Closed ValWood closed 5 months ago
These definitely have contributes_to at SGD e.g.
After reviewing the annotations, they all seem to be annotated with contributes_to, which seems to me to be the rule in this case. In any case, with PAINT we can only use the primary annotations as they were made. We can neither add nor remove a tag such as contributes_to. Have I misunderstood something? If the question is whether to propagate contributes_to in PAINT, I'd say yes in this case. Best regards, Marc.
I think contributes_to should propagate...I thought it did ? @pgaudet
The annotation that PAINT propagates depends on whether the original annotation had a contributes_to or not.
If there are annotations with and without 'contributes_to', then the PAINT curator picks which to propagate.
Where is the screenshot from ? In AmiGO I see contributes_to for all rpb10 RNA polymerase annotations:
but not on the pombase page:
Do you display this information? Looks like something may have gotten lost.
May be a PomBase bug, tagging @kimrutherford
We don't load qualifiers from the GOA GAF file at the moment, except for NOT. Should we load all of these?:
I'm confused, I thought the only annotation qualifiers were colocalizes_with contributes_to NOT
We should load contributes to from PAINT We don't use colocalized_with (are there any external annotations that use it?)
I'm confused, I thought the only annotation qualifiers were
You're right: https://geneontology.org/docs/go-annotations/#annotation-qualifiers
It's probably something to do with GPAD/GPI: https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#allowed-gene-product-to-go-term-relations
We should load contributes to from PAINT
It looks like all the contributes_to qualifiers come from PAINT. I'll make sure they're loaded for tomorrow's update.
We don't use colocalized_with (are there any external annotations that use it?)
There are 4 colocalizes_with annotations from http://snapshot.geneontology.org/annotations/pombase.gaf.gz:
PomBase SPCC736.14 dis1 colocalizes_with GO:0035371 GO_REF:0000033 IBA PANTHER:PTN000288762|UniProtKB:Q14008 C TOG/XMAP215 microtubule plus end tracking polymerase Dis1 protein_coding_gene taxon:4896 20170228 GO_Central
PomBase SPCC895.07 alp14 colocalizes_with GO:0035371 GO_REF:0000033 IBA PANTHER:PTN000288762|UniProtKB:Q14008 C TOG/XMAP215 microtubule plus end tracking polymerase Alp14 mtc1 protein_coding_gene taxon:4896 20170228 GO_Central
PomBase SPAC17C9.13c cut8 colocalizes_with GO:0031965 GO_REF:0000033 IBA PANTHER:PTN008622754|FB:FBgn0036994 C tethering factor for nuclear proteasome Cut8 protein_coding_gene taxon:4896 20221209 GO_Central
PomBase SPAPJ760.02c abp1 colocalizes_with GO:0005884 GO_REF:0000033 IBA PANTHER:PTN000850943|FB:FBgn0036372|RGD:70885|RGD:619839 C cofilin/tropomyosin family, drebrin ortholog Abp1 protein_coding_gene taxon:4896 20190524 GO_Central
those are OK, I'm not sure they need colocalizes_with but I can look at those later. We can close this on the GO tracker and move to PomBase.
I thought is was, but it seems not:
CC @krchristie