Manager Call 2018-11-21

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Annual report

What do we need from MODs ? We have been asking staff, personnel changes, publications, curation statistics from the current year. Looks like we have only included publications and overall number of publication curated in the last report. How about asking:

  • Number of FTEs on the project ?
  • Publications and presentations
  • Any highlights they would like to share in the annual report
    • Do we need any additional information ?

Follow up on priorities

  • Release: came out on Nov 16:
    • Suzi A, will you announce ? Do we have a process?
    • Why was it delayed? Do we need more resources on releases ?
    • Release tasks update (Seth)
  • GO website migration: Suzi L/Laurent-Philippe: Aim: Dec 1 -> Is this still the plan ?
  • Noctua+GO-CAM repository: Moving legacy annotations to GO central: Jim, Ben, Chris, Seth: strategy

Next hackathon

Early February in LA?

Proposed aims (David, Kimberly, Pascale):

  • import of legacy annotations & GP2term relations
    • also for importing legacy annotations - mapping existing annotation extensions to GO-CAM models

Action items


Chris slides - overview


  • Need to get all annotations out of Protein2GO, have under GO Central control
    • Only curatable annotations would be in Noctua, so not IBA IEA etc (Master of IBA is in PAINT DB)
      • This doesn't mean they can't be used in models, can be brought in like any annotations currently can specifics need to be worked out (will this make duplicates?)

Idea: IEAs brought into Noctua converted into ISS since they've been manually reviewed- no, because ISS needs a w/f. Use a new/different code? Generally agreed this is now a manual annotation (manually reviewed)

  • Is a priority, but no dates/deadlines yet
  • Difficulty due to variations in causal connectivity & scale

Noctua database based on models: everything belongs to exactly one model

  • this doesn't work with standalone annotations
  1. Refactor architecture so 'model' is optional
  2. work with this for now and hopefully improve in the future

Scenario: what if models are merged, then changes made upstream... what happens?

Would like to do experiments for different types of grouping (1 model/statement or gene up to 1/genome), but that takes a lot of resources and time Problems likely with all options, so some experimentation is needed

1 model/gene is way to start
Start on worm (maybe dicty?)
Test case: can groups review/edit existing annotations (tool name currently Annotation Review)

How are annotations brought in, say, from Intact?

New models ought to be based on processes, not gene-by-gene, although seems likely curators will want to go gene-by-gene

Experiments on dicty need to be run on Noctua Dev

  • Do some QC to make sure Noctua resembles intent of curators
  • tool needs to handle large amounts of data (MGI beta catenin)

Rough timeline should be available by Cambridge, including working Dev version with a genome loaded

Why aren't AGR curators currently using Noctua?

  • No ability to review
  • presentation to users- goes back into GPAD, so time in Noctua isn't yet worth it

Plan for moving legacy annotations to Noctua db

  • Strategy:
    • start with (Paul proposes NOT to do dictybase, since it's not in Alliance) and wormbase, perhaps also MGI (to have some Alliance members)
    • Move ALL Their annotations in (to discuss- IEA and IBA)
    • David and Kimberly will select a set of genes to test whether the load worked correctly
  • Timeline for the first database?
  • Goal: Getting WormBase data in by the next GO meeting

On call

Chris, Seth, David, Kimberly, Paul, Suzi L, Suzi A, Judy, Ben, Jim, Huaiyu, Laurent-Philippe, Pascale