5 May 2020 PAINT Conference Call

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Revision as of 10:52, 5 May 2020 by Mi (talk | contribs) (GAF 2.2 more qualifiers)

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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:

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:

  1. What to do when TC is violated in the experimental annotation? Example:http://amigo.geneontology.org/amigo/gene_product/FB:FBgn0003507
  2. What to do when incorrect qualifier is used? Example: http://amigo.geneontology.org/amigo/gene_product/MGI:MGI:2137670
  3. 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 involved_in GO:000001". And this will propagate an IBA "Gene:00001 involved_in GO:000001". The exception, of course, is for NOT qualifiers.

PAINT IBDs (thus inferred IBAs too) will use the qualifiers as below (except for NOT qualifier):

  • biological process - use "involved_in" for all annotations as default.
  • cellular component - use "is_active_in" for all annotations as default.
  • molecular function - use "enables" as default, but "contributes_to" can be used where it is appropriate.

PANTHER 15 migration in PAINT

Will do the migration

Discussion points