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)
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)
We should strive for v1.4 release before AIRR-C Meeting VI:
Set AIRR v1.4 Milestone due date to April 22, which is the Friday
before the April ComRepo meeting, so ComRepo has some time to
discuss before the AIRR-C meeting.
Major v1.4 issue for the ADC is the identifier definitions.
Everyone please update their issues and pull requests with the
correct Project and target Milestone.
We will review v1.4 Milestone and decide on including in the March
Standards WG meeting.
Terminology document: There is now a consolidated list of terms in a
Google Sheet, please review and comment until 2022-02-27.
GermlineSet cannot contain multiple version of an allele,
as there is no full-fledged support in the schema. However,
the release_version and release_date field can be used
to indicate that changes took place in an AlleleDescription
between different GermlineSet records.
In case "temporary labels" are assigned to alleles, these
labels will - similar to regular gene symbols - be used in
for annotation in the Rearrangement.[vdj]_call fields.
There is no coordinated process to increment the
release_version of an AlleleDescription and/or a
GermlineSet. Users will copy a germline set from a germline
set repository (e.g., OGRDB) and put it into their study to
ensure tight linkage. If users change either of these records,
during their analysis procedure they are expected to change the
version and date, but these changes will remain local to the
study using these modified records. If and how these changes
flow back to the germline set repository is beyond the scope
of the Standards WG. It should be noted that extended alleles
will be considered to be like new alleles, and thus also
trigger a version increase. William will add some guidance on
this in the Docs.
Extended discussion around identifiers and references (#562):
It seems to be clear that _id for ancillary objects (e.g.,
SequenceDelineationV)are not necessary.
The main purpose of _id fields for now is to allow the local
linkage between objects within a study, which is expected to
include a copy of the utilized GermlineSet und Genotype
records. This requires uniqueness of the ID, but not
resolvability.
Updated versions of a utilized GermlineSet may be retrieved
via the germline_set_ref, which may contain a CURIE. This
reference needs to be resolvable, but not necessarily unique.
It is not expected that AIRR-seq repositories use this
reference to resolve queries (e.g., for a GermlineSet), as
the records included in a study are considered to be most
accurate ones for this study,
The generic part of the discussion around IDs, PIDs, GIDs,
persistence and resolvability has been moved to #347.
Next call on Mon, 2022-02-21. Mind the (day-light saving time) Gap!