Minutes_Standards_2024 03 - airr-community/airr-standards GitHub Wiki

Standards Call 2024-03

Agenda

  • General discussion: When are we "done" and what is a realistic timeline for this?
  • Discussion Contributor record (#741)
  • Structure of Cell and associated objects (#768)
  • Lineage schema (Background: #378, #333, #317; Proposal: #769)
  • Update DataProcessing for v2.0? (#313, #434, #453; Related: #578)
  • Structure of AIRR Docs (#730, #745), See pull request (#763)
  • New Event record and its embedding in the Schema (#749)
  • Manifest schema (#548).

Minutes

Meta

  • Date: Mon, 2024-03-04 19:00 UTC
  • Present: Jason, Ulrik, Christian, Brian, Chaim
  • Regrets: ...

Topics

  • General discussion:
    • Goal is to have 2.0 (nearly) done by June, focus on core features
    • Stop pushing Issues to v2.1, there should be no issues linked to this milestone in June
    • Document things that will not be dealt in v2.0, so that they could be resuscitated for v3.0 (eg, wiki, project, or milestone for archived issues)
    • Paper writing should start in summer, all issues within the scope of v2.0 will be collected and solved in v2.1
    • We foresee that smaller development steps will take place post v2.1, but this will happen in sprint-style by smaller groups, so the WG could still dissolve at Porto.
    • How to coordinate these changes will need to be discussed.
  • Contributor record (#741): Done and merged. Realized that R and python test files out of sync, will be handled #775
  • Cell et al. (#768): There is agreement that "Option #3" is what we want to go for, i.e.,
    • Cell is not a container
    • Objects are linked together via cell_id
    • Cell is maintained as an separate object that contains cell-specific metadata that does not fit into any other object
    • We will keep the Cell->``Receptor`` linkage (within cell) as Receptor is a global object
    • We will rename CellExpression and CellReactivity to Expression and Reactivity
  • Event object will be pushed to post v2.0, but we will come up with a plan to address it.
  • We will close #763 and annotate the appropriate issues/PRs with the Documentation project.
  • Lineage schema PR will be made with unit test data. #333 will be closed.
  • Manifest object will be revisited on a later call.
  • DataProcessing redesign will not make it into v2.0.

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