Present: Brian, Christian, Corey, Francisco, Florian, Marcos, Sri
Decisions
Renaming "Organism" field to "Species" was approved. After we
discussed this again, the renaming was put to a vote. It was decided
to perform this renaming in the upcoming v2 release of MiAIRR and the
AIRR schema (see #266).
Relation between MiAIRR Set 6 and DataRep rearrangement. See
minutes of MiniStd Call 2019-11 for a summary. DataRep is fine
with the suggested procedure (DataRep governs the fields, MiniStd
simply declares whether a field is "minimal" in terms of reporting).
We approved this as the new mode of operation, which will be
included in the documentation until the v2 release, although it is
formally independent of it.
Follow-up
Human Population Genetics XT: Due to time restrictions this was not
yet brought up in a GLDB call. Therefore comments on the respective
tickets (#264, #265) were requested via the GLDB mailing list
until our next call.
Makeing renaming of fields trackable: Renaming (not only deprecation)
is now included #248 and defined as a To-Do for v2.0 (#305).
Addition of further gene call fields to rearrangement (#258):
This is a bigger discussion involving ComRepo, DataRep and GLDB.
However, as it does not affect the existence of the [vdj]_call
fields, which we require for Set 6, it is not a MiniStd topic.
Inclusion of species information for cell and locus annotation: As
discussed during the MiniStd Call 2019-09 and decided in
MiniStd Call 2019-10, we want to introduce fields to provide
species information for the cell_* and locus fields to
address issue #137. The respective changes were introduced in PR
#260, however it turns out that it is problematic to add
ontology-controlled fields to the rearrangement object (#278),
i.e., for locus. Therefore only cell_species was added to the
schema, while locus_species has been reverted (via #281). Will
follow up with DataRep and ComRepo on potential solutions.
Current NCBI submission stats: Pulled from NCBI based on the "AIRR"
keyword (note that not all submitted studies include this). Results
in table191201 are queried via
https://www.ncbi.nlm.nih.gov/nuccore/?term=AIRR%5BKeyword%5D
and show TLS record counts aggregated by BioProject ID:
BioProject
records
PRJNA545339
12
PRJNA336331
1
PRJNA488042
20
PRJNA520929
62
PRJNA338795
93
New topics
Define cell and receptor objects: The ongoing work to create
API endpoints to access single-cell data (#211) has sparked some
discussion about the cell and receptor entities and their
respective (potential) IDs cell_id and pair_id (see lengthy
discussion in #273). We agree that it would be important to
include a representation of these objects in the schema and adapt the
API endpoints accordingly. Will follow up in MiniStd Call 2020-01.