Review problem taxon constraints

[balhoff]

I removed these constraints from only_in_taxon.tsv because they slipped through QC checks and were causing unsatisfiable classes:

GO:0010098  suspensor development   NCBITaxon:6072  Eumetazoa
GO:0031154  culmination involved in sorocarp development    NCBITaxon:33680 Myxogastria 
GO:0031152  aggregation involved in sorocarp development    NCBITaxon:33680 Myxogastria 
GO:0099138  altruistic chimeric sorocarp development    NCBITaxon:33680 Myxogastria 

One reason is that Myxogastria wasn't yet in our taxon import.

[pgaudet]

GO:0010098, suspensor development >> suspensor is a plant structure ; do we inherit TC from PO? Others (GO:0031154, GO:0031152, GO:0099138) are currently Only in Taxon | 33083 | Dictyostelia, which is a Eumycetozoa, not a Myxogastria

The common parent would be Evosea

@ValWood how did you pick up these as terms needing TCs? (since they already had TCs...)

Thanks, Pascale

[ValWood]

They came through the function prediction pipeline. They did make predictions on obsolete terms too, but I thought that I checked them all. The suspensor development doesn't have one.

It's weird that I would put these 3 anyway since the taxon constraint would go on the parent "sorocarp development" not on each child. I think I must have mixed up my checked list with the list of all the terms which had predictions.

[pgaudet]

We may get a TC from PO for GO:0010098, suspensor development - I dont dare loading the Protégé plugin

I think @dustine32 generates a full list of all TCs for PAINT - @dustine32 is there some place we can access a current version of this file?

Thanks, Pascale

[ValWood]

I don't see a tax constraint for GO:0010098, suspensor development in QuickGO though. I would see it there from any source wouldn't I?

[pgaudet]

No, quickgo does not show TC coming outside of GO.

Le mar. 23 mai 2023, 09:42, Val Wood @.***> a écrit :

I don't see a tax constraint for GO:0010098, suspensor development in QuickGO though. I would see it there from any source wouldn't I?

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[dustine32]

@pgaudet Here is the current file used by PAINT, generated using gaferencer and based on the 2023-03-06 GO release ontology: http://data.pantherdb.org/TaxonConstraints/TaxonConstraintsLookup.txt

A newer file based on the 2023-05-10 GO ontology should be available in a few days.

[balhoff]

@pgaudet @ValWood

[pgaudet]

Thanks @balhoff - @ValWood this is what the taxon plugin does (but it makes Protégé very slow)

[ValWood]

Can this be closed?

[balhoff]

@ValWood if you are satisfied with the taxon constraints on those terms, then yes please close.

[ValWood]

The sorocarp terms have constraints. GO:0010098 suspensor development doesn't

@pgaudet mentions above this may come from PO. I don't know how that works. Happy to close if it will come from elsewhere.