Catalytic activity, acting to interconvert metabolites (was: small molecule interconversion)

[pgaudet]

From @dosumis on February 9, 2017 16:12

Intention is to distinguish catalytic processes acting on an 'information biomacromolecule' (CHEBI:33695) from those acting on other molecules. We can't do this logically with the way ChEBI is built (we don't have a class representing the complement of 'information biomacromolecule' (CHEBI:33695). But we could derive a small molecule list using a closed world intepretation of ChEBI (e.g. via graph reasoning). @cmungall - Can you script adding a derived class like this to GOCHE?

_Copied from original issue: geneontology/molecular_functionrefactoring#35

[pgaudet]

From @ValWood on February 28, 2017 11:48

Super!

(The small-molecule metabolism list is really useful for metabolic modellers etc)

[pgaudet]

At the ontology call we discussed that 'small molecule' was difficult to define. A suggestion is to use 'metabolite' -> 'Catalytic activity, acting to interconvert metabolites' Is that any better ?

[ValWood]

"metabolite" is what we are trying to capture with this term. However this would translate to "metabolite metabolic process", it looks weird but I guess it's clear enough.

[pgaudet]

Discussed with @amorgat - she has no objection to using 'metabolite'.

If there are no objections from the ontology group, I will go ahead and implement that.

Thanks, Pascale

[pgaudet]

Discussed with @thomaspd Plan is to

• use Rhea cross-references
• look up reaction participants
• for reactions in which none of the participants are children of CHEBI:33695 information biomacromolecule, then this reaction will be classified as a 'catalytic activity, acting to interconvert metabolites'.

We'd like to have a script to do this at each GO release (ie including updated Rhea).

[amorgat]

@pgaudet @thomaspd If I understand your concern correctly, I think that you don't have to query ChEBI ontology for that task. Rhea reactions involving macromolecules have participants of the type GENERIC (GenericPolypeptide / GenericPolynucleotide) or POLYMER. Reactions with ALL participants of the type CHEBI can be classified as a 'catalytic activity, acting to interconvert metabolites'.

[pgaudet]

Great ! That's very useful.

We now need to define a strategy.

[amorgat]

@pgaudet where can I find documentation on GO release cycle / procedure?

[pgaudet]

http://wiki.geneontology.org/index.php/Release_Pipeline

[amorgat]

@pgaudet thanks!