Manager Call 2018-11-07

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Meeting URL


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)

Priorities and strategy

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 (?)
        • Pascale: we also need to think about doing QC on the automatic tools that would predict connectivity - that will take quite some time too, so prefers a more simple solution
        • Chris suggests doing an experiment in which we test integrating unconnected annotations, for example starting with dictyBase
        • Proposed import process: take triples out of each model
      • improve RO – who should do that? Including testing property chains:
        • Chris: We can have a bit of Jim's time on this.
        • David: What will we do about the different 'participants' relations - are we just moving forward ? Chris: yes
      • work on reasoning
      • fixing issues with pipeline (including GPAD output)
        • required GPAD2, which will require some plumbing and will break for a lot of people: people importing GPAD
    • Noctua Roadmap
  • GO rules (includes QC): Pascale/Eric: Improving reports: end of 2018, implement/fix some rules 4 rules /month?
  • Tools:
    • GO API implementation (Laurent-Philippe / Deepak)
    • Bioinformatics Guide (how to):
      • Ontology manipulation / traversal (parents, children, slim, related terms, etc)
      • Search / Browse / Aggregate annotations (e.g. per gene, taxon, pathway, aspect, etc)
      • Interactive Online Notebooks:
        • Jupyter (Python)
        • R Markdown (R)


  • 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


  • Complete proteomes
  • Contributing groups

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