Closed bkmartinjr closed 5 months ago
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@pablo-gar - thanks for the assay term changes.
Question/open issue: the Census schema also defines special handling for the normalized layer, for any "Smart-Seq" assays. Can we add the definitive list of which EFO terms are considered a Smart-Seq assay? Ideally this would be included in the Census schema (or referenced as you did with the assay filter terms).
@bkmartinjr - In regards to issue #993 there is this point:
Confirm no use of CL:0000003, aka native cell. These cells will now be marked as unknown in both obs.cell_type and obs.cell_type_ontology_term_id columns. See related task: https://github.com/chanzuckerberg/cellxgene-census/issues/1019
Once a test build is produced, are we to check this manually in the python interpreter by doing a count of CL:0000003
in obs.cell_type_ontology_term_id
and native cell
in obs.cell_type
and checking that the count is zero?
Or should this be captured in some type of of post build acceptance test where some sanity checks about the data are done?
@prathapsridharan re:
are we to check
This is entirely an upstream issue in the DP process, and the builder does not enforce (or check) for this level of metadata compliance with the CxG schema. These checks for compliance with the CxG schema are the provenance of the schema validation toolkit used by Lattice, et al.
We could do this kind of checks, but it is redundant, and adds linkages across layers in the system that don't add much value IMHO.
@atarashansky - we have included your requested organisms info (#796) in Census schema 2.0.0. Current content will be:
In [4]: census['census_info']['organisms'].read().concat().to_pandas().set_index('soma_joinid')
Out[4]:
organism_ontology_term_id organism_label organism
soma_joinid
0 NCBITaxon:9606 Homo sapiens homo_sapiens
1 NCBITaxon:10090 Mus musculus mus_musculus
Please feel free to leave comments on both the Schema MD file changes and the code.
Light QC on test build shows no issues
Checks
obs
and addition to census["census_info"]["organisms"]
.See notebook https://colab.research.google.com/drive/1kb2ZR0MPxVsWBgJlIgrtJrkGPx5wqxIk
Builder support for Census schema 2.0.0 / CELLxGENE schema 5.0.0
Fixes: #993 Fixes: #1022 Fixes: #796
Primary changes: