search

chanzuckerberg / single-cell-curation

Code and documentation for the curation of cellxgene datasets
MIT License
38 stars 23 forks source link

Integrate all required ontology processing into ontology preparation #357

Closed brianraymor closed 1 year ago

brianraymor commented 2 years ago

Context

The cellxgene-schema CLI downloads and processes pinned ontologies to address the schema requirements.

There is separate (distributed in the code base) ontology processing occurring for filter by metadata, filter with ontology awareness, gene expresssion, and cell census.

We should investigate integrating all required ontology processing into the ontology preparation step for the cellxgene-schemaCLI to eliminate duplication of code and ensure that all features are based on the pinned versions of the ontologies.

See Proposal: Standardization of ontology-derived process and assets of CELLxGENE Discover.

@atolopko-czi also writes:

I've attempted to capture the currently ad hoc, manual Schema Upgrade Process. This can serve as requirements for what processes and configuration updates need to be automated and simplified in order to address this story.

brianraymor commented 1 year ago

Issue moved to chanzuckerberg/single-cell #446 via Zenhub