1 March 2023 PAINT Conference Call

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


PANTHER17 release update

  • PANTHER17 was released. See minutes in the November PAINT call.
  • A bug was identified in December that missed some forward track of IBDs. As a result, the number of lost IBAs will decrease once the bug is fixed.
    • Only affects IBDs that were not forward-tracked via PTN and instead tracked to a descendant node. More specifically, these IBDs that were supported by multiple evidence genes were missed due to a buggy redundancy check.
    • 1132 affected families
    • 4184 distinct PTN/GO term/qualifier combinations
    • The bug is fixed in the code. Plan is to load these into our test DB then generate IBA test GAFs to get a better idea of how many IBAs will be added.
  • NEW bug! Annotation forward tracking to descendant nodes does not consider LEAF nodes. This should have been allowed for NOT annotations since often there are NOT PAINT annotations placed directly on leaf nodes.
    • Code fix ticket here: https://github.com/pantherdb/panther_build/issues/24
    • Rerunning after the code fix and checking the diff reveals what was missed:
      • 130 NOT IKR/IRD annotations
      • 29 families affected
    • Notably, one of the example leaf nodes is in this new list: DROME_Wsck (PTN000701347 - DROME|FlyBase=FBgn0046685|UniProtKB=P83097).
      • Its sibling leaf node IXOSC_8024579 is also in the new list.
      • The list of missed LEAF NOT annotations is on the GO drive here.
The NOT annotation in the 15.0 tree
The DROME gene in the 17.0 tree

Overwriting EXP NOT annotation

See Pascale's email on 2/23 about this ticket: https://github.com/geneontology/go-annotation/issues/4464

Here is a summary of the discussion.

  • The issue raised in the ticket is the result of the change in tree and a bug that didn't handle such changes. If the bug is fixed, the NOT annotation should be applied to the sequence. Therefore there should be no conflict.
  • Since the NOT conflicts were fixed in drosophila and pombe by manual curation in fall 2021, there has not been any complaints to this issue.
  • Most of the conflicts in mouse and other vertebrates or mammals seem to be from the NOT annotation to isoforms in manual curation.
  • Here are the decisions.
    • We will address the tickets, and correct the errors.
    • We will identify the possible bugs in the migration through these tickets.
    • We will review all the NOT conflict annotations.
    • We will continue to export IBA to allow conflict for now, and continue to monitor the tickets. Will revisit this topic in a few months.

PAINT paper

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

The consortium members are providing feedback to the manuscript. The deadline is 3/2. We will meet on 3/6 to discuss about the feedback.