Minutes_Standards_2022 03 - airr-community/airr-standards GitHub Wiki
Standards Call 2022-03
Agenda
IMPORTANT: Due to non-synchronized DST switching we will meet
one hour earlier for those people in Europe, but the usual time
for those in North America.
Review of v1.4 milestone : Goal is to present the v1.4 release at
the AIRR VI meeting, discuss and decide what (and what not) to
include.
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)
Call 2021-08 notes: Follow up on ComRepo feedback (also see
Call 2021-12), suggested restructuring:
TSV output SHOULD be supported for all data that is commonly
represented in tabular structures
All API endpoints SHOULD return JSON encodings
For some API endpoints it is possible to request TSV files
For any endpoints supporting TSV encodings these will be clearly
documented in the API Spec and/or Documentation
Endpoints that do not support TSV can reject TSV requests
If API endpoint returns a field then the content of that field in
JSON and TSV MUST be equivalent
Bottom line: API Endpoints that are JSON or JSON+TSV should be
defined in the spec/docs - the repositories don't get to choose.
Cell schema (#409) and associated pull request (#574)
Restarted activity on (#404): Should we try to have a closer
integration of the Receptor object and MHCGenotype from the
Germline schema?
Germline-related objects: Most immediate issues are solved. MHC will
need more time and will be considered to be a separate issue. Will
introduce split between MHC class I and II alleles. Also, we need
a vocabulary for the experimental support for a given allele call.
Will continue discussion in #573.
Revisited issues of the v1.4 milestone: Push a couple of those
to v2.0 (e.g., Manifest), remaining issues should be doable until
mid-May.
Contributor object: Agreement that this consolidation is in
general the right thing to do. As CRediT is now receiving increasing
support from publishers and ORCiD, we will adopt this vocabulary for
the contributor role. Submission specific roles currently foreseen
in the AIRR Schema (study contact, data collection, data submission)
will are independent of CRediT and will therefore use separate tags/
keywords. As this object will create incompatible changes the target
will be pushed to v2.0. (#552)
Only touched briefly on Cell (#409) and Receptor (#404)
object, will follow-up on Github and in the next call.