cellxgene-census

Programmatically query the CZ CELLxGENE Census (61M+ cells) when you need cross-tissue, disease, or cell-type expression data for population-scale queries and reference atlas comparisons.

Quality

83%

Does it follow best practices?

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Securityby

Passed

No findings from the security scan

Quality

Content

78%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

Highly actionable content with a complete runnable example and clear sequencing, though somewhat redundant in its Implementation Details. The main weakness is progressive disclosure: the existing reference bundle files are never linked from the skill body.

Suggestions

Link the existing bundle files from the body, e.g. under an Advanced section: 'Schema details: See [census_schema.md](references/census_schema.md)' and 'Common query patterns: See [common_patterns.md](references/common_patterns.md)'.

Trim Implementation Details sections that re-explain what the commented example already demonstrates (filtering semantics, expression-layer columns) to improve conciseness.

Add a lightweight validation checkpoint for the out-of-core path, such as confirming the query returns rows before iterating or handling an empty result.

Dimension	Reasoning	Score
Conciseness	Mostly efficient with a complete runnable example and tight section headers, but the Implementation Details section re-explains filtering semantics, access-pattern choice, and expression-layer columns already shown in the commented code, which could be trimmed.	4 / 5
Actionability	Provides a complete, copy-paste-ready Python script covering metadata exploration, in-memory AnnData loading, and out-of-core iteration, plus exact install commands — fully executable across the common cases.	5 / 5
Workflow Clarity	The example lays out a clear numbered 1-4 sequence (open pinned census, explore metadata, load AnnData, out-of-core query) with version pinning for reproducibility, but lacks explicit validation/error-recovery checkpoints for the large-scale iteration path; the destructive/batch cap does not apply since this is read-only querying.	4 / 5
Progressive Disclosure	The body has good section structure, but the two provided bundle files (references/census_schema.md, references/common_patterns.md) are never referenced or linked from SKILL.md, leaving them orphaned, and portions of Implementation Details could live in those references rather than inline.	3 / 5
	Total	16 / 20 Passed

Description

87%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

A strong, specific description that clearly states what the skill does and when to use it with concrete trigger phrases and a distinct niche. Minor gaps are the lack of common single-cell synonyms and the fact that all capabilities fold into one query action.

Dimension	Reasoning	Score
Specificity	Names the domain ("CZ CELLxGENE Census (61M+ cells)") and the concrete action ("Programmatically query") plus several specific use modalities (cross-tissue, disease, cell-type expression, population-scale queries, reference atlas comparisons), but all reduce to one core query action rather than a list of distinct operations.	4 / 5
Completeness	Explicitly answers both "what" ("Programmatically query the CZ CELLxGENE Census") and "when" ("when you need cross-tissue, disease, or cell-type expression data for population-scale queries and reference atlas comparisons") with concrete trigger phrases, satisfying the Use-when requirement.	5 / 5
Trigger Term Quality	Strong natural terms for the target audience ("cross-tissue", "disease", "cell-type expression data", "reference atlas", "population-scale queries"), but omits common synonyms users would also say such as "single-cell", "scRNA-seq", or "scRNA".	4 / 5
Distinctiveness Conflict Risk	The "CZ CELLxGENE Census (61M+ cells)" niche is highly specific with distinct triggers and minimal overlap risk against other skills.	5 / 5
	Total	18 / 20 Passed

Validation

93%

Warnings & errors only

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 15 / 16 Passed

Validation for skill structure

Criteria	Description	Result
frontmatter_unknown_keys	Unknown frontmatter key(s) found; consider removing or moving to metadata	Warning

	Total	15 / 16 Passed

Repository: aipoch/medical-research-skills
Path: scientific-skills/Evidence Insight/cellxgene-census/SKILL.md
Commit: 63c61d3

Reviewed: 9 hours ago

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