Which annotation validation rules are currently implemented? (e.g Taxon checks are not running)

[ValWood]

We are a bit confused about which checks are currently running/not running.
I have reported the absence of taxon checks in a few ticketes (related to PAINT and other annotation outliers)

midori just inserted some errors into our files and reported back that
" It also reported using 14 rules for annotation validation ... of 23 documented. The taxon check, rule 13, appears to be one of the ones that's not used."

v

[ValWood]

added "bug" for taxon checks....

[pgaudet]

@cmungall @dougli1sqrd
Can we clean up the rules documentation for the GOC meeting ? I'm happy to help of needed.

Thanks, Pascale

[pgaudet]

We also need to for each rule page to pointed to its error report in the documentation.

[ValWood]

Are taxon constraints back
geneontology/go-ontology#15701

[ValWood]

Taxon constraints don't appear to be implemented...

There are lots of annotations to "multicellular organismal process" for fungi in GO/AmiGO (1511)

[ValWood]

and locomotion (92)

[ValWood]

Can the taxon constraints be reimplemented soon.
This seems to be causing problems "all over the shop"
For example:

#1873
#1836
#1807
#1724
and others

What exactly happens with taxon restricted terms? At the moment I don't think these are reported in the logs ( @mah11 is that correct?).
But shouldn't these be a "hard check" ? Taxon restricted annotations should be reported to the provider, but dropped from GO.

@pgaudet could you bring this up on the editors call?

[pgaudet]

It is a known issue that taxon checks are not running, see geneontology/go-site#660

Hopefully this can be fixed soon, I agree this is critical.

[ValWood]

It's driving me crazy :)

[selewis]

Me too. The taxon checks are needed in three places #1 in PAINT, #2 in Huaiyu's code when he is staging the PAINT releases, and #3 in the primary pipeline.

The first two can't happen until @mugitty (Anushya) and @huaiyumi move their code into github. Help us motivate them please!

[ValWood]

@mugitty @huaiyumi this will be really really helpful...

But these checks are not working anywhere in GO (irrespective of PAINT) so is this the blocker for everything?

[selewis]

Everything - taxon checks need to be resuscitated.

[pgaudet]

This ticket should be subsumed by geneontology/go-site#670

But first, taxon checks are high priority. @dougli1sqrd @cmungall how soon can the be re-instated?

[ValWood]

What is the current status of taxon checks? Are they all running now? Is this ticket still required?

[ValWood]

duplicate of geneontology/go-site#670
but if taxon check not implemented, ho long will they take?

[pgaudet]

There are reports for taxon rules violations in the 'reports' files but I am not sure they are correctly implemented, see geneontology/go-site#734

Pascale

[pgaudet]

I think this can be closed.