7 April 2015 PAINT Conference Call

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PAINT conference call minutes, April 7th, 2015

Participants: Li, Rama, Suzi, Moni, Huaiyu, Donghui, Paul T., Chris

Agenda and Minutes

  • Timing for phasing out species specific GAFs (Karen) - This was raised by Karen at the last meeting, but deferred because Suzi was not at the call.
    - At the last PAINT meeting, during discussion of Rama's question about use of the "Ref Genome" versus "GO Central" sources, Suzi talked about the plan to change the flow of GO annotations from PAINT to MODs so that they will all go to UniProt, and then get picked up by MODs from there, instead of from species specific GAFs, if I understood correctly.
    - The MGI GO group discussed this at our weekly meeting, and we would like to know what is the time frame for eliminating the species specific GAFs? We need a minimum of 30 days notice in order to get software changes in place to be able to accommodate this change. Has a plan been announced to the Consortium as a whole?
  • SVN depository - When is it going to be ready for curators to commit the paint curation. (Rama)
    • Suzi said she was running a script to revert some of the changes. Some of the recent commitment complicated the process. Please do not commit anything at the moment. The process should probably be completed later today.
  • PANTHER 10. release and test on PAINT (Huaiyu)
    • Huaiyu: PANTHER 10 is very close to be released. We probably should test it before it is used for paint curation. Do we need a new build of paint? The library location will be different from the current one since regular curation will continue to use 9.0. We will set up a test location for 10.0.
    • Suzi: The families that are no longer in the new library should be deleted from svn. There should not be a new build. Everything can be configured in PAINT for testing.
    • Will discuss this offline.
  • Family presentation (Donghui) PTHR15074:

(1) two duplicated nodes show functional divergence (biological process): DNA repair vs negative regulation of transcription

  • - Euteleostomi_PTN000386639 participates in DNA repair (GO:0006281)
    - Euteleostomi_PTN000386639 participates in cellular response to DNA damage stimulus (GO:0006974)
    - Euteleostomi_PTN000424568 participates in negative regulation of transcription from RNA polymerase II promoter (GO:0000122)
    - Euteleostomi_PTN000424568 participates in negative regulation of transcription, DNA-templated (GO:0045892)

(2) how to handle annotations to both nucleus and cytosol

    • Minutes: The pubmed reference should be checked for the cytosol annotation. The rule is to annotate the cellular component where the protein performs the function.