10 July 2024 PAINT Conference Call

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Present

Marc, Pascale, Huaiyu, Dustin, Anushya

Agenda

Plan to transition PAINT to PANTHER19.0

PANTHer19.0 was released in June, 2024. Let's start to plan the transition.

  • 17.0->19.0 Node forward tracking stats:
    • Speciation - 1088886 / 1157989 (94.0%)
    • Duplication - 314883 / 381302 (82.6%)
    • HT - 5678 / 6872 (82.6%)
    • Leaf - 1841304 / 2013571 (91.4%)

Comparing these stats to the previous migration of 15.0->17.0, forward tracking of all speciation and HT was better in 17.0->19.0 with duplication being about the same and leaf being lower.

  • 15.0->17.0 Node forward tracking stats:
    • Speciation - 1025670 / 1137262 = 90.2%
    • Duplication - 306836 / 371052 = 82.7%
    • HT - 4548 / 6973 = 65.2%
    • Leaf - 1847433 / 1973248 = 93.6%

"Do not annotate" terms

Anushya gathered all the IBDs and the families that will be impacted if these annotations are removed. Here is the file: https://drive.google.com/file/d/1mQsaiwkU-K_Vp356rVXnyLDL87dzyT50/view?usp=sharing There are 505 families, 444 with human genes. Here are the questions.

  • How do to proceed? Do we just remove them or they should be curated with replacement terms.
    • Minutes: Marc and Pascale have curated nearly all of the families. Anushya will regenerate the file for the update.
  • How to prevent this from happening again in the future?
    • Minutes: We can add a "do not annotate" label to the terms so that they will be filtered out during curation and automated updates. This may involve some updates on the database schema.
  • Shall we do it before or after we transition to PANTHER19?
    • Minutes: Since more of the families have been re-curated, we will finish it before the PANTHER 19 transition.

Functionome paper revision update

TBD.

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