12 April 2023 PAINT Conference Call

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Present

Marc, Dustin, Anushya, Paul T, Huaiyu, Pascale


Agenda

PANTHER17 release update and family review

  • we are exploring ways to make the PANTHER trees more stable.

Minutes

  • PAINT migration from 15 to 17 resulted in a large number of families that require review (~1000). This is due to three reasons. First, v.16 was skipped, so that migration process was a bit complex (node forwardly tracked from 15->16->17, while annotations were tracked from 15->17). Second, tree topology changed in certain trees (e.g., PTHR11207, PTHR10024). Mainly, duplication nodes were moved. Third, the node forward tracking algorithm doesn't handle such topology changes.
  • The leaf node mapping is nearly 96% from 16->17 and 95.2% from 15->17. We would expect better mapping of internal nodes. However, the small number of changes (instability) in UniProt maybe the reason that caused the drastic changes of the tree topology. There may also be issues in the tree building algorithm.
  • It was agreed that the ultimate solution would be to make the tree more stable. There are ways to improve the tree building algorithm but will require substantial amount of computing time. This may not happen until v.19.
  • It was discussed whether we should skip the 17 PAINT review, and freeze the annotations in 15, or we should continue the review.
  • It was decided that we continue to the review of 17 trees while we are working on the tree building algorithm.

GO Consortium Meeting

Do we have anything to present?

Minutes

  • We should update the consortium about the migration to v.17, and the issues related to the migration.
  • Huaiyu will come up with an outline in a few days, and then get input from everyone.

PAINT paper

Here is the link to the draft. https://docs.google.com/document/d/1UHaO-ti3WN7r4zcbZnyRyMYUEhJh-d5NqljTktzLQyg/edit?usp=sharing

  • status: being reviewed by SynGO Consortium members until April 21. We will submit after comments have been addressed, hopefully prior to ISB!
  • review test website at http://3.211.50.244/

Minutes Didn't have time to discuss in this call.