5 May 2020 PAINT Conference Call: Difference between revisions
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https://github.com/pantherdb/fullgo_paint_update/issues/45 | 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== | ==PANTHER 15 migration in PAINT== |
Revision as of 13:17, 5 May 2020
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