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?
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.