Transmembrane transporter RHEA xrefs to add about go-ontology

[pgaudet]

Hi @sjm41

Thanks for these.

Simple 1:1 mappings:

Be careful that some GO terms are more specific, e. g. ABC transporters. The RHEA should be put as broadMatch for these.

Mappings involving multiple RHEAs to a single GO term - add both RHEAs as NarrowMatch xrefs?

Sure, unless RHEA has a more general reaction that corresponds to the GO term. I assume it doesn't, since you suggest these.
Note that GO does not capture stoichiometry.

Potential mappings involving a mismatch of some sort.

looking..

[pgaudet]

Potential mappings involving a mismatch of some sort.

These are all a bit unique. One thing that seems to happen often is that in GO the chemical is not precise enough; please check with it the ChEBI used by RHEA is consistent with the annotations, and if they are, please change the term definition and ChEBI in the LD.

You can list any remaining questions once the ones covered above are done.

OK ?
Thanks, Pascale

[sjm41]

Also need to wait for response to query about meaning of RHEA entries like "RHEA:70719 L-alanine(in) = L-alanine(out)"
#27277 (comment)

[pgaudet]

Sorry @sjm41 I missed the question in #27277 (comment)

So, the real question here (and it's a wider question) is whether GO terms like this new one:
id: GO:0160173
name: histamine transmembrane transporter activity
def: Enables the transfer of histamine from one side of a membrane to the other.
are intended to represent:
(1) a generic (potentially grouping) GO term that can be used to annotate any protein that transports the given substance, with/without additional ions/substances involved;
or
(2) a much more specific 'uniporter' activity that should only be used to annotate proteins that only transport the single given substance.

The answer is (a). In GO, this represents a grouping term with no mention of the mechanism. Uniporter would be a different term. However, generally if there is a unique mechanism, we dont usually create the general grouping class.

In the beginning of RHEA, they didn't use to capture mechanisms for transporters, but I think thy now do, which creates a bit of confusion because not everything is uniform. @amorgat @kaxelsen please correct me if this is wrong.

Thanks, Pascale

[sjm41]

Thanks @pgaudet for confirming the GO meaning. As I said in #27277 (comment), I thought that was the case for GO. It's the meaning of the RHEA entries like RHEA:70719 or RHEA:73879 I'm really unsure about, and whether they have the same meaning as (ie. should be xrefs to) generic GO grouping terms (like GO:0160173) or not:

the same question applies to RHEA reactions like "RHEA:73879 "histamine(out) = histamine(in)". On the face of it, that RHEA has the same definition as the GO:0160173 ("Enables the transfer of histamine from one side of a membrane to the other.") term so could be added as an (exact) xref. But is RHEA:73879 intended to be (1) a generic grouping term for all types of histamine transporter, or (2) specifically for histamine uniporters involving no other chemical? In fact, maybe such RHEAs are intended for 'passive transporters (channels)' given that no other chemical is involved?

[pgaudet]

If RHEA doesn't specify, then the RHEA term means 'x transmembrane transporter activity' in GO.

[sjm41]

Elisabeth Coudert at RHEA has clarified that 'compound(out)=compound(in)' RHEA transport reactions are not intended to be grouping terms in RHEA, but rather indicate channel/uniporter transporters.
Having checked this with @pgaudet, this means that:
i) GO should not have/put these types of RHEA xref on generic/grouping GO terms
ii) These types of RHEA should always be tagged 'broadMatch' xrefs on the corresponding channel/uniporter GO terms.