2 April 2019 PAINT Conference Call

Discussion points

PANTHER/PAINT Pipeline issues

• There are still 4 open tickets in the PAINT pipeline project:

https://github.com/orgs/geneontology/projects/23 Status update on these?

• Duplicate annotation problem is back:

https://github.com/geneontology/go-annotation/issues/2247 PTN000163972

• Are we loosing NOT annotations in updates ? See comments in PTHR16517 (and when I opened the family on March 19, there were NO NOT annotations)

Implement taxon constraints with PAINT

Timeline ??

Curation priorities

New families and fixing GitHub tickets (40 open as of Feb 27) - UPDATE:

Tool feature requests

• Undo
• Links to AmiGO for all genes

Tree issues ?

PTHR10791: https://github.com/geneontology/go-annotation/issues/2210 Pascale - saw may cases where sequences from yeast and other distantly related organism seem to be misplaced- ie duplications should be calculated to be older.

Example tickets

Problem with updates ?

Or was this curated like this ?? https://github.com/geneontology/go-annotation/issues/2251

Specificity of transporters

First issue: Questionable dispute

• https://github.com/geneontology/go-annotation/issues/2209
• Val points out that transporter substrate may evolve rapidly; we need to be careful when we annotate.
• In this case the annotation was propagated to only a small node; what do people think about this propagation?

Second issue: questionable tree annotation

• Review annotations to this family: PTHR43341
  • why did the curator NOT propagate 'amino acid transporter activity' ?
  • Weird propagation in a small pombe duplication node
  • No membrane annotation
  • Hardly any BP propagated

• Could this be due to some automatic update ?