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pubmed-database

Search PubMed for scientific literature, including published clinical trials. Fetch abstracts and full text. Link published research to biological databases (gene, protein, nucleotide, PubChem) to discover associations between papers and specific compounds or genes. Verify medical spelling, match raw citations, and cache result sets for bulk processing. Interfaces NCBI E-utilities and PMC BioC APIs.

Quality

82%

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SKILL.md
Quality
Evals
Security

Quality

Content

80%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 is highly actionable with executable CLI examples and excellent progressive disclosure through real one-level-deep references. Its main weakness is workflow clarity: bulk API operations lack an explicit error/validate feedback loop, which caps that dimension at 3.

Suggestions

Add an explicit validation/feedback loop for bulk API calls, e.g. 'On a non-zero exit or 429: wait and retry with backoff, then re-run; confirm the output file was written before chaining the next call.'

Add a checkpoint before chaining (e.g. verify the output JSON is non-empty / has the expected key) so batch failures are caught early.

Optionally trim the duplicated MANDATORY reference-reading warning to a single statement to gain a point in conciseness.

DimensionReasoningScore

Conciseness

Lean and purposeful with no padding or basic-concept over-explanation; only minor trim possible — the MANDATORY reference-reading warning restates the same caution found in the function-group links, so it is efficient but not perfectly tight.

4 / 5

Actionability

Provides fully executable, copy-paste CLI invocations ('uv run scripts/pubmed_api.py ./search_results.json search_pubmed "BRCA1" --max_results 5') plus concrete jq recipes and exact positional/flag syntax covering the common chaining and slimming cases.

5 / 5

Workflow Clarity

The context-management steps are clearly sequenced (filter early, slim, bulk single-turn, ground, terminate), but the skill centers on batch/bulk API operations and lacks an explicit validate/retry checkpoint for API errors (e.g. 429 backoff → verify), which the rubric caps at 3 for batch operations.

3 / 5

Progressive Disclosure

A clear overview body links one level deep to 8 real reference files (all verified present) plus the CLI script, with a 'Structure of the skill folder' listing and well-signaled function-group links; content is appropriately split and easy to navigate.

5 / 5

Total

17

/

20

Passed

Description

75%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.

The description is specific and distinctive, enumerating the skill's concrete capabilities clearly, but it never states when Claude should invoke it. Adding an explicit 'Use when...' clause would lift the completeness dimension past its current cap.

Suggestions

Add an explicit trigger clause, e.g. 'Use when the user asks about PubMed, NCBI databases, published clinical trials, biomedical abstracts, or linking papers to genes/compounds.'

Include natural user synonyms and file extensions currently missing — 'NCBI', 'PMID', 'PMC', '.bib', 'citation matching' — to broaden trigger-term coverage.

Keep the existing third-person voice and action list; they are already strong on specificity and distinctiveness.

DimensionReasoningScore

Specificity

Lists multiple concrete actions — 'Fetch abstracts and full text', 'Link published research to biological databases (gene, protein, nucleotide, PubChem)', 'Verify medical spelling, match raw citations, and cache result sets' — giving comprehensive coverage of the CLI's capabilities.

5 / 5

Completeness

The 'what' is clear and detailed, but there is no 'Use when...' or equivalent explicit 'when' clause; per the rubric, a missing explicit trigger clause caps completeness at 3.

3 / 5

Trigger Term Quality

Strong natural-domain terms ('PubMed', 'scientific literature', 'clinical trials', 'abstracts', 'full text', 'gene', 'protein', 'PubChem') but omits a few user-level synonyms/extensions like 'NCBI', 'PMID', '.bib', or 'citations file'.

4 / 5

Distinctiveness Conflict Risk

Names a clear niche ('PubMed', 'NCBI E-utilities and PMC BioC APIs') with distinct triggers and minimal overlap risk against other skills.

5 / 5

Total

17

/

20

Passed

Validation

100%

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

Validation — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository

google-deepmind/science-skills

Path

skills/pubmed_database/SKILL.md

Reviewed

Table of Contents

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