Minutes_Standards_2022 01 - airr-community/airr-standards GitHub Wiki

Standards Call 2022-01

Agenda

  • Germline-related objects: Introduced and further updated in PRs #530, #566 and #568. Still numerous open questions (#559, #562) that require a discussion about scope, intended use cases, and potential MiAIRR inclusion.
  • Generic Contributor object: Schema has now multiple data structures that annotate researchers involved in a study and their roles. We should try to consolidate this. (#552)
  • Travis/Github Actions: Travis has been turned-off, any issues observed? (#484, #541, #546)
  • Any points to raise at the ExCom/Co-Leads meeting in February?
  • AIRR VI is coming up, any organizational things that this WG wants to discuss?
  • Call 2021-08 notes: Follow up on ComRepo feedback, see Call 2021-12.
  • Cell schema (#409) and associated pull request (#574)
  • keywords_study (#515, #569)
  • Terminology documents (see Call 2021-10, #549).

Minutes

Meta

  • Date: Mon, 2022-01-24 19:00 UTC
  • Present: Aditi, Artur, Brian, Chaim, Christian, Edward Lee, Felix, Jason, Jingyun, Ken, Kira, Marc, Scott, Ulrik, William
  • Regrets: --

Topics

  • Travis/Github Actions: GA seems to work fine and provides higher granularity in pass/fail messages directly visible from the PR. Jason will turn of Travis for good and test re-enabling checks on the master branch.
  • Germline-related objects: Long discussion, managed to clarify several points:
    • The property holding the allele designations is termed label, as this reflects the intented use of this field in combination with a (yet to be developed) PID for the respective allele.
    • All GermlineSet objects used in a study MUST be included as a local copy within a study (not the Study object), to ensure that links based on label cannot break. germline_set_ref is provided as a backup to allow verification and check for updates.
    • While the biological genotype is a property of a subject, the inferred Genotype is derived from a sample. Furthermore, as inference on a given repertoire may be carried out against different GermlineSet, we need to move it further down in the object hierarchy to DataProcessing.
    • The [VDJ]_call fields reference by default to the alleles in GermlineSet. A specific Genotype record is acting as a modifier to the GermlineSet, in which undocumented_alleles are additions (MAY be used by the gene caller), while all alleles belonging to one of the deleted_genes are excluded for them analysis (MUST NOT be used). Alleles in the GermlineSet that are neither among the documented_alleles not excluded (see above) are considered to be potentially legit but undetected.
  • Generic Contributor object: Has seen good progress on #552. Will try to finalize this in the next call, please have a look and see whether there are any further comments.
  • No points for the ExCom/Co-Leads meeting.
  • AIRR-C VI will take place mid-May, hopefully as hybrid meeting. We will propose to the General Assembly to re-new the mandate of this WG for the next cycle. We would really like to see some turn-over of the co-leads, therefore everyone who has been participating in this WG over the currect WG is invited to volunteer.
  • All further agenda points were pushed to the next meeting.

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