2 Mar 2021 PAINT Conference Call
Curation priority/need review status
The discussion can be found in the email trail from Feb 10-14 with subject "PAINT migration "requires review" logic". Discussion points:
- We will only keep the "require review" status created during the 14 to 15 migration, and erase the rest.
- In the future, we will have more explicit messages for the review. For annual migration, there are three situations that will trigger a require review status.
- Families with nodes that cannot be mapped from previous library to new library. Such families will require recuration.
- Forward-tracked nodes changed families. Curation status goes to the new family, not the old family (since it may have been dropped). The review is to check whether the annotation can be propagated tp an ancestral node or to a more specific term, etc.
- Families with annotations forward-tracked to child nodes. Review if the annotation can be propagated to an ancestral term.
- Need to decide about the monthly updates.
- We will clean up the "require review" status. Only those from 14 to 15 migration will be kept. Dustin will create a document to list the families in each of the three categories. The families are ordered based on the number of PTNs affected in the family.
- In the future, we will continue to use the label for migrations between PANTHER builds. We can either label the priority on the status or use a separate document as we do this time.
- We will also use numbers of IBAs to determine whether a family needs to be reviewed.
- For monthly update, we will continue to use the output from the validator pipeline.
Plan to migrate PAINT to PANTHER 16
There was a suggestion to skip it due to the error in Xenopus tropicalis genome from UniProt.
- Pascale: unable to save PTHR13723 with many NOTs https://github.com/geneontology/go-annotation/issues/3296
- From same ticket: Steven mentions getting no answer in the Panther tracker - can we make sure to answer people?
The feedback is welcome. However, we may not be able to split or merge based on the tickets. We will use both the MSA and HMM scoring results as references to determine if a split or merge should be done or not.
Improve annotation forward tracking (postponed)
This is a topic we discussed at the last call. Sometimes nodes are not tracked between PANTHER builds due to the current rules. Huaiyu has proposal to improve the rules, and will discuss here.