pgaudet

The other issue is that the mapping file doesn't contain the mapping type, so it is not possible to use that file to make annotations.

Right - we need all the cross-references in all the files, otherwise it creates more confusion.

Fixed see got example GO:0061775 - RHEA:13065 [Broad] : not in the mapping file anymore https://release.geneontology.org/2024-11-03/ontology/external2go/rhea2go Not in the [go-basic.obo file ](https://release.geneontology.org/2024-11-03/ontology/go-basic.obo) [Term] id: GO:0061775 name: cohesin loader activity namespace:...

#3 narrowMatch xrefs are going to be added to go-basic.obo, but won't be tagged with a narrowMatch qualifier so will be indistinguishable from exactMatch xrefs in this file. The type...

Can you use the go-plus file? This will be included as a skos property. Also, can you not rely on UniProt to provide the RHEA and EC mappings?

> What is the reason/advantage of doing this? This allows RHEA > GO mapping, and for this, narrowMatches are safe. However I didn't realize anyone did GO > RHEA mapping...

@balhoff Can you tell how many terms have narrow, broad and exact/nothing?

Good point! These are weird ones that we keep to be exhaustive WRT EC. How about making them 'related'? Related synonyms are not exported (like Broad).

Hi @balhoff We also need a check that makes sure that 'comments' don't start with http or https - since in Protege 'comment' is often the default annotation, we often...

Can you also check that GO:0080076 caffeoyl CoA:S-adenosyl-L-methionine O-methyltransferase activity (no xref) is different from GO:0042409 caffeoyl-CoA O-methyltransferase activity (RHEA:16925, EC:2.1.1.104) ? GO:0080076 caffeoyl CoA:S-adenosyl-L-methionine O-methyltransferase activity: Catalysis of the...