lamindb.examples.cellxgene

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”, and “cell culture” ULabels (tissue_type)

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

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

Generates a Schema for a specific CELLxGENE schema version.

Parameters:

  • schema_version (Literal['4.0.0', '5.0.0', '5.1.0', '5.2.0', '5.3.0', '6.0.0']) – The CELLxGENE Schema version.

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

  • organism (Literal['human', 'mouse', 'zebra danio', 'rhesus macaquedomestic pig', 'chimpanzee', 'white-tufted-ear marmoset', 'sars-2'], default: 'human') – The organism of the Schema.

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

Return type:

Schema