2 April 2019 PAINT Conference Call
- 1 Present
- 2 Discussion points
- 2.1 Are we loosing NOT annotations in updates ?
- 2.2 PANTHER/PAINT Pipeline issues
- 2.3 Filtering 'protein binding' from PAINT
- 2.4 Curation priorities
- 2.5 Tool feature requests
- 2.6 Tree issues ?
- 2.7 Example tickets
- 3 Action items
Huaiyu, Dustin, Michael, Paul, Marc, Pascale
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
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.
New families and fixing GitHub tickets (40 open as of Feb 27) - UPDATE: > 10 left
Tool feature requests
- 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.
Specificity of transporters
First issue: Questionable dispute
- 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 ?
- Huaiyu: get stats for the NOT annotations before May 7, 2018 and after May 8, 2018
- Huaiyu, Dustin, Pascale: Documentation of pipeline: https://github.com/pantherdb/fullgo_paint_update/issues/18
- Anushya: Taxon constraint bug for unrecognized specie
- Anushya: Record every action (every annotation/NOT, etc) that curator does when curating a tree in the Curator Notes
- Dustin: Figure out which trackers to use for PAINT feature requests and Panther family review requests