Manager Call 2018-11-07: Difference between revisions

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**** Chris: We will not be able to bring in everyone's annotations in by Cambridge
**** Chris: We will not be able to bring in everyone's annotations in by Cambridge
**** Back end: how much work will that be? Issues, we need to figure out how to partition annotations. We have some research work about this, there are many possible ways. We need to decide on the strategy.  
**** Back end: how much work will that be? Issues, we need to figure out how to partition annotations. We have some research work about this, there are many possible ways. We need to decide on the strategy.  
**** Paul: is there a solution where nothing is connected at first (ie, 1 model for every annotation)? This would avoid create dependencies on connections AT FIRST. Advantage is that every group could move to Noctua as soon as that' sin place. Otherwise we will likely be delayed.
**** Paul: is there a solution where nothing is connected at first (ie, 1 model for every annotation)? This would avoid create dependencies on connections AT FIRST. Advantage is that every group could move to Noctua as soon as that's in place. Otherwise we will likely be delayed.
**** David: we need to have a plan for how models/individual annotations will be handled/re-merged
**** Kimberly: AI we should make a Google doc - TO DISCUSS at the next managers call (?)
*** improve RO – who should do that? Including testing property chains
*** improve RO – who should do that? Including testing property chains
*** work on reasoning
*** work on reasoning

Revision as of 12:34, 7 November 2018

Meeting URL

Agenda

Montreal GOC Meeting Action Items and priorities

Reminder: SAB recommendations - high level priorities

  • Major uses of GO
    • mRNA expression analysis
    • Proteomics data analysis
    • Genetic data analysis
    • DNA methylation analysis
    • Other: (~50%) primarily comp biol and biomed informatics
  • Keep doing: ontology + annotations = model of biology, broad accessibility to all
  • And get even better: more expressive annotations, more QA and review, more collaboration, more APIs and better response times

SAB recommendations:

  • increase focus on QA
  • Leverage authors of curated papers (~150K papers have been used, link from PubMed to GO for annotated papers) ----review (and curate new)
  • Review of older annotations, highly annotated genes
  • Develop GO-CAM use cases, promote in tool developer community
  • Empower developer community (push use of recent GO annotations/ontology in tools, developer guide, website guide, APIs, build an R package to update GO annotations)

Big picture/projects

What are our main priorities? What is the strategy to achieve them?

Kimberly, David, Pascale: Proposal for 2018/early 2019 priorities:

  • GO website migration: Suzi L/Laurent-Philippe: Aim: Dec 1
    • Requires many technical tasks that mostly require Seth
  • Data release pipeline: Pascale/Seth: Are there any blocking issues remaining? If not, we can de-prioritize this for now
    • Many steps are inefficient and slow
    • More work needs to be done: Most work is done by Eric right now - can anyone else help on that ? Paul can find more resources - what do we need ?
    • In the longer term: We need a person who will be responsible for the pipeline - possibly 25% (long-term estimate)
  • Noctua+GO-CAM repository: Kimberly/Seth/David:
    • A developer is needed full time to develop until the Cambridge meeting:
    • Tasks: (just a teaser):
      • getting in all existing annotations in - including implementing gp2term relations implemented
        • Chris: We will not be able to bring in everyone's annotations in by Cambridge
        • Back end: how much work will that be? Issues, we need to figure out how to partition annotations. We have some research work about this, there are many possible ways. We need to decide on the strategy.
        • Paul: is there a solution where nothing is connected at first (ie, 1 model for every annotation)? This would avoid create dependencies on connections AT FIRST. Advantage is that every group could move to Noctua as soon as that's in place. Otherwise we will likely be delayed.
        • David: we need to have a plan for how models/individual annotations will be handled/re-merged
        • Kimberly: AI we should make a Google doc - TO DISCUSS at the next managers call (?)
      • improve RO – who should do that? Including testing property chains
      • work on reasoning
      • fixing issues with pipeline (including GPAD output)
    • Noctua Roadmap
  • GO rules (includes QC): Pascale/Eric: Improving reports: end of 2018, implement/fix some rules 4 rules /month?
  • Tools: etc

Projects:

  • Data release pipeline: Pascale/Seth
  • GO rules (includes QC): Pascale/Eric
  • GO website migration: Suzi L/Laurent-Philippe
  • Noctua: Kimberly/Seth
  • GO-CAM integration with other pathway resources: Paul/Ben/David
  • QC: ->
  • Annotation & ontology: no specific project

External

  • CHEBI
  • Complete proteomes
  • Contributing groups

Next hackathon

January?

Proposed aims (David, Kimberly, Pascale):

  • import of legacy annotations & GP2term relations

Action items

https://docs.google.com/document/d/13BIc-zYaxIkIfK21Jhfk74pNq2jvtjepFdSGd6twpdw/edit#