pgaudet

Implement gorule-0000022 QC check for annotations to retracted publications

39

_From @vanaukenk on December 19, 2016 14:32_ Hi, Following on from a help desk ticket: http://jira.geneontology.org/browse/GO-1431 Can we explore adding a QC check for annotations to retracted publications? A possible...

gorule-0000057 is not implemented but showing up in reports

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Hi @mugitty According to @dustine32 , gorule-0000057 was never implemented (see https://github.com/geneontology/go-site/issues/1553), but it's showing up in reports, see http://current.geneontology.org/reports/assigned-by-gorule-report.html Can you please remove it from the pipeline? Thanks, Pascale

Implement gorule-0000005 IEA, ISS, ISO, ISM, ISA, IBA, RCA annotations ae not allowed for direct annotations to to 'protein binding ; GO:0005515 or GO:0005488 binding

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Need to first check with curators /QC group. @vanaukenk @ValWood @sylvainpoux @selewis

New GO rule to validate entities with upstream's GPI files

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It would be very useful to validate files against the GPIs that groups provide.

Should contains: !gaf-version: !generated-by: database listed in dbxrefs.yaml !date-generated: YYYY-MM-DD or YYYY-MM-DDTHH:MM Example errors in https://github.com/geneontology/go-site/issues/2246 reactome-src.gaf.gz:date-generated: 2023-12-01 reactome-src.gaf.gz:generated-by: Reactome reactome-src.gaf.gz:Project-release: Version 87 zfin-src.gaf.gz:0.001!date-generated: 2024-03-14 - [ ] complete the...

Only rules with status = implemented should show in in the rules report in the pipeline This applies to snapshot and release. On the test code, rules with status 'approved'...

Spec out gorule-0000051 : binding and protein binding need 'with' (or extension)

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- 'GO:0005515 protein binding' >>> UniProt or a MOD ID (FlyBase:, WB:; RGD:; etc) maybe use dbxref as a start?? - 'GO:0005488 binding' >> CHEBI We could consider making the...

Fix Rules display so that labels and headers are fixed

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@mugitty People cannot read this easily

Create a GPAD2.0 test file

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Based on the GAF1.2 test file, which is here: https://github.com/geneontology/go-site/blob/master/docs/gorules_test_errors.gaf Working Google spreadsheet: https://docs.google.com/spreadsheets/d/1Sa2gWpx_wFAHWf36mHM1W9_FJuUg77zBrsVAplbAEak/edit#gid=1312805589 Note that this excludes all checks for gorule-0000001 for now (need to check in the GAF1.2...

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

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P2GO rule