Manager Call 2018-09-05

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Call in info


New Project management strategy

  • Product owner
  • Tech lead
  • Lead architect
  • 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

Did we figure out the payment? No, still on my plate (Seth)

What's the time line for deployment? TBD, but pretty much instantaneous when done. (Seth)

New GAF Submissions

SuziA: Update on documentation for new groups to submit data:

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?
    • 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:

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

  • Please have a look.

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


  • 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


  • On call: Chris, David, Judy, Kimberly, Laurent-Philippe, Nomi, Pascale, Seth, Suzi L., Suzy A.

NAR Paper

  • Deadline is fast approaching
  • If we are going to submit, we need someone to champion ASAP
  • Check the Google doc link above for proposed topics

New project management strategy

  • At the USC hackathon (week of August 27th), we agreed to use the top-level projects in the Gene Ontology repo as a way to articulate:
    • what projects we are working on
    • who are the leads
    • if the project has a delivery date or is ongoing
    • what grant aim the projects corresponds to
    • the overall priority
    • what personnel the project has
  • Percentage of personnel time should be entered
    • Should this be dictated top down or entered by the people doing the work?
    • It would be helpful if the personnel time reflected expectations/priorities from the GO PIs
  • Product owner and technical lead should prioritize tickets for the next sprint
  • Should we dismantle the automatic placement of new tickets into the 'To Do' list? Probably.
  • Should infrastructure also be a project? Would this correspond to maintenance?
  • We discussed the appropriate time frame for projects; six months (between GOC meetings) seems a reasonable place to start
  • We will review the status of the projects during at least one managers call a month

Feedback form update

  • Seth - will be implemented soon

New GAF Submissions

  • Suzy A - still has questions about GAF submission
  • We need documentation for new groups as well as long-standing submitters
  • We need new guidelines on the website
  • This documentation needs to be a project or part of a project?
  • Action item: document steps for new submitters before they submit a GAF (Suzy A and Seth)

Use cases

  • For GAF submissions

Ontology Editors' Meeting

  • Will spend at least one day working on the GO-Reactome-Rhea alignment
  • Need to decide on what else we should have on the agenda

Job descriptions for each role

  • Please review and add updates/edits as needed