Updating EC mappings

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 see also https://docs.google.com/document/d/1YZeKpDjSecKu7P7IQsOzcdnxRDWSUYqoyyCBhvHvU3g/edit#heading=h.btlj3dag0fdq

Guidelines for updating transferred or obsolete ECs

In Protégé, search for the old and the new EC numbers in the ontology.

  • Case 1: The old EC is assigned to a single GO term and the new EC is not used in the ontology
  • Case 2: The old EC is assigned to a single GO term and the new EC is already used in the ontology
  • Case 3: The old EC is assigned to more than 1 GO term
  • Note that there are cases where the EC had been transferred to a third EC; in this case all ECs must be checked.

Case 1 The new EC is not used in the ontology and the old CE is assigned to a single GO term

  • Check if there is a RHEA cross reference
  • Compare the current term definition with that that of RHEA and the new EC
  • Confirm that the term text definition matches
  • If EC and RHEA do not match:
    • If the GO definition is more general: check annotations, and see if the term can be redefined without impacting the annotations
    • If the GO definition is more specific or more general: see whether the GO definition needs to be this specific, or if it can be aligned with the RHEA/EC definitions. This can usually be confirmed with existing annotations

Actions

  1. Update the EC dbxref: can specify source = skos:exactMatch (or narrowMatch or broadMatch, as appropriate)
  2. Check synonyms xreferences and update the EC as appropriate. Check the EC entry to confirm: EC has removed a lot of synonyms in recent years. Take the opportunity to remove excessive synonyms and nomenclature no longer in use (for example “D-fructose:acceptor 5-oxidoreductase activity”).
    • If you keep some synonyms that are now removed from EC, remove the dbxref from these synonyms
  3. Update definition (Note that EC often uses “<=>”, but GO uses just “=”. The GO definitions for enzymatic activity usually starts with “
  4. Update definition xref. Ideally we only keep RHEA as a database cross reference (keep PMIDs). When the RHEA is a narrow or broad match, do not use the RHEA definition as a definition xref; use EC or whatever other database or publication is most appropriate.
  5. Check parentage: any of the first 3 digits of the EC number changed, the term probably needs to be moved. Check the correct parent for the partial EC containing the first 3 digits (for example https://enzyme.expasy.org/EC/1.1.1.-) , and change the term parent as approriate
  6. Check other xrefs (Metacyc, KEGG, etc) to make sure these are still valid. The easiest way to do this is to use the links from the ‘Mappings’ tab in AmiGO.

Case 2 The new EC is already used in the ontology and the old CE is assigned to a single GO term

To be completed

1.3.1.30 Transferred entry: 1.3.1.22.

Case 3: The old EC is assigned to more than 1 GO term

To be completed

Examples

Case 1 1.1.99.11 Transferred entry: 1.1.5.14. Matches a single GO term, GO:0047904 'fructose 5-dehydrogenase activity' GO:0047904 Definition: Catalysis of the reaction: D-fructose + A = 5-dehydro-D-fructose + AH(2). RHEA:22304 definition: a ubiquinone + keto-D-fructose = 5-dehydro-D-fructose + a ubiquinol EC: 1.1.5.14 definition: a ubiquinone + keto-D-fructose <=> 5-dehydro-D-fructose + a ubiquinol

Note that both RHEA and EC match, but the GO definition is more general Single annotation (IDA) UniProtKB: M1VMF7. This entry maps the new EC and the correct RHEA - Changed definition to match RHEA and EC - Updated EC cross references - Cleaned up synonyms - Changed parent from ‘GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors’ to ‘GO:0016901 oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor’



Other case 1

1.14.99.33 Transferred entry: 1.14.19.39.



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