2 April 2019 PAINT Conference Call

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Present

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)


Reporting families building issues

Where can we track requests such as the one here: https://github.com/geneontology/go-annotation/issues/1952 Or we can use another label in the annotation tracker (but I am not sure this is checked before new trees are built?)


Filtering 'protein binding' from PAINT

Since we don't propagate 'protein binding', it should be filtered out from PAINT. The advantage is that families ONLY annotated to protein binding would not show up as curatable.


Curation priorities

New families and fixing GitHub tickets (40 open as of Feb 27) - UPDATE: > 10 left

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

Specificity of transporters

First issue: Questionable dispute

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 ?
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