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scientific-db-pubmed-database

Direct PubMed and NCBI E-utilities search workflows for biomedical literature, MeSH queries, PMID lookup, citation retrieval, and API-backed literature monitoring. Use when a task needs biomedical literature from PubMed rather than general web search.

Quality

92%

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SecuritybySnyk

Low

Low-risk findings worth noting

SKILL.md
Quality
Evals
Security

Quality

Content

90%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.

An excellent, lean skill body: executable code, concrete query syntax, correct subheading ordering, API-key hygiene, and reproducible-search logging. The only improvements are an explicit error-recovery loop for API calls and offloading the lookup-table catalogs into a reference file.

Suggestions

Add an explicit error-recovery step for E-utilities calls (e.g., on non-200 or transient failure, back off and retry before giving up).

Move the field-tag and filter catalogs into a references/ file (e.g., FIELD_TAGS.md) and link to it, keeping SKILL.md as the overview.

Include a brief rate-limit rule (requests/second with and without an API key) near the code example so the 0.35s sleep is justified.

DimensionReasoningScore

Conciseness

The body never explains what PubMed or MeSH is; it is entirely operational — field-tag tables, executable query strings, a working Python client, and checklists. Only trivial overlap with the description in the intro exists, so nothing material could be trimmed; this fits the 'every token earns its place' anchor.

5 / 5

Actionability

The E-utilities section provides a copy-paste-ready Python function with env-var API key handling, timeout, and raise_for_status(), plus exact endpoint names and concrete query examples like 'diabetes mellitus[mh] AND treatment[tiab] AND systematic review[pt]'. Fully executable guidance covering common cases matches level 5.

5 / 5

Workflow Clarity

A clear query-construction sequence ('Start with the research question, split it into concepts, then combine'), a numbered E-utilities pipeline, a review checklist with validation checkpoints, and an output-discipline log template. It falls short of level 5 because there is no explicit error-recovery loop (e.g., HTTP failure → backoff/retry) for API workflows.

4 / 5

Progressive Disclosure

Sections are well organized and the References are clearly signaled one-level-deep external links (no bundle files exist). However, the full field-tag catalog and filter lists (~60 lines of lookup tables) are inlined in the single SKILL.md; moving them to a reference file would better split content, which is the minor gap that holds this at level 4.

4 / 5

Total

18

/

20

Passed

Description

92%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: concrete, comprehensive action list in third person, with an explicit 'Use when…' trigger that even disambiguates against general web search. The only gap is missing a few natural synonyms (papers, abstracts, MEDLINE) users might say.

Suggestions

Add common user phrasings such as 'papers', 'abstracts', or 'MEDLINE' to broaden natural trigger coverage.

DimensionReasoningScore

Specificity

Enumerates five concrete actions — 'PubMed and NCBI E-utilities search workflows', 'MeSH queries', 'PMID lookup', 'citation retrieval', and 'API-backed literature monitoring' — with no vague filler. Coverage is comprehensive across the skill's capabilities, matching the level-5 anchor rather than the 'minor gaps' of level 4.

5 / 5

Completeness

Both parts are explicit: the 'what' is the concrete action list, and the 'when' is spelled out with concrete trigger phrasing — 'Use when a task needs biomedical literature from PubMed rather than general web search'. This mirrors the level-5 example structure, so it is not the level-4 case where the 'when' could be more specific.

5 / 5

Trigger Term Quality

Natural trigger terms are present ('PubMed', 'biomedical literature', 'MeSH', 'PMID', 'citation', 'NCBI E-utilities'), but common user phrasings like 'papers', 'abstracts', 'MEDLINE', and 'life-sciences literature' are absent. Good keyword coverage with a few natural terms missing fits level 4, above level 3's 'missing common variations'.

4 / 5

Distinctiveness Conflict Risk

The description carves out a clear niche (PubMed/NCBI E-utilities) and explicitly distinguishes it from 'general web search', minimizing conflict risk with generic search or literature skills. Distinct domain-specific triggers place it at level 5.

5 / 5

Total

19

/

20

Passed

Validation

93%

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

CriteriaDescriptionResult

metadata_version

'metadata.version' is missing

Warning

Total

15

/

16

Passed

Repository

affaan-m/ECC

Path

skills/scientific-db-pubmed-database/SKILL.md

Reviewed

Table of Contents

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