GO MF
    • manual check
    • add to live GO
    Considerations:
    • interval between imports
    • do we recommend people submit new reactions via Rhea rather than GO?
    • do we also have a TG template for new catalytic reactions?

Current SOPs for handling enzyme updates and new terms

Amelia's Guidelines for New Enzyme Requests

http://wiki.geneontology.org/index.php/Curator_Guide:_Enzymes_and_Reactions


Multi-step catalytic reactions

E.g. 1.14.14.86

Links to enzyme resources

  • Rhea: Expert-curated knowledgebase of chemical and transport reactions of biological interest - and the standard for enzyme and transporter annotation in UniProtKB.
  • Intenz IntEnz (Integrated relational Enzyme database) is a freely available resource focused on enzyme nomenclature. IntEnz is created in collaboration with the Swiss Institute of Bioinformatics (SIB). This collaboration is responsible for the production of the ENZYME resource.
  • Enzyme Commission - IUBMB
  • EC enzyme nomenclature
  • KEGG reactions
  • MetaCyc