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No annotations should be made to uninformative high level terms total: 69 It would be easier if we could see just the ones we need to fix in this list

ValWood

GO procedure for if/when OMIM CURIE/identifier changes to "MIM"

10

I've been asked to provide feedback on OMIM changing its CURIEs to "MIM". Looking at the primary GO upstream data (GAFs and GPADs), there does not appear to be any...

kltm

Change TC to TCDB.

1

See also https://github.com/geneontology/go-ontology/issues/27025 Note: this can be merged in advance of https://github.com/linkml/linkml/pull/1907 because I kept TC as a synonym

cmungall

PomBase inferred GAF missing annotations

30

We've noticed this the last few times we've committed the PomBase GAF to GO: the gene_association.pombase.inf.gaf file produced by the Jenkins job has far fewer inferred annotations than the equivalent...

mah11

Computed annotation to 'do not annotate terms'

6

Hi Issue discussed at ontology call: http://wiki.geneontology.org/index.php/Ontology_meeting_2016-04-07 I noticed that MGI has some annotations to 'sperm part' coming from the GOC pipeline. For example, Spag17 has an GOC sourced annotation...

krchristie

New gorule-0000048: If the annotation has the ND evidence code check whether any manual annotations in the same GO category as the supplied term already exist for this gene product

4

P2GO rule

pgaudet

gorule-0000013 not filtering out IEA annotations

1

GORULE:0000013 states: Experimental annotations (1) failing the taxon constraints are reported in the error reports but unchanged; non-experimental annotations (2) are filtered out of the pipeline products. (1) EXP evidence...

pgaudet

GO Rule for handling unrealizable annotations as found out by gaferencer

10

In Gaferencer, we can tell if an annotation conflicts with its extensions by gaferencer stating that the annotation is unrealizable. We know it's a taxon issue if the `taxonProblem` field...

dougli1sqrd

Clarify GORULE:0000045 With/from: Verify that the combination of evidence (ECO) codes conform to the rules in eco-usage-constraints.yaml

1

"With/from: Verify that the combination of evidence (ECO) codes conform to the rules in eco-usage-constraints.yaml" This is not very useful to people - where is this file found? It looks...

cmungall

Add ECO code mappings to GO_REF files (gorule-0000043)

1

From https://github.com/geneontology/go-site/issues/904 Given a GO_REF, there are a set of valid ECO/Evidence IDs for that GO_REF. This mapping is present in the description of GORULE:0000043. But we can add this...

dougli1sqrd