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pubmed-search

Search and analyze biomedical literature from PubMed using the free E-utilities API. Use when researching medical topics, discovering clinical papers, fetching article metadata by PMID, performing deep paper analysis, or downloading open-access PDFs from PubMed Central. Triggers: pubmed search, search biomedical literature, find medical papers, PMID lookup, pubmed metadata, clinical literature search, biomedical research, life sciences papers, PMC download, ncbi search.

Quality

89%

Does it follow best practices?

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SecuritybySnyk

Low

Low-risk findings worth noting

SKILL.md
Quality
Evals
Security

Quality

Content

81%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 well-structured, highly actionable skill body with executable commands for every subcommand, explicit error-recovery loops, and appropriate offloading of setup detail to a one-level-deep reference. Its weaknesses are redundancy — the Mindset section restates three points that the Anti-Patterns section already covers — and a broken link to requirements.txt.

Suggestions

Delete the 'Mindset' section (or reduce it to one line): all three of its points are already covered more usefully by the 'Anti-Patterns' WHY/BAD/GOOD entries, removing ~10 lines of duplication.

Add a requirements.txt file at the skill root (or fix the 'Dependencies' reference to point at the actual location, e.g., inside scripts/) so the broken reference link resolves.

Move the inline PubTator MCP server JSON block into references/setup-and-troubleshooting.md alongside the other configuration detail, keeping only the one-line 'prefer the MCP' guidance in the body.

DimensionReasoningScore

Conciseness

No basic-concept padding, but the same three points are repeated across sections: MCP-first appears in 'When Not to Use', 'Recommended MCP Server', 'Mindset #2', 'Workflow step 1', and an anti-pattern; rate-limit handling appears in 'Mindset #1', 'Workflow step 4', and its own anti-pattern; open-access caution appears in 'Mindset #3' and an anti-pattern. The 'Mindset' section duplicates the Anti-Patterns section almost entirely and could be cut. This is 'mostly efficient but includes some unnecessary explanation or could be tightened' — not 4, where only minor trimming would be needed.

3 / 5

Actionability

Fully executable, copy-paste-ready commands cover every common case: all five subcommand invocations with real flags ('search --keywords "CRISPR gene editing" --results 10', 'metadata --pmid "33303479" --format json', etc.), a concrete 429 recovery command ('sleep 30 && ./scripts/pubmed_search.py search ...'), and a ready-to-use MCP server JSON config. Not below 5: specific examples cover the common cases with no gaps.

5 / 5

Workflow Clarity

The five-step sequence is clear and includes explicit validation and feedback loops for the risky batch operation: step 4 handles 429s with a wait-30s-retry-once loop and an explicit prohibition on tight retries, 'ALWAYS add a short delay between batch calls' guards bulk fetching, and step 5 is a user-confirmation gate before triage. Not 4: checkpoints are explicit rather than implicit — error recovery (429), rate-limit prevention, and the human gate are all stated.

5 / 5

Progressive Disclosure

Good structure: setup detail is appropriately split into references/setup-and-troubleshooting.md (one level deep, clearly signaled twice, and the file exists), and the References section enumerates all bundle files. Minor gaps: the 'Dependencies: requirements.txt' link is broken (no requirements.txt exists in the bundle), and the inline MCP server JSON config arguably belongs in the references file. Not 5: the broken reference link is a real navigation gap; not 3: content splitting and signaling are otherwise well done.

4 / 5

Total

17

/

20

Passed

Description

96%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.

An excellent description: third-person voice, explicit 'Use when' clause with concrete scenarios, and a comprehensive natural-language trigger list that maps to all four script subcommands. The only weakness is mild overlap risk from broad triggers like 'biomedical research' against general academic-search skills.

DimensionReasoningScore

Specificity

The description lists multiple concrete actions covering every subcommand of the skill — 'Search and analyze biomedical literature', 'discovering clinical papers, fetching article metadata by PMID, performing deep paper analysis, or downloading open-access PDFs from PubMed Central' — mapping to search/metadata/analyze/download with comprehensive coverage. Not below 5: no concrete action from the body's workflow is missing; not above: 5 is the scale maximum.

5 / 5

Completeness

It explicitly answers both questions: 'what' ('Search and analyze biomedical literature from PubMed using the free E-utilities API' plus the enumerated capabilities) and 'when' ('Use when researching medical topics, discovering clinical papers, fetching article metadata by PMID...'). This matches the anchor-5 example structure of concrete what + explicit when with trigger phrases. Not 4: the 'when' clause is fully explicit with concrete trigger scenarios, not merely present.

5 / 5

Trigger Term Quality

The trigger list is comprehensive and natural: 'pubmed search, search biomedical literature, find medical papers, PMID lookup, pubmed metadata, clinical literature search, biomedical research, life sciences papers, PMC download, ncbi search' — covering synonyms a user would actually say (pubmed, medical papers, PMID, PMC, ncbi). Not 4: coverage includes synonym variations users would naturally type, not just a few keywords.

5 / 5

Distinctiveness Conflict Risk

Mostly distinct: PubMed-specific triggers ('PMID lookup', 'PMC download', 'ncbi search') create a clear niche, but broader triggers like 'biomedical research' and 'life sciences papers' carry minor overlap risk with general academic-search skills (e.g., semantic-scholar or google-scholar search) that the description does not distinguish. Not 5: minor overlap remains with closely related literature-search skills; not 3: the dominant triggers are unambiguously PubMed-specific.

4 / 5

Total

19

/

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

allowed_tools_field

'allowed-tools' contains unusual tool name(s)

Warning

metadata_version

'metadata.version' is missing

Warning

relative_links

Relative link issues: 1 missing

Warning

Total

13

/

16

Passed

Repository

pantheon-org/tekhne

Path

skills/documentation/research/pubmed-search/SKILL.md

Reviewed

Table of Contents

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