17 March 2015 PAINT Conference Call

PAINT conference call minutes, March 17rd, 2015 Participants: Marc, Karen, Li, Chris, Huaiyu, Rama, Paul T., Moni

CALL DETAILS

Voice over GO line (Jackson), video over Blue Jeans (Stanford).

Agenda

• Timing for phasing out species specific GAFs (Karen)

  - 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 accomodate this change. Has a plan been announced to the Consortium as a whole?

• Log your curation
  • Use the google spreadsheet: https://docs.google.com/spreadsheets/d/1uHgcaXO7t9__9GuXgBibT0H-YlnU252IsRGWIyhCWN8/edit?usp=sharing
  • Put your initial in the Curator column (Col B) when you start to curate a family
  • Put the date in the "Date completed" column when you finish the curation and commit it into svn.
• Is the svn repository restored ? See email from Suzi last Friday
• Family presentation (Huaiyu) - PTHR11437
  • It is an RNase A family (EC 3.1.27.5)
  • MF
    • The first enzyme in this family was found in bovine pancrease, so it is also called pancreatic ribonuclease. However, other members in the family are found in other tissues, such as liver and kidney. Therefore, the term pancreatic ribonuclease is not proper as an ontology term for molecular activity.
    • Propagated endonuclease activity to the root.
    • The rest of MFs are all binding terms, so did not propagate.
  • CC
    • RNase A is secreted and is involved in defense response. See review http://ini.sagepub.com/content/19/1/86.long
    • Propagated extracellular space to the root.
    • Secretary granules and cytoplasm are not propagated because they are based on immunostaining.
  • BP
    • Propagate RNA phosphodiester bond hydrolysis, endonucleolytic and RNA catabolism to the root.
    • Positive regulation of cell proliferation is related to angiogenesis. Should it be propagated?
    • Propagate angiogensis to the angenin clade.
    • Propagate defense response to bacterium and antobacteral humoral response to the root.

Minutes

• Timing for phasing out species specific GAFs (Karen) - Needs Suzi on the call
• Log your curation

  - Paul - The purpose of this is also to measure progress, The metric is the total number of independent GO terms by literature curation in a family. During the jamboree last summer, on average, people went through about 130 terms per day. Based on the number of families and the annotated GO terms in those families, it is about 3-4 families per day. The metric will be reported to NIH.

• Is the svn repository restored ?

  - A bug was found in the touch up script, so it has to be reverted to the pre-touch versions.

  - Paul gave a brief summary of what touch up does.

  - Check the tree change and see whether an annotated PTN node is no longer in the new version of the tree.

  - Check the ontology terms to see if there are any annotated terms that are obsoleted. If so, whether there is a replacement term.

  - Check the do-not-annotate tag.

  - Check the taxon constraint because it fails sometimes.

  - Check the experimental support to the annotation. The PAINT annotation has to be supported by at least one experimental annotation.

• Tree presentation (PTHR11437)

  - Pancreatic ribonuclease activity

  - Chris: Should submit a ticket about the term name

  - Karen: Go ahead and propagate the term, but submit a ticket, so that when the term is updated it should be replaced by the new term.

  - About regulation of endothelial cell proliferation

  - Both Marc and Karen agreed that the term should not be propagated.