mirror of
https://github.com/chanzuckerberg/cellxgene.git
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Marcus Kinsella
78176f9711
Add the `cellxgene schema apply` and `cellxgene schema validate` subcommands. The first takes an h5ad file and a yaml with config information and produces a new h5ad that follows the cellxgene data integration schema. The second takes an h5ad and checks if it follows the schema version written into its metadata. Both are currently marked as "experimental" as the primary intended users are still at CZI.
96 lines
2.7 KiB
YAML
96 lines
2.7 KiB
YAML
title: Corpora schema version 1.0.0
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type: anndata
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components:
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uns:
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type: dict
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keys:
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version:
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type: dict
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keys:
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corpora_schema_version: null
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corpora_encoding_version: null
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title:
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type: string
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contributors:
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type: stringified list of dicts
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layer_descriptions:
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type: dict
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keys:
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X: null
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organism:
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type: string
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nullable: false
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organism_ontology_term_id:
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type: curie
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prefixes:
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- NCBITaxon
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var:
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type: dataframe
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index:
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type: human-readable string
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unique: true
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obs:
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type: dataframe
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index:
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unique: true
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columns:
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tissue:
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type: human-readable string
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nullable: false
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tissue_ontology_term_id:
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type: suffixed curie
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nullable: true
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prefixes:
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- UBERON
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assay:
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type: human-readable string
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nullable: false
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assay_ontology_term_id:
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type: curie
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nullable: true
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prefixes:
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- EFO
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disease:
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type: human-readable string
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nullable: false
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disease_ontology_term_id:
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type: curie
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nullable: true
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prefixes:
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- MONDO
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- PATO
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cell_type:
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type: human-readable string
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nullable: false
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cell_type_ontology_term_id:
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type: curie
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nullable: true
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prefixes:
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- CL
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- UBERON
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sex:
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type: string
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enum:
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- male
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- female
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- mixed
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- unknown
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- other
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ethnicity:
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type: human-readable string
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nullable: false
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ethnicity_ontology_term_id:
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type: curie
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nullable: true
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prefixes:
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- HANCESTRO
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development_stage:
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type: human-readable string
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nullable: false
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development_stage_ontology_term_id:
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type: curie
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nullable: true
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prefixes:
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- HsapDv
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- EFO
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