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japonicusdb / japonicus-config

Configuration for JaponicusDB
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Apply PomBase GO filters to japonicus #38

Closed ValWood closed 3 years ago

ValWood commented 3 years ago

We filter obvious errors, and report them back to the provider. All Pombase filters should apply.

pombe-embl/goa-load-fixes/ filtered_mappings filtered_GO_IDs

Test http://japonicusdb.kmr.nz/gene/SJAG_03360 GO:0019746 | hopanoid biosynthetic process | IEA with IPR006400 should disappear as

 IPR006400 is currently a filtered mapping

A test for GO ID is GO:0007118 GO:0007114 http://japonicusdb.kmr.nz/term/GO:0007114

kimrutherford commented 3 years ago

All Pombase filters should apply.

Will you every need to add japonicus specific IDs for filtering?

kimrutherford commented 3 years ago

All Pombase filters should apply.

I made that change and re-loaded.

GO:0019746 | hopanoid biosynthetic process | IEA with IPR006400 should disappear

That seems to be gone now.

ValWood commented 3 years ago

Fab!

ValWood commented 3 years ago

I was going to filter these (some many to many where there is specific annotation that we would not want to transfer)>

However, there is not GO annotation transferred from orthologs for these. (I am looking for examples to check that I can filter on. pattern matches to Pombe and S. cerevisiae gene IDs..)

ValWood commented 3 years ago

Question for Kim.

kimrutherford commented 3 years ago

Sorry, what is the question?

ValWood commented 3 years ago

I think this is a duplicate ticket. Filters are implemented apparently.