20 September 2023 PAINT Conference Call

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Present

Pascale, Marc, Dustin, Anushya, Huaiyu, Paul

Agenda

PANTHER17 tree review

Here is the spreadsheet with missing human IBAs between v.15 and v.17. Missing annotations can be due to multiple reasons. A common one is the replaced GO terms are not used for the obsoleted term.

Minutes

  • Report on just annotations lost in migration due to obsoleted term even when there was a replacement term available. (Dustin)
  • Find all IBDs that lost the annotation due to obsoleted term and add the replacement terms. This data, either loaded in the database or as a file, can be used for 18 migration.

Shortening the cycle between new experimental annotations and PAINT

Currently, once new experimental annotations are released by GO, it takes up to one month to be visible in PAINT tool. The question is whether the cycle can be shortened. Below are a few ideas.

  • Snapshot is loaded weekly.
  • Noctua annotations could be loaded directly.
  • Literature curation is done directly in PAINT.

Minutes The extensive discussions boil down to the following two GitHub tickets:

We should continue the discussion within those tickets.

PANTHER18.0 release

PANTHER18.0 will be released this month. We need to determine when to release it to PAINT.

Minutes

  • It is related to the first item in the agenda.
  • Paul suggested to wait until v.19.0. However, the main variable about v.19 release is the update to generate alignment using MAFFT.
  • No decision was made.

S. japonicus taxon issue

See GitHub issue: https://github.com/japonicusdb/japonicus-curation/issues/57#issuecomment-1721024110

Basically, Pombase extracts S. japonicus annotations from JaponicusDB with the species taxon ID 4897, while PAINT uses the S. japonicus data from the Reference Proteome with a strain taxon ID 402676. The ticket is asking whether PAINT can support the species taxon ID.

  • We could retain RefProt's strain taxon in PAINT but use the strain->species taxon relationship in NCBITaxon ontology to export the species taxon in the GAF. Obviously, this would complicate the pipeline a bit.

Minutes

  • We probably can't just replace the taxon ID in PAINT, because the genomes for the species (taxon:4897) and the strain (taxon:402676) are different, and therefore the sequence IDs can be different.
  • The proper fix is probably to ask Reference Proteome to switch from the strain to the species genome. Huaiyu will contact Maria about it.