Flattening to Anndata - cell label

[dosumis]

When flattening to AnnData cell_label should keep the original obs key.

This keeps compatibility with the CZI schema and allows for different flattening schemes.

e.g. Siletti - non neurona Anndatal

has the obs key::value pair

{ "supercluster_term" : "Oligodendrocyte precursor" }

in CAS annotation object with curated annotation metadata:

labelset	cell_label	cell_ontology_term_id	cell_ontology_term	rationale	rationale_doi	positive_gene_evidence
supercluster_term	Oligodendrocyte precursor	CL:0002453	oligodendrocyte precursor cell	Supported by marker expression and annotation transfer from Middle Temporal Gyrus dataset (Jorstad et al., 2023)	DOI:10.1126/science.adf6812	PDGFRA, SOX10

loading CAS to anndata & flattening to obs:

supercluster_term	supercluster_term--cell_ontology_term_id	supercluster_term--cell_ontology_term	supercluster_term--rationale	supercluster_term--rationale_doi	supercluster_term--positive_gene_evidence
Oligodendrocyte precursor	CL:0002453	oligodendrocyte precursor cell	Supported by marker expression and annotation transfer from Middle Temporal Gyrus dataset (Jorstad et al., 2023)	DOI:10.1126/science.adf6812	PDGFRA, SOX10

[dosumis]

Update - turns out this is what the cap_anndata_schema specifies. This just needs to be reflected in the flattening script. Keeping ticket for reference while flattening code is updated.