2 April 2019 PAINT Conference Call

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Huaiyu, Dustin, Michael, Paul, Marc, Pascale

Discussion points

Are we loosing NOT annotations in updates ?

  • See https://github.com/geneontology/go-annotation/issues/2141: looks like when Xiaosong removed and added back annotations in May 2018, NOTs annotations were not restored
    • Another issue here is that AmiGO shows data from 2017-02-28 also ! (see screenshot in ticket)
  • See comments in PTHR16517 (and when I opened the family on March 19, there were NO NOT annotations)

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

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 ?

Action items

  1. Huaiyu: get stats for the NOT annotations before May 7, 2018 and after May 8, 2018
  2.  Huaiyu, Dustin, Pascale: Documentation of pipeline: https://github.com/pantherdb/fullgo_paint_update/issues/18
  3. Anushya: Taxon constraint bug for unrecognized specie
  4. Anushya: Record every action (every annotation/NOT, etc) that curator does when curating a tree in the Curator Notes
  5.  Dustin: Figure out which trackers to use for PAINT feature requests and Panther family review requests