Block annotations to root terms in GPAD output

[hattrill]

In the Noctua snapshot gpad: http://snapshot.geneontology.org/products/upstream_and_raw_data/index.html

there are annotations to root terms e.g. FB FBgn0033814 enables GO:0003674 GO_REF:GO_REF:0000015 ECO:0000307 20230829 FlyBase model-state=production|noctua-model-id=gomodel:646ff70100003749|contributor=https://orcid.org/0000-0003-3212-6364

These should not be exported from Noctua.

Could annotations to root nodes GO:0005575 GO:0008150 GO:0003674 be blocked from the Noctua gpad output.

[vanaukenk]

@hattrill

We can't completely block root node annotations from the Noctua GPAD, since some of the groups, e.g. MGI, ZFIN, who use Noctua for all of their annotation have 'genuine' root node annotations that they want back out.

In looking at the model from the annotation in your comment, though, I'm wondering if what you wanted from these annotations was the statement that 'gene x' is active in ' GO CC'. In other words, were these meant to produce standard GO CC annotations?

Which annotation workbench, e.g. form, VPE, graph, was used to create these annotations?

Thx.

[hattrill]

Hi @vanaukenk Sorry, I did not realise that the rules had changed. The original spec for Noctua was that root terms would not be exported as there had to be something in the MF slot.

Recent ones would probably have been made in VPE but any older ones would have been made in form or graph

[hattrill]

@vanaukenk
These would generally be ones where we have a model with BP and may be CC, but no clear mechanism in that situation. can I just delete these MF in form and have a "null" in the slot?

[vanaukenk]

@hattrill

The rules haven't actually changed - if a root node annotation is in Noctua with the appropriate GO_REF:0000015, they will be exported.

What is not exported are root node annotations that don't have GO_REF:0000015 as evidence, which are, for example, the MF root node annotations created when curators use the BP annotation interface of the Noctua form.

If you want to just make a standard CC annotation, I'd recommend using the CC annotation interface in the Noctua form where you can select is active in as the gp2term relation and don't have to otherwise worry about the underlying GO-CAM data model.

This is exactly the kind of thing we hope to remedy with the new standard annotation UI, which should be available for more general testing in a few weeks.

[vanaukenk]

@hattrill

If you want to go over this on today's annotation call, I'm happy to do that.

[hattrill]

Hi @vanaukenk if I remove the GO_REF:0000015?

[vanaukenk]

@hattrill

Annotation Zoom?

[hattrill]

Nothing to fix