Include a high level term for cell types in the Cell Census

[pablo-gar]

It would be helpful if the cell type annotation had a high-level ontology term mapping, similar to how the tissue and tissue_ontology_term_id have a 1-to-1 mapping to a high-level tissue for increased usability of the Cell Census: tissue_general and tissue_general_ontology_term_id.

This was originally suggested by Angela Pisco

[brianraymor]

And we have prior art for cell types from filter with ontology awareness.

[atolopko-czi]

@pablo-gar tissue_general is already in the census (Core code). OK to close this issue or is there more to it?

[pablo-gar]

This is a request that came from Angela and it relates to having cell_type_general or something alike.

[bkmartinjr]

This issue is in regard to cell type, not tissue type - it is not resolved.

[atolopko-czi]

This issue is in regard to cell type, not tissue type - it is not resolved.

rewrote description to aid my next reading. :)

[lubianat]

@pablo-gar is this something you would like to be provided by the Cell Ontology? Or something you'd prefer to curate internally?

We were discussing having a related broad 'category' for each term in this ticket:
INCATools/ontology-development-kit#859 (comment)

[pablo-gar]

Per triage schema this is not a Census-specific issue and it needs to be addressed holistically for all CELLxGENE Discover features. that depend on cell type mappings.

The solution will likely live in an upcoming ontology service. The Census will use this ontology service to provide mappings in a TBD manner

[pablo-gar]

@lubianat we decided to keep this work in house for the time being. Thanks for the reference