18 August 2015 PAINT Conference Call

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PAINT conference call minutes, August 18th, 2015

Participants: Rama, Pascale, Marc, Karen, Donghui, Huaiyu, Paul T. Suzi

Agenda and Minutes

Impact of new PANTHER release to painted PTNs

This is a continuation of the discussion at July 21 call.

In the new PANTHER release, PTN ids may disappear from the original painted families due to the following reasons.

  1. The PTN is moved to a different family, but the original family is still there.
  2. The families are merged with another family and the original families are no longer in the new library.
  3. The PTNs are obsoleted. The original family may or may not be in the new library.

In #1 and #2 above, the destination PTHR may have been curated in PAINT already.

A file on google drive has been created for these nodes. Below is the file format. A. The PTN ids in the paint curated families that are no longer in the same family in the new library. B. The PTHR id in the old library (in PAINT curation folder also) C. The PTHR id in the new library. “-“ if the PTN id is not tracked forwardly (obsoleted). D. “-“ if the old PTHR is no longer in the new library. The family needs to be removed from svn. E. “+” if the destination PTHR in the new library is already in the PAINT curation folder. In this case, the GAF of the destination family needs to be modified.

There are five scenarios.

  • The family is merged to another family that has been curated in paint (blue shade, or row 2-23) - The PTN needs to be added to the GAF of the new family. The old family should be removed from svn.
  • The PTN has been obsoleted (pink shade, or row 24-87) - The family needs to be removed from svn.
  • The family is merged to another family that has not been curated in paint (green shade, or row 88-165) - The new family should be added to the svn with the GAF file. How about other files of that family? How to label it so that the curators will know that this family has not been curated? The old family needs to be removed from svn.
  • The PTN is moved to a new family that has been curated in paint and the old family is still in the new library (row 166) - The PTN needs to be added to the GAF of the new family in the paint svn, and removed from the old family.
  • The PTN is moved to a new family that has not been curated in paint and the old family still in the new library (yellow shade, or row 167-173) - The new family needs to be added to svn and that GAF needs to be created. Again, same questions as in #3 above.

minutes

  • Huaiyu explained the problem
  • Suzi suggested to simply create gaf by simply copying the line with the merged PTN ids from the original gaf.
  • Huaiyu disagreed because there could be more complicated scenarios in the merge (e.g., PTNs without paint annotation, etc.)
  • Pascale suggested to have a discussion at the GO meeting.

Correcting lingering "GO Central" source in PAINT GAFs

These remain a source of errors. How and when are we going to fix these?

Propose of new PAINT call format

Proposal 1: We will continue to have the call twice a month, with one for family presentation, and the other for updates, priorities and general discussions. Proposal 2: We will reduce the call to once a month with the same format as now, i.e., general discussion plus family presentation.

minutes Suzi and Karen both prefer to keep the current format. The rest agreed.

PAINT progress report and google spreadsheet has been updated

PAINT curation progress report has been updated. It reflects the progress on August 13th 2015.

The Google spreadsheet for search and log annotations has been updated also. It reflects the families and GO annotations from PANTHER 10.0 release.

Family presentation

Donghui presents PTHR15074.