Contributes_to

[hattrill]

Check that contributes_to have been fixed, so that we can discontinue block to EC numbers from DB ticket for EC and Web ticket Sheet for checking made by SM.

SM gave http://flybase.org/reports/FBgg0001650.html as an example of where we could assign ECs to gene products with contributes _to and it would be correct.

Also

• [ ] Add check in GAF metrics to keep track on contributes_to and NOTs

[sjm41]

I haven't looked/updated that sheet for quite a while.... will try to do so this afternoon.

I have been doing regular cross-checks between GO annotations and the enzyme gene groups with each release - based on those checks, I believe all the enzymatic 'contributes to' annotations are now correct (or as correct as they can be). On that basis, I believe we can now drop the 'contributes to' block on EC annotations. But would be good to update/check that separate google sheet you mention above.

[hattrill]

That sounds good - if you are happy, I am happy.

You've got a much better handle on this. So go ahead with plan for GenBank submission and dropping the ban on contributes_to EC. Hopefully, IU can easily modify their pipeline to mirror this.

I am going to add some simple counts to my GAF checking to monitor changes.

[hattrill]

awk '{print $4}' gene_association.fb > qualifiers; grep "NOT" qualifiers | wc -l; grep "contributes_to" qualifiers | wc -l; 603 503

[sjm41]

I regenerated the list of contributes_to annotations based on FB2022_03, filtered out all non-enzymatic annotations and did a quick analysis of what was left: https://docs.google.com/spreadsheets/d/1UG8HJe_OP7tksCYGa97aOHGizyN1vTD2Pl_TQAn2Jbg/edit?pli=1#gid=2102854116

Computing EC annotations based on 'contributes to' annotations would:

• add new & informative EC annotations to ~60 genes
• add incorrect EC annotations to 2 genes (from incorrect PAINT propagations - both since fixed, but not corrected yet in FB)
• add approx 40 annotations of EC:7.1.2.2 (= bi-directional ATPase/ATP synthase reaction) to non-catalytic subunits of (i) mitochondrial complex V and (ii) the Vacuolar ATPase. This is because the two associated GO terms (GO:0046933 & GO:0046961) are 'compound terms' combining proton-transporting and ATPase/synthase activities and EC:7.1.2.2 is (~ correctly) an xref on both those terms.

Overall, I can live with the EC:7.1.2.2 propagation (it's not completely wrong, and it's a consequence of how GO manages those terms). So I will ask that 'contributes to' annotations are now considered in the EC computation scripts.