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Implement GPAD/GPI cross check so that bad identifiers are eliminated early and do not make it to output

12

When a GPAD and its associated GPI are parsed, a check should occur (GORULE:0000001) and if a matching identifier is not found the annotation is eliminated. Currently, when a GAF...

kltm

Annotation rule small change to annotation intersection rule - gorule-0000007

13

At present the file I create allows exceptions for GO terms and for specific genes. I would like to migrate the specific gene IDs to panther family IDs So- in...

ValWood

gorule-0000007 Shared Annotation Matrix: provide documentation

12

Matrix: Add more explanation text to the matrix rule check data html page so curators know what they’re actually looking at on this page. @ValWood Can you provide some text...

pgaudet

Species search for GO CAM on public website (geneontology.org/go-cam)

2

When searching species/organism on https://geneontology.cloud/home Drosophila gets one hit -cGAS-Sting pathway (Drosophila) and D.mel gets 9 -all with D.mel in title and taxid:7227 0 and drosophila melanogaster 0 (there are...

hattrill

Need to run checks (GORULES) on 'goa_uniprot_all_noiea' data

7

These are not in our reports (http://release.geneontology.org/2019-06-09/reports/gorule-report.html) Looks like the data is going in AmiGO and in all our products without checks ?

pgaudet

@tmushayahama has lots of code that checks the validity of triples as they are created and edited. These checks should reference existing GO Rules, and if such a rule does...

dougli1sqrd

Implement gorule-0000038 gorule required: ISS annotations must refer to a sequence with an EXP annotation

2

A- Any term which has ISS annotations but no EXP annotation (to term OR descendant) Suggested by @cmungall in https://github.com/geneontology/go-ontology/issues/17435 B- We have also historically requested any ISS/ISO where the...

ValWood

Add check for extensions-constraints

10

https://github.com/geneontology/go-site/blob/master/metadata/extensions-constraints.yaml See also https://wiki.geneontology.org/Annotation_Relations#Annotation_Extension_Relations

ValWood

Check valid taxa when parsing data (GAF column 13; GPI column 7)

5

Taxon=0 has been observed: https://github.com/geneontology/pipeline/issues/239#issuecomment-1701406534 This should not be allowed; ideally the allowed taxa should come from the taxa loaded (if this is doable)

pgaudet

Bumps [org.eclipse.jetty:jetty-servlets](https://github.com/eclipse/jetty.project) from 9.2.3.v20140905 to 9.4.52.v20230823. Release notes Sourced from org.eclipse.jetty:jetty-servlets's releases. 9.4.52.v20230823 Sponsored Release This is a release of the End of Community Support Jetty 9.x series that was...

dependabot[bot]