Minutes_MiniStd_2020 03 - airr-community/airr-standards GitHub Wiki
MiniStd Call 2020-03
Agenda
Follow-up
DataRep has decided to rename organism to species. Their
change will likely go into v1.3 and therefore predate our change,
which is slated for v2.0. DataRep will also discuss how to annotate
the renaming (#248).
Object definition cell and related data schema: Schema is now
available for review in #358. We however need to discuss about:
"True" Repertoires and "Meta"-Repertoires (the former ones
contain each cell object only once, the latter ones can contain
them multiple time (either copied or linked).
If a Rearrangement is defined as an observed nucleic acid
how do we represent UMI- and CellID-based collapsing. Is there
a separate object for it?
MiAIRR requirement levels:
There is a general consensus in DataRep and ComRepo to move away
from the current RFC2119 terms, as they can create confusion with
the OpenAPI required term.
A current suggestion are the RDA-inspired terms essential,
important and useful (see #342).
John noted that we need to distinguish between terms for
individual fields and qualification of the whole metadata record
for a given use case. Therefore, for most fields the requirement
levels could be differ between use cases. Therefore he suggests
that there are mainly two options that would potentially work:
Use a binary criterium (e.g. MiAIRR compliant), which
applies if and only if all required fields are provided. The
non-nullable requirement could be relabeled as a question of
the ontology/vocabulary for the field.
Spell out the individual requirement for each use case (or
group of use cases).
Switch to Github for agendas and minutes: First round of feedback.
New Topics
Merger of AIRR Standards WGs: ComRepo, DataRep and MiniStd currently
have 4--5 calls every month in which a core group of 5--6 people
frequently talk about similar topics to an extended group of
participants. We would like to see whether we can increase the
efficiency of this process by having one joint meeting per month,
covering the topics of MiniStd and DataRep and the API parts of
ComRepo. In addition the original WG can have additional calls
between the general calls (maybe with a fixed schedule and cancel
if not necessary). If this works out and lead to more fun, less
meetings and/or increased productivity, we would propose an
official merger of the WGs at the next AIRR-C meeting.
Minutes
Meta
Date: Fri, 2020-03-20 13:30 UTC
Present: Ahmad, Christian, Felix, Florian, Francisco, Lindsay,
Marcos, Sri
Decisions
MiAIRR requirement levels:
The requirement level optional will be renamed to defined.
Levels will be introduced via #342.
We will start with a binary definition of "MiAIRR compliance",
which will REQUIRE that all essential fields are present and
contain non-NULL-LIKE values and will REQUIRE that all
important fields are present (but can be NULL-LIKE).
In general, our documentation will encourage people to provide
information on important fields. However, for the sake of
compliance, entry screens MAY default these fields to NULL-LIKE.
The definitions will be documented via #319. This should
include the distinction between field- and use case-based
requirements.
We will start working on use cases in the intermediate future,
probably once AIRRv2 is out.
Follow-up
Object definition cell and related data schema:
Proposed schema is now available for review in #358.
There is a consensus that overlapping populations/repertoires need
to be addressed and that two tiers of Repertoire objects could
be a solution. Will follow up in #361.
rearrangement should rather represent the rearranged DNA, i.e.
one biological entity per cell, while transcript and reads
are derivatives or measurement artifacts. This would mean that
rearrangement is always after UMI- and CellID collapsing. This
needs further dicussion with the other AIRR Standard WGs, will
follow-up in #360.
Migration of agenda and minutes to Github: No objections so far, will
finalize migration until next call.
New Topics
Merger of AIRR Standard WGs: Feedback is positive. Will work out a
new call schedule with the other WGs and notify ExCom.