16 December 2014 PAINT Conference Call

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December 16th, 2014 PAINT call minutes

Participants: Rama, Donghui, Li, Moni, Pascale, Suzi, Chris, Paul, Huaiyu



  1. It was promised and assured that the data coming from either the FTP site or the PaintServer would be identical
  2. But it is not identical
    • The attribute file is different (orthoMCL is included from the PaintServer, FTP site doesn't include PTN#s, etc.)
    • The weights file is missing from the FTP site
  3. The web service is too slow and unreliable to use for a Jenkins job (even if it is just once a year)
  4. Without a reliable way to obtain these data the code to update moldy old GAF files can't be written.
  5. It's been months - please fix!


  • Suzi: The attr files from the FTP don't have the same format as those from the webservice. The PTN numbers are missing. Also there is no wts files on FTP.
  • Huaiyu: The FTP download is for our users. It is not ideal to change format since our users may have already built processes to parse our files. We did this in 2011 by adding PTN ids to the attr files just for paint, but those files were not in our regular FTP download. We can generate the files again.
  • Suzi: Anushya should know the file format.

NOT annotation in PAINT

Huaiyu brought this up two meetings ago. In this meeting, he will show the family PTHR10024 (please have join.me ready) and three different scenarios of NOT annotations in PAINT.

  • The NOT is only applied to the term, but not to its parent terms.
  • The NOT is applied to the term and all its parent terms.
  • The NOT is applied to the term and some of its parent terms.


  • Huaiyu showed PTHR10024 as an example. The PTN000740742 (Syt8) ortholog group lost the calcium binding activity,, thus no longer have calcium ion dependent phospholipid binding activity, but still has the phospholipid binding activity (a parent term). The PTN000797819 (Syt15) may not be involved in regulation of exocytosis, but still involved in calcium dependent exocytosis. So the NOT is placed to the term "regulation of calcium ion dependent exocytosis". One of its parent term "regulation of exocytosis" should be negated, but another parent term "calcium dependent exocytosis" should not.
  • Suzi did not quite agree with it, and would like to continue the discussion off-line because the time ran out.

Are taxon constraints functioning properly in PAINT (Karen)

The Panther family is PTHR10619. It was committed a month ago on Nov 5th.


Did not discuss. Postpone to the next meeting.

Feature requests

NOT & IRD (Pascale) NOT Are not allowed when there is a positive annotation in a clade (as far as I can tell). Can this be changed, at least for use with the IRD code  ?

Show PAINTed parent terms in the matrix (Huaiyu) By default, only the most specific terms are listed in the matrix. When a parent term is propagated, it is now visible in the matrix, but the term is listed in the Annotation window. This is a bit confusing. My suggestion is that all PAINTed terms should be shown in the matrix window.


Did not discuss. Postpone to the next meeting.