Projects update meeting 2022-10-05

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  • Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia
  • Present: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia
  • Regrets:

GOC meeting

  • Next week (Oct 11-13)
  • The following week will be a no GO calls week (week of Oct 17th)
  • Breakout groups:
    • Annotation: Reannotation Strategies (34)
    • Annotation: Annotating to Process or Regulation of Process (34)
    • Annotation: Strategies for Annotation Prioritization (33)
    • Software did not receive a lot of votes (13), but the people who voted for it don't overlap as much with the annotation groups
      • AI Kimberly: to send an email to announce that few people signed up for the GO-CAM curation session that we will have another breakout of curation strategies


  • Tremayne now 50% ? (including Alliance)

Priorities until the end of the year

Main tasks’ document: where we list on which project we are each working on. This is based on the proposed priorities here:

AI for everyone: Look at the list of project and (a) add any missing project you are working on or (b) remove projects you are not working on (these can also be moved to later in the year) Entering your % effort on the project for this period

Ongoing projects update


Seth was to update the API specs document to specify the deliverables for the first part (ongoing), and to make a new document for the next part, "API reabsorb GO-CAM"

Bug fixes Visual Editor

  • 1 remaining ticket: fix UI to have 'Pathway Editor' rather than 'Visual Pathway Editor'
  • Can we get an estimate of when that will be done?

Relations to link MF


Annotation Extension Relations in Noctua


  • AI Project to be discussed in more detail - Jim, Seth, Tremayne, Dustin, Kimberly

Species-specific downloads

  • Seth and Pascale to draft a projects specs document
  • Seth: what is the exact expectation? just a more sensible export?
  • Strategy: 142 species - was planning to have a central database (also to do global checks)
  • Low hanging fruit /easier: can take files we get at the end of the pipeline and sort them out in bins as a post-processing step
  • AI spec out the project - Seth and Pascale/Paul PI ?

Improvements to Noctua Form (new/future project)

David will get feedback from curators

To discuss next time

Improving GO-CAM browser usability

The plan was to do this: Update minerva to handle “maximal-causal-chain-length” and “display-as-pathway-override”

but some 'hack' was applied to more quickly only Display only causal models on GO-CAM site Apply causalmf param to fetch causal gocam-models.json

  1. Do we still want to do the work in Update minerva to handle “maximal-causal-chain-length” and “display-as-pathway-override”, or down-prioritize this?
  2. Some questions about the way the current fix behaves - which is different from Alliance; is this what we want ? Note that this is already deployed
  3. Link out: Currently goes to the Graph viewer; proposal to go to the Alliance Pathway Viewer

Tasks to enable people outside the GO consortium to curate GO-CAM models

Following up on last week's discussion about a few new requests for GO-CAM accounts

MOU individual users

Suzi: MOU for non-MOD users of GO-CAM who request accounts

  • Discuss document and plan next steps

User accounts

  • To manage new and external users, we proposed to create DEV accounts and have a mechanism to move DEV models to PROD directly. How much of a priority is this? If this is a high priority, who should be assigned to this?