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pubmed-database

Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API implementations.

55

Quality

64%

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SecuritybySnyk

Low

Low-risk findings worth noting

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tessl review fix ./plugins/AI-Agents-Safe-Coding-Skills-claude/skills/pubmed-database/SKILL.md
SKILL.md
Quality
Evals
Security

Quality

Content

50%Scale 1-5

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

This skill is comprehensive in coverage but severely over-explains concepts Claude already knows (PubMed basics, Boolean logic, what MeSH terms are, PICO framework). The actionable content—query syntax examples, API code, and field tags—is genuinely useful but buried in verbose explanatory text. The workflows lack validation steps critical for batch API operations, and the main file inlines too much reference material that should live in the referenced supporting files.

Suggestions

Cut the 'Overview', 'When to Use This Skill', and conceptual explanations (what PubMed is, what Boolean operators do, what PICO stands for) — Claude knows these. Focus the body on syntax, field tags, and API specifics Claude wouldn't know.

Move the MeSH subheadings list, publication types list, export formats, and limitations sections into the reference files, keeping only the most critical items inline with pointers to references.

Add explicit validation steps to the programmatic workflow: check HTTP status codes, validate JSON response structure, handle empty result sets, and implement retry logic with example code.

Reduce the five high-level workflows to 2-3 with concrete commands/code at each step, rather than abstract descriptions like 'Identify key concepts and synonyms'.

DimensionReasoningScore

Conciseness

Significantly verbose for a Claude skill. Extensively explains concepts Claude already knows (what PubMed is, what Boolean operators are, what PICO stands for, what MeSH terms are). The 'When to Use This Skill' section is unnecessary padding. Sections like 'Limitations and Considerations' and 'Tips and Best Practices' contain mostly general knowledge. The file is well over 300 lines when it could convey the same actionable content in under 100.

2 / 5

Actionability

Provides concrete, executable query examples and a working Python code snippet for the E-utilities API. Field tag examples, MeSH subheading usage, and citation matching formats are specific and usable. Minor gaps: the ECitMatch example lacks a full API call, and some workflows are high-level steps without executable commands.

4 / 5

Workflow Clarity

Five workflows are listed but they are all high-level step lists without validation checkpoints or error recovery. The programmatic workflow (Workflow 3) mentions error handling as a final step but doesn't show how to validate responses or handle failures. For API batch operations, the absence of explicit validation/feedback loops caps this at 3.

3 / 5

Progressive Disclosure

References three files in a references/ directory (api_reference.md, search_syntax.md, common_queries.md) with clear descriptions of when to consult each, which is good structure. However, no bundle files were provided, so we can't verify these exist. More importantly, the SKILL.md itself inlines a large amount of content (MeSH subheadings, publication types, export formats, limitations) that should be in reference files, making the main file bloated.

3 / 5

Total

12

/

20

Passed

Description

78%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.

This is a strong description that clearly identifies its domain (PubMed REST API), lists concrete capabilities, and explicitly distinguishes itself from a related skill (biopython). The main weaknesses are minor: the 'when' clause could include more user-facing trigger phrases (e.g., 'searching PubMed programmatically', 'NCBI literature queries'), and a few natural synonyms are missing from the trigger terms.

Suggestions

Add user-facing trigger synonyms like 'NCBI', 'literature search', 'biomedical articles', or 'PubMed search' to improve discoverability when users describe their task in non-technical terms.

Expand the 'Use this for...' clause with more concrete scenarios, e.g., 'Use when building custom PubMed search tools, querying NCBI E-utilities directly, or needing fine-grained control over PubMed API requests.'

DimensionReasoningScore

Specificity

Lists several specific actions: 'Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management' and mentions 'direct HTTP/REST work or custom API implementations.' Minor gaps remain—e.g., what exactly does 'citation management' entail—but coverage is good.

4 / 5

Completeness

The 'what' is clearly stated (REST API access to PubMed with specific capabilities). The 'when' is present ('Use this for direct HTTP/REST work or custom API implementations') and includes a boundary condition distinguishing it from biopython, but the 'when' clause could be more explicit about user-facing trigger scenarios.

4 / 5

Trigger Term Quality

Includes strong natural keywords like 'PubMed', 'REST API', 'MeSH queries', 'E-utilities', 'batch processing', 'citation management', and 'HTTP/REST'. Missing some user-facing synonyms like 'literature search', 'biomedical articles', or 'NCBI', which users might naturally say.

4 / 5

Distinctiveness Conflict Risk

Highly distinctive: it explicitly carves out its niche by differentiating from biopython/Bio.Entrez, targeting direct REST/HTTP API access to PubMed specifically. The boundary guidance ('For Python workflows, prefer biopython') actively reduces conflict risk with a related skill.

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.

Validation9 / 11 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

9

/

11

Passed

Repository
administrakt0r/AI-Agents-Safe-Coding-Skills
Reviewed

Table of Contents

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