5 May 2020 PAINT Conference Call
Present
Following up on previous actions
Obsolete Uniprot entries should be filtered (ie not exported in GAFs generated by PAINT) at each PAINT release
Pascale created a ticket: https://github.com/pantherdb/fullgo_paint_update/issues/46
Alex linked the PAINT error report; is this enough to implement the filter ? --- Discussion:
- Alex can provide this every month
- Dustin will look into making some meta data file in the PAINT repo https://github.com/pantherdb/db-PAINT
Taxon constraints
The test version is available at http://panthertest3.med.usc.edu:8083/
We plan to release it before the GO meeting.
Related questions:
- What to do when TC is violated in the experimental annotation? Example:http://amigo.geneontology.org/amigo/gene_product/FB:FBgn0003507
- What to do when incorrect qualifier is used? Example: http://amigo.geneontology.org/amigo/gene_product/MGI:MGI:2137670
- Taxon constraint file may not be perfect.
GAF 2.2 more qualifiers
How are we going to handle these in PAINT?
https://github.com/pantherdb/fullgo_paint_update/issues/45
PAINT will "ignore" qualifiers when judging whether an experimental annotation can be used for supporting a PAINT annotation. Meaning, PAINT annotations will not require supporting experimental evidence to have same qualifiers. So for example, an exp GO annotation "Gene:00001 acts_upstream_of GO:000001" can be used to support an IBD "PTN0000001 part_of GO:000001". And this will propagate an IBA "Gene:00001 part_of GO:000001". The exception, of course, is for NOT qualifiers.
PANTHER 15 migration in PAINT
Will do the migration