Manager Call 2018-09-19

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Meeting URL

Agenda

Montreal GOC Meeting

New Project management strategy

  • ACTION: Each team (product owner / project lead) needs to prioritize the tickets and decide which will be done for the next Milestone (October GO meeting).

Feedback form update

https://github.com/geneontology/go-site/issues/750 What's the time line for deployment? TBD, but pretty much instantaneous when done. (Seth)

  • Will be ready for Montreal meeting

New GAF Submissions

SuziA: Update on documentation for new groups to submit data: https://github.com/geneontology/go-annotation/issues/2067

  • For now: old and existing group
  • How they prepare/review annotations, where to get their reports
  • Will add information for new groups

Ontology Editors' Meeting

Geneva- Week of December 10th

The meeting will focus on (Depending on who can attend):

  • creating good logical definitions in both a general context and in the context of the GO-Reactome-Rhea alignment
    • Filling in missing GO-Rhea xrefs
    • moving from reactions to biochemical pathways
    • implementation of a method to keep in synch with all three resources
    • GO-CAM templates for pathways??
  • potential implementation of Design Patterns and the revival of some type of TermGenie ability
  • GH ticket work and mini-project planning
  • Attendees
    • David H (Can make it)
    • Kimberly (Can make it)
    • Karen
    • Harold (Can make it)
    • Pascale (Can make it)
    • Barbara (Maybe make it)
    • Alan B (Rhea, can make any day)
    • Anne (Rhea, prefers Monday or Tuesday)
    • Chris
    • Peter D(Can make it)
    • Ben?
    • Jim?

Pascale: needed to follow up with Paul regarding funds to hold these

Job descriptions for each role

Pascale and Kimberly stared to create job descriptions for all managers roles:

https://drive.google.com/drive/folders/1F7e2D7T4hleIq8VaH7YW60D9wxQnRFRV

Every manager should add what they believe are their tasks. And then we discuss it here.

  • Please have a look.

Noctua as a teaching tool?

Seth can create students accounts. (We should document how to use these)

Fate of pre-composed terms

  • explicit binding terms
    • X-binding terms will be decomposed as binding and has_input X.
      • Annotation
        • Moving forward
          • Groups that have the ability to use AEs in their own tools will make structured annotations.
          • Groups that do not have the ability to use AEs in their own tools will use Noctua.
        • Existing Annotations
          • On an predetermined date, all existing annotations to pre-composed x binding terms will be converted to binding and an AE.
          • For terms that have a value in the 'with' field with an IPI evidence code, those will be converted to IDA and the 'with' value will be moved over to the AE.
          • For terms that do not have an IPI and a value in the 'with' field, the terms will be converted based on the term. For generic gene products we will use a PRO identifier. For gene families we will use a Panther ID???
  • compound terms between two existing GO classes
    • Compound terms will be decomposed into their elemental terms with appropriate relationships.
      • Annotation
        • Moving Forward
          • Groups that have the ability to use AEs in their own tools will make structured annotations or co annotate.
          • Groups that do not have the ability to use AEs in their own tools will use Noctua.
        • Existing Annotations
          • Existing annotations will be converted to multiple simple conventional annotations (we need to derive rules for this) OR
          • Existing annotations will be converted to simple GO-CAM models from which annotations will be derived. OR
          • Existing annotations will be converted to conventional annotation with AEs, capturing the context of the original term.
  • Considerations
    • With respect to groups that have been using these terms and annotations, can we provide them with tools that will allow them to continue to conduct their analyses?

NAR paper

https://docs.google.com/document/d/13rV4qIHcTJt7lTv_N5_6AbG3OlSU0jODjMU7-jP-e8c/edit#


(Highlights:

  • Substantial improvements to parts of the ontology, particularly the molecular function branch
  • Addition of qualifiers for biological process annotations, allowing users for the first time to distinguish when a gene product functions as an integral part of a process, versus when it has a more indirect causal effect on a process
  • New evidence codes that allow users to filter out annotations from high-throughput experiments
  • A publicly accessible repository of richer, connected GO annotations (we call GO-CAM, for GO-Causal Activity Models), that provide richer annotations and bridge GO annotations and pathway representations
  • New production pipeline and QC effort, and examples of improvements)

See Google doc for the up to date version.

Minutes