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name: accessors-extensions description: "Use anndata reference accessors for validation, plotting, data selection, and typed AnnData extension namespaces." disable-model-invocation: true metadata: disco-role: operating license: BSD 3-Clause

Accessors and Extensions

Use this sub-skill when code needs portable references to arrays inside AnnData objects or a small typed namespace attached to AnnData instances.

Route Here

• Build and inspect anndata.acc references such as A.obs["batch"], A.var["symbol"], A.obsm["pca"][:, 0], A.layers["counts"][:, "gene-a"], A.obsp["connectivities"][:, "cell-a"], or A.X[:, :].
• Check whether a reference/accessor is present in an object with ref in adata or A.obsm in adata, then extract values with adata[ref].
• Parse or serialize references with A.resolve(...), A.to_json(ref), and A.from_json(data) for validation/configuration layers.
• Register a typed extension namespace with anndata.register_anndata_namespace(name) for library-style helpers on AnnData.

Route Elsewhere

• For AnnData shape, view, obs/var, layers, obsm, obsp, and container mutation semantics, use ../data-model/SKILL.md.
• For .h5ad, Zarr, lazy/backed reads, or element I/O, use ../storage-io/SKILL.md.
• For anndata.concat, concat_on_disk, AnnCollection, or batch-combination choices, use ../combining-data/SKILL.md.

References

• references/api-reference.md lists the accessor classes, signatures, object relationships, and extraction contracts.
• references/accessor-recipes.md gives practical recipes for membership checks, extraction, JSON/string parsing, and validation-friendly reference handling.
• references/extension-namespaces.md covers the namespace decorator, class shape, validation, caching, and conflict avoidance.
• references/troubleshooting.md maps common accessor and namespace failures to fixes.
• scripts/demo_anndata_accessor.py is a tiny runnable demo for refs, extraction, JSON/string parsing, and namespace registration.

Operating Rules

• Treat AdRef objects as object-independent references; validate ref in adata before extraction when user input or optional fields are involved.
• Prefer public AnnData APIs and small typed namespace methods; extension namespaces are for library code, not ad-hoc per-notebook state.
• Keep plotting/data-selection APIs accepting either AdRef instances or parseable strings, then normalize to refs with A.resolve(..., strict=True).