2 June 2020 PAINT Conference Call

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Present

Discussion points

June GO release: with PANTHER 15

But we will let the release go ahead regardless.

New species for Panther 16?

See Val's email Those 3 are high priority:

  • Magnaporthe oryzae - apart from the intensity of molecular studies, it causes rice blast and rice is the world's most important cereal crop.
  • Fusarium graminarum (aka Giberella zeae) - head blight of wheat and barley; very active research community.
  • Candida glabrata - yeast pathogen of humans. Unlike C. albicans, it is pathogenic in the yeast, rather than the filamentous form.
    • Paul will reply to Val.

Following up on previous actions

Update on filtering obsolete Uniprot entries at each PAINT release

https://github.com/pantherdb/fullgo_paint_update/issues/46

  • Alex sends a file with the obsolete entries, but that file is based on the upcoming UniProt release, so that sometimes we filter IDs that are still valid. We decided that this is not a problem to over-filter; if uniprot decides to obsolete an entry, it's bad, so it's OK to filter.

Update on Taxon constraints

The test version is available at http://panthertest3.med.usc.edu:8083/

We plan to release it before the GO meeting.

Questions discussed last time:

  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.


  • Anushya: Wants to test the new version of the software on Panther 15. Error messages are based on 14.1.