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cellxgene-census

Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell atlas. Best for population-scale queries, reference atlas comparisons. For analyzing your own data use scanpy or scvi-tools.

58

Quality

69%

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tessl review fix ./backend/cli/skills/databases/cellxgene-census/SKILL.md
SKILL.md
Quality
Evals
Security

Quality

Content

56%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.

The body delivers highly actionable, mostly executable code with a sensible explore-then-query workflow, but it is bloated by three sections that duplicate either the description or the references/common_patterns.md bundle file. Restructuring so the SKILL.md body is a lean overview pointing into the reference files would fix both the conciseness and progressive-disclosure deductions at once.

Suggestions

Cut the 'Common Use Cases' section (lines 429-486) and fold any non-duplicated cases into references/common_patterns.md — they almost entirely restate the Core Workflow Patterns and reference examples.

Replace the 'Key Concepts and Best Practices' section (lines 311-383) with a short list and pointers to the corresponding Best Practices items in references/common_patterns.md, which already covers them.

Move the hard-coded census_version='2023-07-25' examples into a note on version pinning (or the schema reference) rather than repeating the dated value inline, keeping time-sensitive details out of the main body.

DimensionReasoningScore

Conciseness

Noticeably verbose with systematic duplication: 'When to Use This Skill' restates the description, 'Common Use Cases' near-duplicates 'Core Workflow Patterns', and 'Key Concepts and Best Practices' repeats the Best Practices section of references/common_patterns.md nearly item-for-item. The hard-coded version '2023-07-25' is time-sensitive and not placed in a deprecation/old-patterns section. Not 3 because the padding is structural and repeated across multiple sections rather than occasional.

2 / 5

Actionability

Concrete, mostly executable code throughout (open_soma context manager, get_obs/get_var, get_anndata with filter syntax, axis_query chunk iteration, experiment_dataloader). Not 5 because the ExperimentDataset train/test split example references an undefined 'experiment_axis_query' variable and several snippets carry '# Work with census data' placeholder bodies.

4 / 5

Workflow Clarity

Clear sequence (open census -> explore metadata -> estimate query size -> choose get_anndata vs out-of-core axis_query) with an explicit size checkpoint ('If too large (>100k), use out-of-core processing') and a troubleshooting section for error recovery. Not 5 because there is no explicit post-query verification step, though the read-only nature of the queries lowers the stakes.

4 / 5

Progressive Disclosure

Both references (census_schema.md, common_patterns.md) are real, one level deep, and well signaled with explicit 'When to read' guidance, but large blocks of content that belong in those files — the Common Use Cases section and the Key Concepts best practices — are inlined in the body. Not 4 because the inlining is substantial and systematic, exceeding a 'minor organization gap'.

3 / 5

Total

13

/

20

Passed

Description

82%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 description with explicit what/when structure, good natural trigger terms, and excellent conflict-avoidance guidance that routes scanpy/scvi-tools use cases elsewhere. The only deductions are limited action coverage and second-person phrasing.

DimensionReasoningScore

Specificity

Names the domain and a couple of concrete actions ('Query the CELLxGENE Census (61M+ cells) programmatically', 'population-scale queries, reference atlas comparisons') but coverage is not comprehensive, and the second-person phrasing ('Use when you need', 'your own data') triggers the rubric's 1-point specificity reduction. Not 2 because the actions named are concrete and domain-specific rather than generic.

3 / 5

Completeness

Clearly answers both what ('Query the CELLxGENE Census (61M+ cells) programmatically') and when ('Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell atlas') with concrete trigger phrases, matching the top anchor exactly.

5 / 5

Trigger Term Quality

Good natural keyword coverage — 'expression data', 'tissues', 'diseases', 'cell types', 'single-cell atlas', plus adjacent tool names ('scanpy', 'scvi-tools'). Not 5 because common user phrasings like 'scRNA-seq' or 'single-cell RNA sequencing' are absent.

4 / 5

Distinctiveness Conflict Risk

Clear niche (the Census atlas) with distinct triggers, and it actively disambiguates from the nearest competing skills via 'For analyzing your own data use scanpy or scvi-tools', minimizing wrong-skill triggering.

5 / 5

Total

17

/

20

Passed

Validation

81%

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

Validation — 13 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

skill_md_line_count

SKILL.md is long (517 lines); consider splitting into references/ and linking

Warning

metadata_version

'metadata.version' is missing

Warning

frontmatter_unknown_keys

Unknown frontmatter key(s) found; consider removing or moving to metadata

Warning

Total

13

/

16

Passed

Repository
synthetic-sciences/openscience
Reviewed

Table of Contents

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