Travis/Github Actions: Github Actions seems to have worked fine for
the last Merges. Jason will disable Travis for now, we will monitor
things until the next meeting
Call 2021-08 notes: Points were potentially discussed but clearly no
decision on them was made. Brian will bring up points 2+3 with
ComRepo later this week. Will revisit this topic in the next call.
Terminology documents: The general idea is to come up with the list
of terms to be used in the future, but they do not necessarily need
to be identical to the ones used in the past. However, the old terms
terms will be included in the list, redirecting to the current term
for the respective entity. Christian will put the merged list of
terms from the various documents on Github by the end of the week for
consolidation.
Cell schema files: Example JSON looks good, should be finally able to
close this soon. Further remarks from the call:
JSON format is rather large (625 MB for a 10X GEX data set), but
compresses well (down to 23 MB). Also, it is simple to import into
MongoDB.
While property is the term used by OpenAPI to describe
entities within an object, feature_id would be the more
generic term used in data science and underscore the following
point that it SHOULD hold a CURIE.
To increase interoperability, property SHOULD hold PIDs that
are appropriate for the data type at hand. This can be Ensembl for
genes or an ID from the Antibody Registry for antibodies used
in cytometry experiments. However, as experimentalists might use
reagents that are not available in a global catalog, also custom
strings MUST be supported. These MUST NOT look like CURIEs. Also
any given cell_id/property pair MUST be unique
We should include an explanation in the docs that technically,
the Cell object schema can be used to represent cells for
which no rearrangement data is available. This could be due to
failed amplification of IG/TR transcripts or due to the cell not
expressing IG/TR at all. However, it should not be used to
replicate arbitrary GEX data sets into the ADC, if there is no
AIRR connection.
keywords_study: Will leave current fields in place, but change
the proposed keywords to consistently distinguish between objects
that exists in the data set in the repository and features of the
experimental setup. Discussion will be continued and finalized in
#569.