Annotation Conf. Call 2018-07-10

Meeting URL

• https://stanford.zoom.us/j/976175422

Montreal Meeting, October Wednesday, 17th - Friday, 19th

• Logistics
• Agenda

GO Conference Calls

Tuesdays

• Still will be Tuesdays at 8am PDT
• Proposed meeting schedule:
  • 1st Tuesday: Alliance Gene Function
  • 2nd Tuesday: GO Consortium
  • 3rd Tuesday: Alliance Gene Function/GO-CAM Working Group
  • 4th Tuesday: GO-CAM Working Group
  • 5th Tuesday: ad hoc, as needed
• One Zoom URL for all - https://stanford.zoom.us/j/976175422

Wednesdays

• Wednesday Noctua call technical call is suspended for the time being
• The software team will be discussing infrastructure and other development issues on their go-dev calls
• When needed, curators will be asked for feedback on Noctua features

Curation Guidelines and Review

Annotation of Transmembrane Proteins

• Guidelines for Annotating Transmembrane Proteins

Late Breaking - ND Annotations

• Proposal from UniProt-GOA team to automatically remove ND annotations from Protein2GO curation database when there is another annotation using the following evidence codes:
  • ECO:0000269 (EXP) and its descendants
  • ECO:0006056 (HTP) and its descendants
  • ECO:0000250 (ISS) and its descendants
  • ECO:0000317 (IGC) and its descendants
  • ECO:0000318 (IBA) and its descendants
  • ECO:0000319 (IBD) and its descendants
• Some feedback:
  • Okay, but not if HTP evidence code is the only remaining code?
  • These should be manually reviewed to make sure remaining annotation(s) are okay
• 437 annotations - okay to manually review??

Transcription Factors

• Merge terms under 'GO:0000991 transcription factor activity, core RNA polymerase II binding' and children
• Annotation Review

Minutes

• On call: David, Dustin, George, Harold, Karen, Kevin, Kimberly, Laurent-Philippe, Li, Liz, Michele, Pascale, Penelope, Petra, Midori, Paul T., Sabrina, Sandra, Seth, Shur-Jen, Stacia, Stan, Suzi A, Suzi L, Tanya

Montreal Meeting, October Wednesday, 17th - Friday, 19th

• Please sign-up if you are attending or would like to attend remotely
• There is also a workshop on Tuesday afternoon for local students and/or users for training on using GO
• We have a meeting room for Saturday, the 20th, if people would like to stay to have f2f working meetings; please think about if/how you could use this time, if needed
  • Val suggests a github/go-ontology jamboree to work on outstanding tickets

GO Conference Calls

• Tuesday calls are dedicated to GO, but will be shared amongst the Alliance, GOC, and GO-CAM working group
• Wednesday Noctua technical calls are currently on hold while the software team works on infrastructure and other development issues

Curation Guidelines and Review

Annotation of Transmembrane Proteins

• We discussed the decision of the working group at the NYC meeting to go ahead with allowing 'intergral to x membrane' annotations based on experimental evidence such as immunofluorescence, etc.
• This decision is still controversial, but the annotation guidelines will state that curators may make these annotations in line with author intent.
• What to do with legacy annotations is still undecided.
  • We want to be consistent with annotation practice, but there is concern that the proposed automated pipeline will generate too may false positives to 'integral to x membrane' terms.
  • We need to examine the output from a test set of annotations to see what the % of false positives would be.
• We also discussed use of a combinatorial evidence code, more informative than just IC, to make these annotations.
  • Issues to consider: what evidence code would then be used in the GAF?
• Note that GO-CAM models allow for multiple pieces of evidence on an assertion, so they can nicely capture all of the supporting evidence.
• The issue here is really what to do with the legacy annotations.