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kegg-database

Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices. Use this for direct HTTP/REST work or KEGG-specific control.

71

Quality

88%

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SecuritybySnyk

Passed

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SKILL.md
Quality
Evals
Security

Quality

Content

76%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.

A highly actionable, well-organized skill body with extensive executable examples and clear references, weakened primarily by absent validation/error-handling checkpoints in its batch and database workflows and minor verbosity.

Suggestions

Add validation checkpoints to the workflows (e.g., check HTTP status codes, guard against empty/malformed response lines before splitting on '\n' and indexing), especially for the batch loops in Workflows 1 and 2.

Trim the Overview sentence defining KEGG and consolidate overlapping guidance between the per-operation 'When to use' notes and the workflow use cases.

Move inline reference material such as the full Pathway Categories list and identifier/format tables into references/kegg_reference.md, keeping SKILL.md a leaner overview that points to them.

DimensionReasoningScore

Conciseness

The body is dense with executable code and structured reference material rather than prose padding, but the Overview line explaining what KEGG is and some redundancy between the operations and workflows sections could be trimmed.

4 / 5

Actionability

Every operation and all five workflows provide copy-paste ready, executable Python with concrete arguments, covering the common cases comprehensively.

5 / 5

Workflow Clarity

The five workflows have clear numbered sequences, but none include validation or error-handling checkpoints; the batch/database loops parse raw API responses without guards, so the workflow_clarity cap at 3 applies.

3 / 5

Progressive Disclosure

Structure is good with well-signaled, verified one-level-deep references to references/kegg_reference.md and scripts/kegg_api.py, but SKILL.md carries substantial inline reference detail (pathway categories, identifier formats, troubleshooting) that keeps it from being a lean overview.

4 / 5

Total

16

/

20

Passed

Description

100%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, well-scoped description that clearly states capabilities, gives explicit trigger guidance, and actively steers away from the overlapping bioservices skill. It is concise yet comprehensive with no padding.

DimensionReasoningScore

Specificity

Lists multiple concrete actions — 'Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion' — giving comprehensive coverage of the skill's capabilities.

5 / 5

Completeness

Explicitly states what it does ('Direct REST API access to KEGG...') and when to use it ('Use this for direct HTTP/REST work or KEGG-specific control'), satisfying both halves with concrete triggers.

5 / 5

Trigger Term Quality

Covers natural domain terms a bioinformatics user would say (KEGG, pathway analysis, drug interactions, ID conversion) with synonyms (REST API / HTTP/REST).

5 / 5

Distinctiveness Conflict Risk

Occupies a clear KEGG-specific niche and actively disambiguates from a competing skill ('For Python workflows with multiple databases, prefer bioservices'), minimizing conflict risk.

5 / 5

Total

20

/

20

Passed

Validation

87%

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

Validation14 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

metadata_version

'metadata.version' is missing

Warning

frontmatter_unknown_keys

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

Warning

Total

14

/

16

Passed

Repository
synthetic-sciences/openscience
Reviewed

Table of Contents

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