lamindb.examples.cellxgene .md

CELLxGENE utilities.

lamindb.examples.cellxgene.save_cellxgene_defaults()

Save default values of the CELLxGENE schema to the instance.

Adds CELLxGENE specific (control) values that are not available in the ontologies: :rtype: None

  • “normal” Disease

  • “na” Ethnicity

  • “unknown” entries for DevelopmentalStage, Phenotype, and CellType

  • “tissue”, “organoid”, “primary cell culture”, and “cell line” ULabels (tissue_type)

  • “cell”, “nucleus”, “na” ULabels (suspension_type)

lamindb.examples.cellxgene.create_cellxgene_schema(field_types='ontology_id', *, spatial_library_id=None)

Generates a Schema for a specific CELLxGENE schema version.

Parameters:

  • field_types (Literal['ontology_id', 'name'] | Collection[Literal['ontology_id', 'name']], default: 'ontology_id') – One or several of ‘ontology_id’, ‘name’.

  • organism – The organism of the Schema.

  • library_id – Identifier for the spatial library. Specifying this value enables curation against spatial requirements.

Return type:

Schema