12 August 2014 PAINT Conference Call

PAINT call minutes, August 12, 2014

Participants: Rama, Karen, Suzi, Huaiyu, Moni, Chris, Pascale

Update on PANTHER family build

• Huaiyu gave an update on the current PANTHER family build.
  • Initial trees includes the entire 213 reference proteome genomes from their yearly release.
  • A script is being developed to prune the trees that contain only a subset of the genome. The resulting trees will be released on the PANTHER website and be used for PAINT curation.
  • We are still deciding the number of genomes to use in the trees for PAINT curation. Three possible options. The first is to use the bare minimum of 12 MOD plus a few representative genomes. The second is the keep the current 85 plus a few plants. The third is in between, that is, to select representative ones from each kingdom, probably around 50. Need everyone's feedback
  • The release day is targeted at the end of the year, but it is possible for PAINT to have pre-release access sometime in October. However, the pre-release won't be available at the PANTHER website nor at the FTP site.
• Suzi: In terms of number of genomes to include, it is better to get feedback from the community, especially from PAINT curators. There are some genomes less well annotated, and they probably should not be included.
• Karen: It will be better if there is a mechanism built in paint that allows curator to mark the nodes with bad sequence annotations (e.g., fragments).
• Suzi: This can be done in the future.
• Huaiyu: Meanwhile, we can just write down the names of the organisms, and pass them to Paul. He is the contact person with Reference Proteome.
• Suzi: It is not ideal to have paint to use the pre-release if it is not in sync with the website or ftp site. It is OK to wait until the official release.
• Both Karen and Rama said they liked the current trees with regard to the number of genomes.

Jamboree update

Will continue to curate and fulfill the hours by the end of September.

Automatic propagation discussio

This is about the email trail initiated by Rachael on the go-discuss mailing list on Aug. 12.

• Pascale: This is about some constraints used by Compara with regard to propagating terms under "behavior". Not sure if it is necessary in paint.
• Chris: It is a proposal to tag certain behavior terms so that they are flagged when one wants to propagate. It is probably more restrictive than the current taxon constraint.
• Suzi: It can be built in paint.
• Pascale: Curators should be able to override it.
• Suzi: Yes, it can be warning.